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.

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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.

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.

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. There are 64 possible codons for the 22 amino acids The genetic code is degenerate There are also “start” and “stop” codons

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 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 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

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

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

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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

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

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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 (exons)

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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

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 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 N- formylmethionine the small ribosomal subunit mRNA strand 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 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.

Translation 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. 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.

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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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

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. Genetic variation (caused by mutation) is necessary for evolutionary change of the species.