CS 262: Lecture 1 - Biology ReviewDNA and RNA Work on molecular biology began in 1954, after James Watson and Francis Crick discovered the structure of DNA. DNA is composed of nucleotides, each containing a phosphate group, a sugar, and a nitrogenous base. Two strands of nucleotides form the famous double helix structure. Most notably, nucleotides are paired such that the ba(C) is always paired with guanine (G). Watson and Crick escaped our attention that the specific pairing we have postulated immediately suggests a possible copying mRNA is very similar to DNA, but singleDNA By convention, DNA is written from the 5’ end to the 3’ end. You can get information about both strands by reading just one strand 5’GGTCT, its reverse complement (the opposite strand, read also from 5’ to 3’). However, the two sequences are not functionally equivalent, since they may encode different amino acids.Chromosomes Every cell in our body contains all of our DNA, which means about 3 billion bases! Since the DNA is so long, it must be packed densely into chromosomes.autosomes, and X and Y sex chromosomes.spheres around which DNA is packed. (Modifications to histones in a particular cell can tell us which DNA is active within the cell.) A nucleosome is a group of histones (pictured to the right). Biology Review and a bit of Sequence AlignmentWork on molecular biology began in 1954, after James discovered the structure of DNA. DNA is composed of nucleotides, each containing a phosphate group, a sugar, and a nitrogenous base. Two strands of nucleotides form the famous double helix structure. Most notably, nucleotides are paired such that the base adenine (A) is always paired with thymine (T), and cytosine (C) is always paired with guanine (G). Watson and Crick famously wrote, escaped our attention that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” RNA is very similar to DNA, but single-stranded and with uracil (U) replacing thymine.from the 5’ end to the 3’ end. You can get information about both and 5’-3’. In the example below, AGACC is chemically equivalent to GGTCT, its reverse complement (the opposite strand, read also from 5’ to 3’). However, the two equivalent, since they may encode different amino acids. of our DNA, which means about 3 billion bases! Since the DNA is so long, it must be . Humans have 2 x 22 X and Y sex chromosomes. Histones are spheres around which DNA is packed. (Modifications to histones in a particular cell can tell us which DNA is active within is a group of histones (pictured to the and a bit of Sequence Alignment nucleotides form the famous double helix structure. Most notably, nucleotides are (A) is always paired with thymine (T), and cytosine famously wrote, “It has not escaped our attention that the specific pairing we have postulated immediately stranded and with uracil (U) replacing thymine. from the 5’ end to the 3’ end. You can get information about both equivalent to GGTCT, its reverse complement (the opposite strand, read also from 5’ to 3’). However, the two equivalent, since they may encode different amino acids.The Genetic Dogma DNA is used to make proteins, the building blocks of life. To make a protein, a subsequence of DNA is transcribed inside the nucleus to single-stranded RNA, which is then translated inside the cytoplasm to a protein. A single gene can lead to many alternate forms of proteins. DNA to RNA to Protein to Cell In humans, DNA is about 3 x 109 nucleotides long, and contains around 22,000 genes. It is transcribed to messenger RNA (mRNA), which is translated to proteins. In addition, these proteins fold into 3-D structures that populate cells in organisms such as George W. Bush. Genetics in the 20th century In the 20th century, scientists formulated a basic description of how life is formed from information in DNA. In addition, evolution could now be studied from a molecular basis. Organisms have now been collected into a tree with parents representing common ancestors. • Humans and chimpanzees both evolved from common ancestors 6 million years ago. • Humans and rodents share ancestors from 80-100 million years ago. • Humans and fish share ancestors from 300 million years ago. Eukarya, including plants, animals, and even single-celled fungi like yeast, have nuclei in their cells; bacteria and archaea do not. Evolution results from errors in DNA transcription coupled with geographic migrations of groups of organisms, which allow populations of the same species to grow increasingly different until they are separate species. Most errors in DNA transcription are neutral or harmful. If harmful, organisms with those mutations tend to have fewer children, and the mutation dies out. Only when the error is beneficial does the mutation become significant in the evolution of a species. 21st Century In the 21st century, sequencing technologies now allow us to do relatively inexpensive sequencing of DNA. In the 20th century, procedures to identify genes were expensive and required considering one gene at a time. Now we can look at many genes at the same time, and figure out which genes are on or off in a specific time period. Between two individuals of the same species, DNA differs by about 1/1000 nucleotides. Molecular biologists are also interested in comparing the DNA of two individuals, a process made much easier with computers.In this course, we will be covering basic algorithms used in these technologies. Computational Biology Computational biology is concerned with organizing and analyzing massive amounts of data. This enables biologists to use data, form testable hypotheses, and make new discoveries about biology. We will study six uses of computational biology: 1. Sequencing Biologists can now identify sequences of around 500 nucleotides, which they then piece together like a puzzle (with 60 million pieces!) to form the entire sequence of DNA in an organism. The process is called Computational Fragment Assembly, and it was introduced in 1980. However, it was only in 1995 that up to a million DNA pieces could be assembled, and only in 2000 was the whole human genome assembled. As of this year, more than 500 genomes have been sequenced. 2. Gene Finding Only about 1.5% of human DNA encodes useful data (i.e. genes), therefore it is tricky to identify genes. Biologists must exploit statistical
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