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Genes and How They Work
Chapter 15
The Nature of Genes
Early ideas to explain how genes work came from
studying human diseases.
Archibald Garrod studied alkaptonuria, 1902
– Garrod recognized that the disease is inherited via a
recessive allele
– Garrod proposed that patients with the disease lacked
a particular enzyme
These ideas connected genes to enzymes.
The Nature of Genes
Evidence for the function of genes came from
studying fungus.
George Beadle and Edward Tatum, 1941
– studied Neurospora crassa
– used X-rays to damage the DNA in cells of
Neurospora
– looked for cells with a new (mutant) phenotype
caused by the damaged DNA
The Nature of Genes
Beadle and Tatum looked for fungal cells
lacking specific enzymes.
– The enzymes were required for the biochemical
pathway producing the amino acid arginine.
– They identified mutants deficient in each
enzyme of the pathway.
The Nature of Genes
Beadle and Tatum proposed that each enzyme
of the arginine pathway was encoded by a
separate gene.
They proposed the one gene – one enzyme
hypothesis.
Today we know this as the one gene – one
polypeptide hypothesis.
The Nature of Genes
The central dogma of molecular biology
states that information flows in one
direction:
DNA
RNA
protein
Transcription is the flow of information from
DNA to RNA.
Translation is the flow of information from
RNA to protein.
The Genetic Code
Deciphering the genetic code required
determining how 4 nucleotides (A, T, G, C)
could encode more than 20 amino acids.
Francis Crick and Sydney Brenner determined
that the DNA is read in sets of 3 nucleotides
for each amino acid.
The Genetic Code
codon: set of 3 nucleotides that specifies a
particular amino acid
reading frame: the series of nucleotides read
in sets of 3 (codon)
– only 1 reading frame is correct for encoding the
correct sequence of amino acids
The Genetic Code
Marshall Nirenberg identified the codons that
specify each amino acid.
RNA molecules of only 1 nucleotide and of
specific 3-base sequences were used to
determine the amino acid encoded by each
codon.
The amino acids encoded by all 64 possible
codons were determined.
The Genetic Code
stop codons: 3 codons (UUA, UGA, UAG) in
the genetic code used to terminate
translation
start codon: the codon (AUG) used to signify
the start of translation
The remainder of the code is degenerate
meaning that some amino acids are
specified by more than one codon.
Gene Expression Overview
template strand: strand of the DNA double
helix used to make RNA
coding strand: strand of DNA that is
complementary to the template strand
RNA polymerase: the enzyme that
synthesizes RNA from the DNA template
Gene Expression Overview
• Translation proceeds through
– initiation – mRNA, tRNA, and ribosome come
together
– elongation – tRNAs bring amino acids to the
ribosome for incorporation into the polypeptide
– termination – ribosome encounters a stop codon
and releases polypeptide
Gene Expression Overview
Transcription proceeds through:
– initiation – RNA polymerase identifies where to
begin transcription
– elongation – RNA nucleotides are added to the
3’ end of the new RNA
– termination – RNA polymerase stops
transcription when it encounters terminators in
the DNA sequence
Gene Expression Overview
Gene expression requires the participation of
multiple types of RNA:
messenger RNA (mRNA) carries the information
from DNA that encodes proteins
ribosomal RNA (rRNA) is a structural component
of the ribosome
transfer RNA (tRNA) carries amino acids to the
ribosome for translation
Gene Expression Overview
Gene expression requires the participation of
multiple types of RNA:
small nuclear RNA (snRNA) are involved in
processing pre-mRNA
signal recognition particle (SRP) is composed of
protein and RNA and involved in directing mRNA
to the RER
micro-RNA (miRNA) are very small and their role
is not clear yet
Prokaryotic Transcription
Prokaryotic cells contain a single type of
RNA polymerase found in 2 forms:
– core polymerase is capable of RNA elongation
but not initiation
– holoenzyme is composed of the core enzyme
and the sigma factor which is required for
transcription initiation
Prokaryotic Transcription
A transcriptional unit extends from the
promoter to the terminator.
The promoter is composed of
– a DNA sequence for the binding of RNA
polymerase
– the start site (+1) – the first base to be
transcribed
Prokaryotic Transcription
During elongation, the transcription bubble
moves down the DNA template at a rate of
50 nucleotides/sec.
