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Chapter Seventeen Nucleic Acids
Copyright © Houghton Mifflin Company. All rights reserved.16a–2 Nucleic acids comprise the genetic machinery of living cells. They are polymers composed of nucleotide monomer units. They were first discovered by F. Miescher in 1869, but their importance was not recognized for nearly a century. There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). They contain ribose and deoxyribose sugars, respectively.
Copyright © Houghton Mifflin Company. All rights reserved.16a–3 Nucleotides: The Building Blocks of Nucleic Acids
Copyright © Houghton Mifflin Company. All rights reserved.16a–4 Nucleotides are three-component molecules containing: (1)a phosphate group, (2)a pentose sugar (deoxyribose or ribose), (3) a heterocyclic nitrogen-containing base (a purine or a pyrimidine). PhosphateSugar Base
Copyright © Houghton Mifflin Company. All rights reserved.16a–5 The Pentose Sugars The only difference is that an OH group is bound to carbon 2’ in ribose, and this is replaced by an H in deoxyribose. RNA has ribose as its sugar, DNA uses deoxyribose.
Copyright © Houghton Mifflin Company. All rights reserved.16a–6 The Nitrogenous Bases There are two basic forms: Purines and Pyrimidines:
Copyright © Houghton Mifflin Company. All rights reserved.16a–7 The Nitrogenous Bases
Copyright © Houghton Mifflin Company. All rights reserved.16a–8 The Phosphate Group O OH O - | | O==P—OH | | OHO - Phosphoric AcidIonized form at pH = 7 Phosphoric acid is H 3 PO 4
Copyright © Houghton Mifflin Company. All rights reserved.16a–9 Nucleotide Formation Nucleotides are formed from their subunits by (you guessed it!) condensation reactions, splitting out waters. Both the phosphate-sugar reaction and the sugar-base reaction split out water molecules.
Copyright © Houghton Mifflin Company. All rights reserved.16a–10 Nucleotide Nomenclature
Copyright © Houghton Mifflin Company. All rights reserved.16a–11 Primary Structure of Nucleic Acids The backbone of a nucleic acid is composed of sugar- phosphate bonds. The bases stick off of the sugar units and their sequence forms the primary structure. Only four types of bases appear in any nucleic acid.
Copyright © Houghton Mifflin Company. All rights reserved.16a–12 The Structure of a Nucleic Acid Note the 3’ and 5’ ends.The primary structure has a direction. The links are 3,5’ “phosphodiester” links. Each phosphate link has a -1 charge. By convention, the strand is read from the 5’ to the 3’ end. Here TGCA.
Copyright © Houghton Mifflin Company. All rights reserved.16a–13 The Double Helix In 1953 in James D. Watson and Francis Crick figured out the structure of DNA— it turned out to be a double helix. They published their results in the journal Nature. Watson later wrote a controversial book called The Double Helix.
Copyright © Houghton Mifflin Company. All rights reserved.16a–14 There Were Clues Earlier ￭ One clue was that in DNA the percentage of the base adenine was always the same as that of the base thymine, and the percentage of guanine was always the same as that of the base cytosine: that is, %A = %T and %G = %C ￭ Also, experiments indicated that nucleic acids were the genetic materials in viruses. ￭ But these clues were largely ignored while most workers focused on proteins as the supposed genetic material.
Copyright © Houghton Mifflin Company. All rights reserved.16a–15 The Two Strands Of DNA are Complementary “A” hydrogen bonds to “T”, and “G” hydrogen bonds to “C,” so one strand is complementary to the other. Example: Strand 1: AGTCAATGCC Strand 2: TCAGTTACGG Remember: We start on strand 1 at the 5’ end and go from there.
Copyright © Houghton Mifflin Company. All rights reserved.16a–16 Replication of DNA In this process DNA molecules produce exact duplicates of themselves. The strands separate and acquire new strands. Enzymes direct the process.
