Transcript Genes chapt15

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.
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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
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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.
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Fig. 15.1-1
Fig. 15.1-2
Fig. 15.1-3
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.
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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.
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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.
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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
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The Genetic Code
• Marshall Nirenberg identified the codons
that specify each amino acid.
• There are 64 possible codons for the 22
amino acids
- The genetic code is degenerate
• There are also “start” and “stop” codons
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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.
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Gene Expression
• 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
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Gene Expression Overview
• Transcription proceeds through three steps:
– 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
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Gene Expression Overview
• Translation proceeds through three similar
steps:
– 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
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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
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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
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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
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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
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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
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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
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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.
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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
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Fig. 15.9-1
Fig. 15.9-2
Fig. 15.9-3
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
•The primary transcript must be edited by:
– removal of non-coding sequences
(introns)
– splicing together the coding sequences
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(exons)
Fig. 15.10
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
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Fig. 15.11a
Fig. 15.11b
Fig. 15.11c
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
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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
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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
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Translation
• In prokaryotes, initiation of translation
requires the formation of the initiation
complex including:
– an initiator tRNA charged withNformylmethionine
– the small ribosomal subunit
– mRNA strand
• The ribosome binding sequence of
mRNA is complementary to part of rRNA
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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
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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.
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Translation
• Elongation continues until the ribosome
encounters a stop codon.
• Stop codons are recognized by release
factors which release the polypeptide from
the ribosome.
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Translation
• In eukaryotes, translation may occur on
ribosomes in the cytoplasm or on ribosomes
of the RER.
- the location depends on the intended
destination of the protein
• 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.
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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.
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Fig. 15.22-1
Fig. 15.22-2
Fig. 15.22-3
Table 15.2
Mutation: Altered Genes
• Point mutations alter a single base.
– base substitution mutations – substitute
one base for another
• transitions or transversion mutations
(missense mutations)
– nonsense mutations – create stop codon
– frameshift mutations – caused by
insertion or deletion of a single base
– silent mutations - do not change protein
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Mutation: Altered Genes
• Triplet repeat expansion mutations
involve a sequence of 3 DNA nucleotides
that are repeated many times
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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
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Mutation: Altered Genes
• Too much genetic change (mutation) can
be harmful to the individual.
• Genetic variation (caused by mutation) is
necessary for evolutionary change of the
species.
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