lecture12 - Lecture 1 Introduction Biology Background The...

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Unformatted text preview: Lecture 1: Introduction: Biology Background The purpose of this lecture is to review the basics of biology relevant to this course. By the end of this lecture, we will have a general knowledge of the structure of biomolecules, how DNA functions, what a gene is, and how computer scientists differ from biologists. We will also have a basic understanding of the abstract model of a cell shown in figure 1 below. Also, we will only learn biology that is necessary in this class. As seen in figure 1, a cell has two areas: an inner area called the nucleus, and an outer area called the cytoplasm or cytosol. The cytoplasm is basically everything that is not in the nucleus. There are many types of molecules in the cell such as DNA and RNA, and many molecular processes. We will have a basic understanding of these by the end of the lecture. All living organisms have genetic material consisting of DNA and RNA. DNA stands for D eoxyribo N ucleic A cid and RNA stands for R ibo N ucleic A cid. They are given these names because they are most often located in the nucleus of Figure 1: A model of the cell. Figure 2: DNA structure. the cell (nucleus = nucleic) and contain a chemical called phosphoric acid. The “Deoxyribo” and “Ribo” refer to the relatively simple molecules called nucleotides that make up DNA and RNA. These nucleotides are considered monomers because they can be chained together to form a polymer, which in this case is a DNA or RNA polymer. In turn, another term for a polymer is a macromolecule. The nucleotides that make up DNA are called deoxyribonucleotides, or dNTP for short, and the nucleotides that make up RNA are called ribonucleotides, or NTP for short. A deoxyribonucleotide consists of the following molecules: a deoxyribose sugar, a phosphoric acid, and a nitrogenous base. The nitrogenous base for a deoxyribonucleotide can be one of the following: Adenine(A), Guanine(G), Cytosine(C), and Thymine(T). On the other hand, a ribonucleotide is similar to a deoxyribonucleotide except that it has a ribose sugar in place of a deoxyribose sugar, and in the nitrogenous base Uracil(U) replaces Thymine(T). Figure 3a and 3b show the general structure of a nucleotide. Note that the carbon atoms in the ribose and deoxyribose are numbered 1’ to 5’ (the carbon atoms in positions 1’ through 4’ are implied, so we don’t have to print a C to represent carbon there). Figure 4 shows the different possible nitrogen bases that DNA and RNA can have, which consist of a subgroup of purines and a subgroup of pyrimidines. Figure 3a: Example of an RNA monomer (ribonucleotide) that has the nitrogenous base Adenine(A) represented in blue. (We actually need 2 more phosphate groups to create ATP.) Figure 3b: This highlights the difference between a ribose sugar from RNA and a deoxyribose sugar from DNA. Two nucleotide monomers can bond at the 3 rd carbon atom of one nucleotide and the 5 th carbon atom from the other. This bond is called a phosphodiester bond, and the...
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lecture12 - Lecture 1 Introduction Biology Background The...

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