Copyright © Houghton Mifflin Company. All rights reserved.16a–17
Copyright © Houghton Mifflin Company. All rights reserved.16a–18 Chromosomes and Genes A chromosome is a DNA molecule bound to a group of proteins. Typically a chromosome is about 15% DNA and 85% protein. Humans have 46 chromosomes in each cell; dogs have 78, frogs 26, mosquitos 6. Chromosomes come in matched pairs: so humans have 23 pairs, one from the father, the other from the mother, in each pair. Each chromosome houses a large number of genes.
Copyright © Houghton Mifflin Company. All rights reserved.16a–19 Protein Synthesis The Central Dogma: Information flows from DNA to RNA to proteins: Information DNA → RNA → Proteins The DNA → RNA step is called transcription. In this step DNA passes on the code for a protein to RNA. The RNA → Proteins step is called translation. In this step (which is actually composed of several steps) the codes in the RNA are used as blueprints in protein synthesis. Note that RNA molecules are usually single-stranded, whereas DNA is double-stranded. RNA molecules also tend to be much smaller than DNA molecules.
Copyright © Houghton Mifflin Company. All rights reserved.16a–20 The Structure of a Cell ■ All higher organisms have “eukaryotic” cells that have a nucleus. Schematic of a eukaryotic cell Mitochondria are the main energy- producing organelles Ribosomes (the small dots) are the organelles where proteins are manufactured.
Copyright © Houghton Mifflin Company. All rights reserved.16a–21 Ribonucleic Acids There are several important types of RNA molecules: Messenger RNA – mRNA molecules carry the codes for proteins from the DNA (in the nucleus) to the ribosomes (which are structures in the cell outside the nucleus). Primary transcript RNA – ptRNA is the “raw material” for messenger RNA. It will be edited to produce mRNA Ribosomal RNA – The ribosomes are structures in the cell where the actual synthesis of proteins occurs. They consist of RNA and protein. This RNA is designated rRNA. Transfer RNA – tRNA molecules transfer specific amino acids to the ribosomes, where the amino acids are joined into proteins. Other RNAs – A number of other types of small RNAs play special genetic roles, such as regulating gene expression.
Copyright © Houghton Mifflin Company. All rights reserved.16a–22 The Genetic Code A gene is a segment of DNA that carries the code for the structure of a protein (or sometimes an RNA molecule). A gene usually consists of a DNA sequence of about nucleotides. The human genome (the entire genetic code on 46 chromosomes) apparently contains about 20-22,000 genes. The “code” consists of three-nucleotide sequences (codons) that stand for individual amino acids. For example, the DNA sequence G-U-C (starting, remember, from the 5’ end) represents the amino acid valene. Other coding sequences are: UUC – phenylalanineUCA – serene CCA – prolineAGA – argenine And so forth: See Table 17.2 for a full list.
Copyright © Houghton Mifflin Company. All rights reserved.16a–23 Additional Comments on the Code The code is almost universal: that is, it used by almost all organisms: plants, microbes, and humans. The code contains start and stop signals. With four different “letters” (A,T,G,C), a three- letter sequence has 4 3 = 4x4x4 = 64 possibilities. A given amino acid may be specified by several sequences. For example, the sequences UCU, UCC, UCA, and UCG all specify the amino acid serine. (The code is thus said to be “degenerate”, i.e., not having a single, unique sequence for each amino acid.)
Copyright © Houghton Mifflin Company. All rights reserved.16a–24 Transcription of the Code from DNA to RNA Four steps: 1.A portion of the DNA sequence unwinds and exposes a gene. This is governed by the enzyme RNA polymerase. 2.Free ribonucleotides align along one of the exposed DNA strands. They pair up with complementary bases on the DNA. 3.RNA polymerase links up these ribonuceotides. 4.Transcription ends when the enzyme encounters a “stop” signal in the DNA sequence. This produces “primary transcript RNA”, ptRNA.
Copyright © Houghton Mifflin Company. All rights reserved.16a–25 Editing of the ptRNA: Formation of mRNA But the RNA sequence (ptRNA) is not quite ready to be used for protein formation – it must be edited. In the editing some parts (introns) are spliced out. Exons are kept and joined.
