BIO 122 Week 7 Class 3 Notes PDF

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Lecture notes from week 7 class 3...

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BIO 122 Notes Week 7 Class 3 Fundamental Theories of Biology and Introduction to the Cell DNA Replication and How Genes Work Part 6 RNA Processing ● In eukaryotes ○ DNA → pre-mRNA → mRNA → Protein ○ Some genes encode an RNA is the final functional product ■ Structural RNAs ■ Regulatory RNAs ● RNA → DNA ○ (some viruses)

● ○ The first clue that the biological information in DNA must go through an intermediary in order to produce proteins, came from knowledge of the cell structure. ■ In eukaryotic cells, DNA is enclosed within a membrane-bound organelle called the nucleus. ● But the cell’s ribosomes, where protein synthesis takes place, are outside the nucleus ○ in the cytoplasm. ○ To make sense of this François Jacob and Jacques Monod proposed ● RNA molecules act as a link between genes found in the cell’s nucleus ● And the protein-manufacturing centers located in the cytoplasm

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■ They predicted that short lived molecules of RNA, which are called Messenger RNA (mRNA) was found to carry information from DNA in the nucleus to the site of protein synthesis (mRNA is one of several distinct types of RNA in the cell) It was later found that the enzyme RNA polymerase synthesizes RNA ■ According to the information provided by the sequence of bases in a particular stretch of DNA The central dogma summarizes the flow of information in cells DNA codes for RNA, which codes for proteins: ■ DNA → RNA → proteins The sequence of bases in a stretch of DNA ■ Specifies the sequence of bases in an RNA molecule ■ Which specifies the sequence of amino acids in a protein Genes ultimately code for proteins

The Central Dogma ● The central dogma summarizes the flow of information in cells ● DNA codes for RNA, which codes for proteins: ○ DNA → RNA → proteins ● Crick’s simple statement encapsulates much of the research reviewed in this chapter. ○ DNA is the hereditary material. ■ Genes consist of specific stretches of DNA that code for produce used in the cell. ● The sequence of bases in a stretch of DNA specifies the sequence of bases in an RNA molecule ○ Which specifies the sequence of amino acids in a protein ● Genes ultimately code for proteins ● Proteins are the workers of the cells ○ functioning not only as enzymes but also as motors, structural elements, transporters and molecular signals. ● Transcription ○ Produces a transcript of a gene ○ mRNA specifies primary structure of polypeptide ● Translation ○ Process of synthesizing specific polypeptide on a ribosome using mRNA template

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● ○ Biologists use specialized vocabulary to summarize the sequence of events captured in the central dogma. ■ 1. DNA is transcribed ● To messenger RNA ● By RNA polymerase ■ Transcription is ● The process by which the hereditary information in DNA is copied to RNA ■ 2. The mRNA is then translated to proteins in ribosomes ■ Translation is ● The process where the order of the nucleotide bases is converted to the order of amino acids ■ Transcription is appropriate because it means ● “MAKING A COPY” ■ Translation is appropriate because it means ● “CONVERTING INFORMATION FROM ONE LANGUAGE TO ANOTHER” – the language of DNA to the language of proteins.

The Genetic Code

● According to the central dogma ○ An organism’s genotype is determined by the sequence of bases in its DNA ○ An organism’s phenotype is a product of the proteins it produces ● To appreciate this point, consider that all proteins encoded by genes are what make the “stuff” of the cell and dictate which chemical reactions occur inside. ○ For example a population of oldfield mouse native to southeastern ○ North America, individuals have a gene for a protein called melanocortin receptor. ■ Melanocortin is a hormone – an important type of molecular signal – that works through the melanocortin receptor to influence how much dark pigment is deposited in fur. ● An important aspect of a mouse’s phenotype – its coat colour ○ is determined in part by the DNA sequence at the gene of the receptor. ● Later work revealed, alleles of the same gene differ in their DNA sequence ○ As a result, the proteins produced by different alleles of the same gene frequently differ in their amino acid sequence ● To drive home the point, look at part (b) of the figure, at the DNA sequence in the portion of the melanocortin receptor and compare it to the sequence in (a). ○ The sequences differ – meaning they are DIFFERENT ALLELES. ■ Now look at the protein products of each allele, and note that one of the amino acids in the protein’s primary structure differs – ● one allele specifies an arginine residue; the other specifies a cysteine residue.

● At the protein level, the phenotypes associated with these alleles differ. The consequences for the mouse are striking; ○ Melanocortin receptors that have arginine in this location deposit a large amount of pigment, but receptors that have cysteine in this location deposit small amounts of pigment. ○ Whether a mouse is dark or light depends, largely, on a single base change in its DNA sequence. ■ In this case, a tiny difference in genotype produces a large change in phenotype. ● The central dogma links genotypes to phenotypes. How Long is a “Word” in the Genetic Code? ● How do the four DNA bases encode the sequence of proteins that contain 20 different amino acids? ○ Once biologists understood the general pattern of information flow in the cell, the next challenge was to understand the final link between DNA and proteins. ○ Exactly how does the sequence of bases in a strand of mRNA code for the sequence of the amino acids in a protein? ■ If this question could be answered, biologists would have cracked the genetic code – the rules that specify the relationship between a sequence of nucleotides in DNA or RNA and the sequence of amino acids in proteins.

● ○ The fist step in cracking the code was to determine how many cases make up a “word”. ○ In a sequence of mRNA, how long is a message that specifies one amino acid?

○ Based on some simple logic George Gamow predicted ■ Each word in the genetic code contains three bases ● His reasoning derived from the observation that 20 amino acids are commonly used in cells and from the hypothesis that each amino acid must be specified by a particular sequence of mRNA ○ His reasoning: ■ There are only four RNA bases (A, U, G and C), so a one-base code could specify only 4 different amino acids. ■ A 2 base code would represent 4 x 4 or 16 different amino acids ■ A 3 base code would represent 4 x 4 x 4 or 64 amino acids ○ A three-base code provides more than enough messages to code for all 20 amino acids ○ A three-base code is known as a triplet code ○ This hypothesis suggests that the triplet code is redundant – that more than one triplet of bases might specify the same amino acid. As a result, different 3 – base sequences in an mRNA – say AAA and AAG might code for the same amino said – say lysine. Triplet Code ● Experimental results consistent with a triplet code ● Codon ○ The group of three bases ○ Specifies a particular amino acid ● Reading frame...