Genes and How They WorkChapter 15

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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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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.

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.

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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 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

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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

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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

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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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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

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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 intron-exon boundaries

– introns – non-coding sequences

– exons – sequences that will be translated

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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 with N-

formylmethionine– 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.

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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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

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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

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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.

However, genetic variation (caused by mutation) is necessary for evolutionary change of the species.