NUCLEOTIDES The building blocks of DNA, nucleotides are used to make up the repeating units in the strands of DNA that represent the genetic code. A nucleotide consists of a sugar, a phosphate, and a nitrogen base. Since there are only four bases, researchers postulated that the enormous amount of genetic variation on the planet had to be in the sequence of the nucleotides within the DNA molecule. This sequence then controls the synthesis of precise proteins in the sequence of amino acids. On one end of the DNA molecule, the 5-carbon sugar has a phosphate attached and is known as the 58 end. On the other end of the sugar is an OH that is identified as the 38 end of the DNA molecule. Bases Four nitrogenous bases make up the bonding sites along the center of the DNA molecule and are bonded to a carbon on the sugar mol- ecule. There are two purines and two pyrimidines. The purine names end in -nine. MOLECULAR GENETICS—DNA AND EVOLUTION 117 Peterson’s n SAT II Success: Biology E/M www.petersons.com A. Adenine A purine, double-ring base with two bonding sites B. Thymine A pyrimidine, single-ring base with two bonding sites C. Cytosine A pyrimidine, single-ring base with three bonding sites D. Guanine A purine, double-ring base with three bonding sites Ribose A 5-carbon sugar, as signified by the -ose ending, ribose is considered the central part of the nucleotide, as the bases and the phosphate bond to it. Phosphate Bonded to another carbon on the ribose sugar, the last phosphate on the molecule is the 58 end. CHAPTER 5 118 Peterson’s n SAT II Success: Biology E/Mwww.petersons.com HISTONES Histones are proteins that help protect the DNA molecule. The DNA molecule is surrounded by eight or nine histones to help it form a protective DNA-histone complex in a tight space in the nucleus. BASE-PAIRING Base-pairing is the pairing of complimentary bases along the DNA strand. The sum of the bonds and the coiling of DNA makes the molecule securely attached along its entire length. Analysis of the assays of the DNA from a variety of organisms caused Erwin Chargaff to note that the percentage of adenine was almost identical to the percentage of thymine in the DNA of a cell. A similar relationship was discovered for cytosine and guanine. This was later referred to as Chargaff’s rule and led Watson and Crick to the ultimate conclusion that the molecule was directed inward—the result of which was their proposal that DNA was a double helix. Linus Pauling, who did so much work with proteins, wrestled with the molecule being directed outward; many others did as well, based on the strength of Dr. Pauling’s reputation. Adenine-Thymine This purine-pyrimidine bonding is the result of each base having two hydrogen bonding sites. Adenine and thymine can bond only with each other in DNA. MOLECULAR GENETICS—DNA AND EVOLUTION 119 Peterson’s n SAT II Success: Biology E/M www.petersons.com Cytosine-Guanine This purine-pyrimidine bonding in the DNA molecule is the result of these bases having three sites for hydrogen bonds. Cytosine and guanine can only bond with each other. H1 bonds The bonds between the adenine-thymine and cytosine-guanine classes of chemicals that form the base sequences in DNA, in addition to other places where we find hydrogen bonds. COMPLIMENTARY STRANDS Since adenine always bonds with thymine and guanine always bonds with cytosine, if one strand of the DNA molecule is known, then the other, complimentary strand can be known. This means that if you have one half of the molecule, you can construct the other half, which is exactly what DNA does during replication. The main strand CHAPTER 5 120 Peterson’s n SAT II Success: Biology E/Mwww.petersons.com is used as a template to produce its complement. The nature of the bonds along the strand make the adenines on one strand line up in the opposite direction of the adenines on the other strand. As a result, the molecule is said to be anti-parallel. 5* end “Hanging out” on one end of the base pairs is the phosphate group, which is the end that starts the “reading” of the molecule when it is being replicated. The direction of replication along the master strand then is from 58 end to 38 end. 3* end Opposite the base on the master strand with its 58 end is the compli- mentary strand with its 38 end oriented outward at the “beginning” of this strand, in an anti-parallel way. REPLICATION A combination of the words “reproduce” and “duplicate,” replication refers to the act of DNA making a copy of itself. This precedes mitosis or meiosis. Mitigated by enzymes, it proceeds as two concur- rent events, one from the 58 end of what is called the leading strand and the other from the 38 end of the lagging strand. The result of replication is said to be semi-conservative, since we end up with half the original DNA in each of the resulting new strands. DNA helicase DNA helicase is an enzyme