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Department
Biology
Course
Biology 2581B
Professor
Prof
Semester
Winter

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Lecture 9 Most human traits do not have 2 opposing phenotypes. Many traits don’t have a definitive dominance or recessiveness. Some traits turned out to be multifactorial – ie. Determined by two or more genes, or the interaction of genes with the environment. Incomplete dominance –ch3 This occurs when the hybrid does not resemble either pure-breeding parent. F1 hybrids that differ from both parents often express a phenotype that is intermediate between those of the pure parents. Flower colour is the best example of incomplete dominance.Across between pure-bred red and pure-bred white snapdragons always produces F1 offspring with pink petals. This is the result of each allele contributing a specific protein in pigment production. Gene expression in Eukaryotes and Prokaryotes –ch8 In eukaryotes transcription takes place in the nucleus and translation takes place in the cytosol. In prokaryotes, both transcription and translation occur in the open intracellular space. The rate of translation is often due to the rate of transcription. This type of relationship is called attenuation, where the rate of one thing determines the rate of another. This attenuation does not occur in eukaryotes because the nuclear envelope physically separates the sites of transcription and translation. Transcription In prokaryotes, transcription begins with the sigma subunit of RNApolymerase binding to the promoter, and the RNApol (RNAP) binding to the complex to form the functional enzyme. This step is called initiation. The sigma factor gets released from the RNAP as the RNAP unwinds the DNAand begins transcription of the mRNA. This step is known as elongation. When the RNAP hits a stop codon, it gets released from the DNA. Initiation of translation In prokaryotes, translation begins at a ribosome binding site on the mRNA, which is defined by a short sequence of nucleotides called a Shine-Dalgarno box, which is right before the start codon AUG. There is nothing to prevent an mRNA from having more than one ribosome binding site. In fact, many mRNA strands have multiple ribosome binding sites, and are called polycistronic – ie. They contain the information of several genes (aka. Cistrons). Sd-box AUG In eukaryotes, the small ribosomal subunit first binds to the methylated cap at the 5’end of the mature mRNAand then migrates to the initiation site. The cap is a methylated backwards guanine. The backwards guanine is added by special capping enzymes and is methylated using enzymes called methyl transferases. The initiation site is almost always the firstAUG codon encountered. The mRNAregion between the 5’cap and the initiation codon is sometimes called the 5’- untranslated region (5’UTR) or 5’-untranslated leader. methyl 5’UTR AUG In eukaryotes, a single mRNAstrand contains the information for translating only one polypeptide. In prokaryotes, the start codon gets translated into an N-formylmethionine (fMet) and in eukaryotes it’s just Met at the N terminus. Post-translational cleavage events cleave off the fMet/Met in both prokaryotes and eukaryotes to give the final mature protein. Eukaryotic mRNA require more processing than prokaryotic mRNA. Not only do they need splicing of the introns during transcription, but they also need the addition of a methyl cap and a poly-Atail. Gene structure C. elegans is a soil-living roundworm that is 1 mm long with its entire genome already sequenced. To find possible genes in the genome, open reading frames are scanned for. ORFs are strings of amino acid-encoding nucleotide triplets that contain the gene and its introns. Once a region that is likely a gene has been found, the researcher then finds out the sequence of amino acids that the gene encodes. That sequence is then searched in a database, and if a similar sequence in a protein of known function in another organism is found, they can conclude that the C. elegans version probably has a similar function. Collagen gene Promotor 5’UTR Exon 2 Exon 3 3’UTR Start Stop codon polyA tail addition site C. elegans are a strange eukaryote in that they will use transplicing of primary transcripts from two different genes to create a new mRNA. Like bacteria, they will transcribe some groups of nearby genes as one long polycistronic transcript. Types of Mutations in exons Silent mutations – a change in a nucleotide that results in the same a.a. being produced Conservative Missense mutations – a change in a nucleotide that results in a different a.a. translated, but with similar chemical properties which make the protein still functional Non-conservative missense mutations – a change in a codon that results in a different a.a. with different chemical properties that results in a non-functional protein. Nonsense mutations – a change in a gene that creates a premature stop signal. Frameshift mutations – the insertion or deletion of nucleotides within the coding sequence. If the insertion or deletion is not divisible by three, then it will shift the reading frame and create a loss- of-function protein. Most eukaryotes have splice-acceptor, splice-donor, and branch sites that allow splicing to join exons together with precision in mature mRNA. If there are changes to these sites, then mature mRNAcannot be formed. Mutations that affect a ribosome binding site would lower the affinity of the mRNAto the small ribosomal subunit, resulting in less or no protein produced. Mutations that affect gene expression Loss-of-function mutation – any mutation inside or outside of the coding region that reduces or eliminates the protein produced Recessive loss-of-function alleles – alleles that completely block the function of a protein (aka. Null or amorphic mutations). These mutations either prevent expression of the protein, or create a non-functional protein. Hypomorphic mutation – a loss-of-function mutation that reduces expression of a gene, or creates a functional protein that is less active. These type of mutations are hard to detect Incomplete dominance – when a phenotype varies continuously with the levels of protein function Haploinsufficiency – when one wild-type allele does not produce enough protein product to result in a normal phenotype. Few phenotypes require both wild-type alleles. Some phenotype are dependent on the amount of the protein being produced. In these cases, being heterozygous for a loss-of-function allele will produce a different phenotype. Ex. T-locus in mice determines length of tail. Aheterozygote with a null mutation will produce only half the amount of protein normally produced, and will grow a tail that is half as long. Dominant negative / antimorphic alleles – alleles of genes that encode subunits that block the activity of the wild-type subunits. Ex.Agene that encodes a polypeptide that associates with three other identical polypeptides to form a four-subunit enzyme. All four subunits are made from the same gene. The presence of a mutant subunit in the four can make a function-less enzyme. The chance of a proper enzyme being made is (1/2)^4 = 1/16 or 6.25% Gain-of-function alleles – a mutation that enhances a proteins function or expression. Hypermorphic mutation – a gain-of-function mutation that creates either more protein than the wild-type allele, or the same amount, but more active protein. Neomorphic mutations – a gain-of-function mutation that creates an entirely new phenotype. This can be because the gene creates a new protein with a new function, or expresses a gene at the wrong time. Ex. Drosophila gene Antennapedia is active during embryonic and larval stages. Dominant mutations of this gene cause expression of it in the head of the insect, causing legs to grow instead of antennae. This is an example of ectopic expression – gene expression at the wrong place or time Mutations in proteins used in development ch18 Null mutations detected in a genetic screen are often the best way to draw conclusions of the importance of a protein in organism development. Gene knockout - Scientists will often used targeted mutagenesis – inducing a null mutation in the gene of interest – to study the effects of the protein product on development. The process involves taking a cloned gene, using recombinant DNAtechniques to destroy its function, and then replace the wild-type gene in the genome with the inactivated cloned copy. Conditional mutation – a loss-of-function mutation that only occurs under certain conditions. Ex. Afunctional mutant protein that losses its function beyond a certain temperature, whereas the wild-type can function in both high and low temperatures. Temperature sensitive proteins allow studying the effect of a protein in a later stage of life. Ectopic gene expression – the expression of a gene at the wrong time or place Lecture 10 Digital analysis of DNAch9 Biotechnology is the entire set of techniques used to examine long stretches of genes. Restriction enzymes are used to generate fragments (or ‘digest’) of DNAthat are suitable for manipulation and characteri
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