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Genetic Molecules | OAT Nucleic Acid • Nucleosides consist of a nitrogenous base and a pentose sugar • Nucleoside A nucleoside consists of a nitrogenous base (red) and a pentose sugar (blue). The nitrogenous base shown here is adenine, making this nucleoside adenosine. • Nucleotides are formed when a phosphate group is bonded to the nucleoside o Adenine, guanine, cytosine, thymine, and uracil We will see their structures later, but you need not memorize them Nucleotides polymerize to form nucleic acids o (more specifics soon) Deoxyribonucleic Acid (DNA) • DNA is a nucleic acid built from nucleotides with 4 nitrogenous bases: o Adenine, guanine, cytosine, & thymine o Uracil is not found in DNA; it is found in RNA, which we will see later • Adenine and guanine are: o Double-ringed o Known as “purines” • Cytosine and thymine are: o Single-ringed o Known as “pyrimidines” • As a pneumonic, remember that “cytosine,” “thymine,” and “pyrimidine” have the letter “y” Nucleotide A nucleotide is formed when a phosphate group (green) is appended to a nucleoside. The nucleotide formed here is adenosine phosphate. • • Nucleotides are frequently referred to by the name of their nitrogenous base o “Adenosine phosphate” above can simply be called “adenine” There are 5 nitrogenous bases we will use: The 4 Nucleotides of DNA Cytosine and thymine are pyrimidines, while adenine and guanine are purines. 1 © 2017 J Co Review, Inc., Accessed by Guest on 06-18-2017 Genetic Molecules | OAT • • Though not found in DNA, uracil is a purine DNA forms when nucleotides polymerize via phosphodiester bonds o These are bonds between a pentose sugar’s 3rd carbon and the phosphate of another nucleotide Ordering 5’ to 3’ Using the blue nucleotide as an example, an arrow pointing from the pentose’s 5-carbon to its 3-carbon points down. This arrow indicates that our nucleic acid should be denoted green blue red and not in the reverse direction. • • One DNA Strand (aka A Nucleic Acid) DNA consists of several nucleotides adjoined between the 3rd carbon on one nucleotide’s pentose sugar and the phosphate group of another nucleotide. These bonds, indicated by black arrows, are called phosphodiester bonds. • • We denote nucleic acids as a list of all its nucleotides o But in which direction? 5’ to 3’ o That is, we order nucleotides in the direction indicated by an arrow from one pentose sugar’s 5 carbon to its 3 carbon In the above nucleic acid, an arrow from a pentose’s 5-carbon to its 3-carbon points downwards o So, we’d order that nucleotide from green blue red • Nucleic acids can be exceedingly long For simplicity, we will no longer draw each nucleotide in its entirety o Rather, we will show the “backbone” of phosphate groups coupled with each nucleotide represented by a unique geometric shape So, the nucleic acid we’ve been working with will be shown as: Simple Nucleic Acid Illustration We will abbreviate the expansive nucleic acid structure to a phosphate backbone (black) coupled with each nucleotide represented by a unique geometric shape and color. Ordered from 5’ to 3’, this strand is AGC, representative of adenine guanine cytosine. 2 © 2017 J Co Review, Inc., Accessed by Guest on 06-18-2017 Genetic Molecules | OAT • • • • The 5’ end of a nucleic acid is capped with a phosphate group The 3’ end is capped with a hydroxyl o (shown in previous illustrations) DNA consists of two nucleic acids lying side-by-side The two strands lie in opposite directions o One strand points 5’ 3’ in one direction, and the other points 5’ 3’ in the other direction DNA Complementary Strands Given the bottom strand of AGCGAT, the top strand must be its complement: TCGCTA. Each A is paired with T, and each G is paired with C. • • DNA Structure DNA consists of two nucleic acids lying side-byside oriented in opposite directions. The two strands are held together by hydrogen bonds (black dotted lines). An adenine on one strand is always coupled with thymine on the other strand. The same is true of guanine and cytosine. • • A DNA nucleotide and it’s “partner” on the complementary strand is called a base pair o We’d say the above DNA is 3 base pairs long Since A is always coupled with T and G is always coupled with C, we can predict the complementary sequence o i.e. suppose know that from 5’ 3’, one strand of DNA has the sequence AGCGAT o The complementary strand must be TCGCTA • But be careful! Since the bottom strand was 5’ 3’ going rightward, the top strand is 5’ 3’ going leftward o And since we report nucleic acids 5’ 3’, the complementary strand is technically ATCGCT We mentioned earlier that the two strands are held together via hydrogen bonds o C and G share 3 H bonds o A and T share 2 H bonds Think, C & G both rhyme with 3 In fact, a common exam question will show a few DNA fragments and ask which is most resistant to decomposition o The answer will be the fragment containing the most C-G base pairs More C-G base pairs means more H bonds, making stronger DNA Identifying the Strongest DNA Sequence The circled DNA fragment, which contains the most C-G base pairs, will be the strongest. 3 © 2017 J Co Review, Inc., Accessed by Guest on 06-18-2017 Genetic Molecules | OAT • • We’ve been drawing DNA as linear side-by-side nucleic acids But in reality, DNA actually forms a 3D double helix • • • (a) (b) True Structure of DNA We’ve depicted DNA as (a) linear side-by-side nucleic acids. In actuality, DNA is twisted into (b) a double helix. This may be easier to visualize in the lecture video, in which the twisting DNA strands are animated. Genes • Several nucleotides within DNA make up a gene o Genes encode RNA, which in turn encode the proteins organisms rely upon to survive o We will learn more about RNA and protein production in the coming sections • • • In the previous illustration, we show 7 nucleotides comprising a gene o But in actuality, several hundred or thousand nucleotides will comprise a gene Prokaryotes, which are simple organisms lacking a nucleus and membrane-bound organelles, have just one copy of each gene Eukaryotes, which are more complex organisms that do have a nucleus and membrane-bound organelles, can have multiple copies of each gene o Eukaryotes even have “spacer” DNA that doesn’t code for RNA In eukaryotes, DNA commonly transcribed into RNA is stored as euchromatin o Which is lightly-packed DNA, which is easy to unfold and reference DNA not commonly needed is stored as heterochromatin o Which is more tightly packed away The entirety of an organism’s genes is called the organism’s genome o Though everyone’s genome is unique, all human genomes differ by less than 0.1% o And, the human genome is only ~2% different from that of a chimpanzee Genes DNA nucleotides make up a gene, which encodes RNA, which encodes proteins. More on this in coming sections 4 © 2017 J Co Review, Inc., Accessed by Guest on 06-18-2017