that begins the unraveling of the DNA molecule at the sites of the hydrogen bonds. DNA polymerase This enzyme arranges the new nucleotides next to their complimen- tary base to make the new strand of DNA. As the name suggests, it makes a polymer out of individual nucleotides. MOLECULAR GENETICS—DNA AND EVOLUTION 121 Peterson’s n SAT II Success: Biology E/M www.petersons.com Leading strand A leading strand is a strand of DNA that starts at the 58 end and is made continuously. It is not named for the fact that it starts first, but for the fact that, since it is made continuously, the construction of it proceeds faster. Lagging strand A strand of DNA that starts at the 38 end. Its production proceeds slower than the leading strand because it is made in pieces that are then bonded to the template to which it will be complimentary. These pieces, known as Okasaki fragments, are bonded into place by DNA ligases. RNA-RNA RNA-RNA is a 5-carbon sugar that possesses an extra oxygen atom [compared with DNA] and replaces thymine with the base uracil, CHAPTER 5 122 Peterson’s n SAT II Success: Biology E/Mwww.petersons.com thus enabling it to pass through the nuclear envelope and take the code of DNA to the cytoplasm. Three types of RNA are made in the nucleus and reunite in the cytoplasm in the process known as protein synthesis. TYPES RNA, the carrier of the DNA code from the nucleus to the rough ER in the cytoplasm, has three forms that play a key role in the synthesis of proteins. These molecules, acting in concert, ultimately produce the proteins that control the life of the cell, even the production of RNA. rRNA Stored in the nucleolus, rRNA helps make up ribosomes that reside on the rough ER. Ribosomes are composed of rRNA and proteins. The mRNA attaches to the ribosomes and thus begins the making of a protein. mRNA mRNA is the lengthy form of RNA that is coded by the DNA molecule and carries that code for synthesis of a particular protein. This sequence will be “read” in the ribosome and serves as the blueprint for the precise sequence of amino acids that will make up the protein coded for in the mRNA. The codon is three consecutive nucleotides on the mRNA that code for a particular amino acid carried by the tRNA. MOLECULAR GENETICS—DNA AND EVOLUTION 123 Peterson’s n SAT II Success: Biology E/M www.petersons.com tRNA tRNA contains the anticodon to the mRNA’s codon, just three nucleotides long; the nature of this molecule was hypothesized before the structure was actually known. The tRNA carries an amino acid to the ribosome, where it bonds to the codon on the mRNA. There are 20 amino acids that make up proteins. The sequence of these amino acids, like the sequence of nucleotide bases in the DNA, is critical. If there was one base pair for every one amino acid, this would result in only four amino acids ever being utilized to make proteins. Two base pairs for every amino acid will code for a maxi- mum of 16 amino acids, four short of the needed 20 to transport all of the amino acids needed for life. It is now known that the tRNA molecules are, in fact, three bases long, providing more than enough variations to code for 20 amino acids as well as stop, start, and some duplication. CHAPTER 5 124 Peterson’s n SAT II Success: Biology E/Mwww.petersons.com TRANSCRIPTION Transcription takes place in the nucleus of eukaryotic cells. It is the first step in protein synthesis, wherein DNA’s information is copied on RNA. Three RNA molecules, rRNA, mRNA, and tRNA, are made during this phase, each from the separate complementary strands of original DNA. They are then transported to the cytoplasm, where the next step is performed—translation. During translation, the sequence of codons on mRNA orders the sequence of amino acids in the protein. Transcription can be likened to what occurs in, say, a court setting, where the court reporter transcribes the spoken word into the written word—same language, different form. MOLECULAR GENETICS—DNA AND EVOLUTION 125 Peterson’s n SAT II Success: Biology E/M www.petersons.com Bases In RNA, uracil replaces the thymine found in DNA. The uracil, like the thymine it replaces, still bonds opposite adenine. Students should be careful not to associate uracil with thymine in a way that the uracil replaces the adenine. It doesn’t; like thymine, it will bond opposite adenine as thymine does in DNA. In RNA, we will get A-U pairing, whereas in DNA, we get A-T pairing. Sugar The 5-carbon sugar, along with the phosphate, is part of the back- bone of nucleotides and is different in RNA. The RNA sugar has one more oxygen than the amount found in the DNA sugar. This makes this site possess an OH radical with no electrical activity. Alterna- tively, DNA possesses an H1 at that site, making its activity different than RNA. Promoters The site on DNA where transcription of RNA is begun, using only one of the DNA strands, the sense strand. The other strand—called the missense strand—is not used during this process. CHAPTER 5 126 Peterson’s n SAT II Success: Biology E/Mwww.petersons.com [...]