Copyright © Houghton Mifflin Company. All rights reserved.16a–26 Some Additional Details Splicing means that a single gene can yield several protein codes, depending on how it is spliced. This is called alternative splicing. Both the exons and introns of a gene are initially transcribed to form ptRNA. Then the ptRNA is spliced to form the mRNA for a given protein. Enzymes direct the splicing. The Human Genome Project (which produced a rough sequence for the human genome) was completed in 2001 with the sequencing of about 3 billion nucleotides and about 22,000 genes. Two groups were responsible for it: an NIH group led by Francis Collins and a private group (Celera Genomics) led by J. Craig Venter. Now many additional organisms have had their genomes sequenced.
Copyright © Houghton Mifflin Company. All rights reserved.16a–27 Transfer RNA Transfer RNA (tRNA) molecules pick up amino acids and transfer them to the ribosomes, where they are aligned and linked up to form proteins. tRNAs attach amino acids at one end and have a recognition portion (anticodon) that pairs up with a complementary sequence on the mRNA that codes for that amino acid.
Copyright © Houghton Mifflin Company. All rights reserved.16a–28 Translation: Protein Synthesis ■ Protein synthesis occurs on the ribosomes, which are cell organelles. The synthetic process requires a number of ingredients: ■ Ribosomes are the sites, or “factories”, where proteins are synthesized. They are comprised of subunits containing about 65% RNA and 35% protein. ■ Messenger RNA molecules act like messengers, bringing the code, or blueprint, for a protein (the “message”) from the DNA gene to the ribosomes. ■ Transfer RNA molecules pick up amino acids and carry them to the ribosomes. There they line them up using their anticodons. Thus they act like workers who gather and assemble the parts. ■ Enzymes act like managers and workers to control and operate the manufacturing process.
Copyright © Houghton Mifflin Company. All rights reserved.16a–29 ■ Enzymes direct the process, and the polypeptide continues to grow as more amino acids are added. ■ Growth continues until a “stop” codon is encountered. ■ Finally, the polypeptide is cleaved from the tRNAs by hydrolysis.
Copyright © Houghton Mifflin Company. All rights reserved.16a–30 ■ Protein synthesis involves a number of different stages. ■ Normally,some additional processing of the protein takes place after it separates from the ribosome. ■ A single mRNA molecule can code for the production of a large number of Identical protein molecules.
Copyright © Houghton Mifflin Company. All rights reserved.16a–31 ￭ Translation of the mRNA code into protein. ￭ tRNAs bring in amino acids and put them in their proper places on the mRNA. ￭ The process continues until the entire protein sequence is formed. ￭ The yellow glob is the enzyme that directs the operation.
Copyright © Houghton Mifflin Company. All rights reserved.16a–32 Comments on “Junk DNA” ￭ For a long time it was thought that large portions of the genome contained useless, or “junk”, sequences of nucleotides. ￭ Now it is realized that these supposed junk regions actually code for different kinds of RNA molecules that help regulate the expression of genes. ￭ Apparently the resulting differences in gene expression are very important in determining differences between different individuals and different species, e.g., between humans and chimpanzees.
Copyright © Houghton Mifflin Company. All rights reserved.16a–33 EPIGENETICS ■ This term refers to effects that go beyond, or fall outside, effects caused by the genetic code itself. Thus epigenetic means ”beyond the genetic code.” ■ Genetics is not destiny. Epigenetic effects account for why identical twins, with the same genetic code, are not completely identical. For example, why does one gets a disease and the other doesn’t. ■ Many epigenetic effects come from the environment. ■ Selective methylation of biomolecules can have dramatic effects, turning genes on or off. ■ Histones are proteins that surround the DNA of the genetic code. These proteins can “hide” parts of the code and prevent genes from being expressed.
Copyright © Houghton Mifflin Company. All rights reserved.16a–34 In general genetic engineering involves placing a gene from one organism into another organism. Example: Bacteria have been genetically altered to produce human insulin, and this can be used to treat diabetics. The bacteria can be grown in large numbers and the insulin is harvested for medical use. Special enzymes are used to extract and insert the desired genes. In some cases genes can be artificially constructed for such purposes. Genetic Engineering
Copyright © Houghton Mifflin Company. All rights reserved.16a–35 Misfolded Proteins ■ Just as misguided people can cause problems, so also can misfolded proteins. ■ Disease-causing misfolded proteins are called prions (pronounced “PREE-ons’). They are believed responsible for the following diseases: Sheep – scrapies Cattle – mad cow disease Humans – human variant Creutzfeld-Jacob disease (and perhaps Alzheimer’s disease, Parkinson’s disease) ■ Stanley Prusiner (UCSF) won the 1997 Nobel Prize for first suggesting that misfolded proteins were responsible for disease. This was, and is, a very controversial idea. ■ A tribe of cannibals in New Guinea honored their dead by eating their brains—and developed a neurological disease (kuru).