The transcription bubble consists of
– RNA polymerase
– DNA template
– growing RNA transcript
Prokaryotic Transcription
Transcription stops when the transcription
bubble encounters terminator sequences
– this often includes a series of A-T base pairs
In prokaryotes, transcription and translation
are often coupled – occurring at the same
time
Eukaryotic Transcription
RNA polymerase I transcribes rRNA.
RNA polymerase II transcribes mRNA and
some snRNA.
RNA polymerase III transcribes tRNA and
some other small RNAs.
Each RNA polymerase recognizes its own
promoter.
Eukaryotic Transcription
Initiation of transcription of mRNA requires a
series of transcription factors
– transcription factors – proteins that act to bind
RNA polymerase to the promoter and initiate
transcription
Eukaryotic pre-mRNA Splicing
In eukaryotes, the primary transcript must be
modified by:
– addition of a 5’ cap
– addition of a 3’ poly-A tail
– removal of non-coding sequences (introns)
Eukaryotic pre-mRNA Splicing
The spliceosome is the organelle responsible for
removing introns and splicing exons together.
Small ribonucleoprotein particles (snRNPs)
within the spliceosome recognize the intronexon boundaries
– introns – non-coding sequences
– exons – sequences that will be translated
tRNA and Ribosomes
The ribosome has multiple tRNA binding
sites:
– P site – binds the tRNA attached to the growing
peptide chain
– A site – binds the tRNA carrying the next
amino acid
– E site – binds the tRNA that carried the last
amino acid
tRNA and Ribosomes
tRNA molecules carry amino acids to the
ribosome for incorporation into a polypeptide
– aminoacyl-tRNA synthetases add amino acids to
the acceptor arm of tRNA
– the anticodon loop contains 3 nucleotides
complementary to mRNA codons
tRNA and Ribosomes
The ribosome has two primary functions:
– decode the mRNA
– form peptide bonds
peptidyl transferase is the enzymatic
component of the ribosome which forms
peptide bonds between amino acids
Translation
In prokaryotes, initiation of translation requires the
formation of the initiation complex including
– an initiator tRNA charged with
formylmethionine
– the small ribosomal subunit
– mRNA strand
N-
The ribosome binding sequence of mRNA is
complementary to part of rRNA
Translation
Elongation of translation involves the addition
of amino acids
– a charged tRNA binds to the A site if its
anticodon is complementary to the codon at the
A site
– peptidyl transferase forms a peptide bond
– the ribosome moves down the mRNA in a 5’ to
3’ direction
Translation
Translation
There are fewer tRNAs than codons.
Wobble pairing allows less stringent pairing
between the 3’ base of the codon and the 5’
base of the anticodon.
This allows fewer tRNAs to accommodate all
codons.
Elongation continues until the ribosome
encounters a stop codon.
Stop codons are recognized by release factors
which release the polypeptide from the
ribosome.
Translation
In eukaryotes, translation may occur on
ribosomes in the cytoplasm or on ribosomes
of the RER.
Signal sequences at the beginning of the
polypeptide sequence bind to the signal
recognition particle (SRP)
The signal sequence and SRP are recognized
by RER receptor proteins.
Translation
The signal sequence/SRP holds the ribosome
on the RER.
As the polypeptide is synthesized it passes
through a pore into the interior of the
endoplasmic reticulum.
Mutation: Altered Genes
Point mutations alter a single base.
– base substitution mutations – substitute one base for
another
• transitions or transversions
• also called missense mutations
– nonsense mutations – create stop codon
– frameshift mutations – caused by insertion or
deletion of a single base
Mutation: Altered Genes
triplet repeat expansion mutations involve a
sequence of 3 DNA nucleotides that are
repeated many times
triplet repeats are associated with some
human genetic diseases
– the abnormal allele causing the disease contains
these repeats whereas the normal allele does not
Mutation: Altered Genes
Chromosomal mutations change the
structure of a chromosome.
– deletions – part of chromosome is lost
– duplication – part of chromosome is copied
– inversion – part of chromosome in reverse
order
– translocation – part of chromosome is moved
to a new location
Mutation: Altered Genes
Too much genetic change (mutation) can be
harmful to the individual.
However, genetic variation (caused by
mutation) is necessary for evolutionary
change of the species.