... given by p2 and q2, and the frequency of heterozygous individuals is given by pq 1 qp 5 2pq The following equations hold: (1) p 1 q 5 1 (the sum of the alleles is 10 0 percent) and (2) p2 1 2pq 1 q2 5 1 (the sum of all the individuals is 10 0 percent) This equation holds true if 1 no natural selection occurs 2 no mutations occur 3 the population is isolated from other populations 4 the population is... called the lysogenic stage, occurs when an infected bacterium does not immediately duplicate viral particles The viral DNA is temporarily incorporated into the cellular DNA EVOLUTION Evolution is the changes in the frequencies of certain genes in a population over a period of time; 11 percent of the SAT II Biology exam has questions on this subject Genetic variation is what drives evolution Much of what... leave the nucleus without having the original code compromised if anything should happen to this RNA Finally, we translate the nucleotide sequences into polypeptide sequences Peterson’s n SAT II Success: Biology E/M 12 7 www.petersons.com CHAPTER 5 mRNA This is known as the codon and reflects the statement of the original code in the DNA This will be placed along the ribosomes for “reading,” the sequential... to conclude how species came to be so varied on the planet Basically, he stated that nature selects those organisms that will survive and pass on their survivability traits Peterson’s n SAT II Success: Biology E/M 13 1 www.petersons.com CHAPTER 5 Natural Selection Natural Selection is Darwin’s idea that species could not simply acquire the trait that allowed them to survive Like the culling of a herd... gamete selection, and crossing over 4 Outbreeding—mating that occurs between unrelated partners 5 Balanced polymorphism—the maintenance of a variety of phenotypes in a population, the most advantageous of which possess survival value The non-advantageous alleles decrease in frequency Peterson’s n SAT II Success: Biology E/M 13 3 www.petersons.com CHAPTER 5 C Allele Frequency Darwin proposed natural selection... www.petersons.com 13 0 Peterson’s n SAT II Success: Biology E/M MOLECULAR GENETICS—DNA AND EVOLUTION virus Transformation occurs when bacteria absorb free pieces of DNA from their environment VIRAL GENETICS Non-living substances, viruses can nonetheless take over a living cell in two stages The first, called the lytic stage, is when the virus penetrates the cell, uses cellular enzymes to duplicate viral particles,... vary is its (A) sugar (B) base (C) deoxyribose (D) ribose (E) phosphate 6 An mRNA is 429 nucleotides long The number of amino acids in the polypeptide chain formed from this mRNA is (A) 14 3 (B) 14 2 (C) 14 1 (D) 429 (E) 428 7 Which of the following is NOT consistent with Griffith’s experiments? (A) injected mixture of R-strain and live S-strain: mouse dies (B) injected mixture of heat-killed S-strain and... specifically a change in a single nucleotide One type of point mutation is base substitution, during which one base along the original DNA sequence is replaced by another base Peterson’s n SAT II Success: Biology E/M 12 9 www.petersons.com CHAPTER 5 Frame shift The entire sequence is shifted one or more frames along the DNA sequence Two types of mutations that cause a frame shift mutation are insertion... favorite subject of SAT II Biology test-makers Genetic equilibrium occurs when allele frequency remains unchanged, meaning there is no evolution: factors—mentioned above as affecting allele frequency—are held constant The frequency for each allele is given by p and q, the frequency of homozygous individuals is given by p2 and q2, and the frequency of heterozygous individuals is given by pq 1 qp 5 2pq The... and A-C-U, respectively Polypeptides The chains of amino acids that make up the polypeptides are, in sum, formed in the following way Once the mRNA is attached to the www.petersons.com 12 8 Peterson’s n SAT II Success: Biology E/M MOLECULAR GENETICS—DNA AND EVOLUTION rRNA in the ribosomes, the tRNA anticodon, with its accompanying amino acids, moves into position on the codon of mRNA The mRNA is then . individuals is given by pq 1 qp 5 2pq. The following equations hold: (1) p 1 q 5 1 (the sum of the alleles is 10 0 percent) and (2) p 2 1 2pq 1 q 2 5 1 (the sum of all the individuals is 10 0 percent). This. pyrimidines. The purine names end in -nine. MOLECULAR GENETICS—DNA AND EVOLUTION 11 7 Peterson’s n SAT II Success: Biology E/M www.petersons.com A. Adenine A purine, double-ring base with two bonding. it makes a polymer out of individual nucleotides. MOLECULAR GENETICS—DNA AND EVOLUTION 12 1 Peterson’s n SAT II Success: Biology E/M www.petersons.com Leading strand A leading strand is a strand of DNA