Copyright © Houghton Mifflin Company. All rights reserved.16a–36 What you absolutely must understand from Chapter 17 ■ Understand that nucleic acids form the genetic machinery of cells, and that they are polymers of nucleotide monomers. ■ Understand that there are two types of nucleic acids: RNAs and DNAs. ■ Understand that nucleotides have three parts: a pentose sugar, a phosphate group, and a nitrogen-containing base. ■ Be able to distinguish ribose from deoxyribose. ■ Be able to distinguish a purine from a pyrimidine. ■ Know that T, C, and U are pyrimidines, and A and G are purines. ■ Know that DNA contains deoxyribose with A, T, G, and C, whereas RNA contains ribose with A, U, G,and C.
Copyright © Houghton Mifflin Company. All rights reserved.16a–37 What you must know (cont.) ■ Know that the nucleotides are called adenosine, guanosine, etc. ■ Understand that the pentose sugars of nucleotides are joined to both phosphate and base units by means of condensation reactions. Know what a condensation reaction is and what its reverse reaction is called. ■ Appreciate what the “primary structure” of a nucleic acid refers to, and that it has a 5’ and a 3’ end. Be able to contrast this primary structure with that of a protein. (What types of links are involved in each? What types of side groups?) ■ Understand that the secondary structure of DNA is a double helix, with two strands wrapped around each other in a spiral, with the bases inside, and held together by hydrogen bonds between the bases. Know what bases bond to each other in this way.
Copyright © Houghton Mifflin Company. All rights reserved.16a–38 What you must know (cont.) ■ Know who first determined the DNA structure and when. Appreciate that they relied on X-ray diffraction studies to find the structure. ■ Appreciate why the fact that the % G = % C in DNA was an important clue for the structure determination. ■ Appreciate that there are three hydrogen bonds between G and C, and just two between A and T. ■ Understand the process by which DNA replicates itself so that two identical copies are made. ■ Understand the terms gene, genome, and chromosome. Know how many chromosomes humans have.
Copyright © Houghton Mifflin Company. All rights reserved.16a–39 What you must know (cont.) ■ Understand the general idea of the “Central Dogma” (even though some exceptions are now known). ■ Understand the different types of RNA (rRNA, ptRNA, mRNA, tRNA) present in a cell and what their roles in protein synthesis are. ■ Understand the general process by which proteins are made in a cell: where it happens and how it happens. ■ Understand the basic idea of the genetic code —that each amino acid is coded for by a sequence of three nucleotides (a codon). Appreciate that the human genome has about 3 billion nucleotides and 22,000 genes. ■ Understand the idea of splicing of ptRNA, and how it allows a single gene to yield several different mRNAs that code for several different proteins.
Copyright © Houghton Mifflin Company. All rights reserved.16a–40 What you must know (cont.) ■ Appreciate that an amino acid may be represented in the code by several different codons. ■ Understand the basic structure of a tRNA molecule and how its attachment site and anticodon region contribute to its action. Appreciate that it forms an ester link to its amino acid, and that this link is later hydrolyzed. ■ Appreciate that protein formation on the ribosome is ended when a stop condon is encountered. Also understand that the whole process is controlled by several enzymes. ■ Understand that a single messenger RNA can be used repeatedly as the blueprint for a number of identical proteins. ■ Understand that genetic engineering generally involves the transfer of a gene from one organism into the genome of another organism.
Copyright © Houghton Mifflin Company. All rights reserved.16a–41 To Do List Read chapter 17!! Do additional problems Review Lecture notes for Chapter Seventeen Do practice test T/F Do practice test MC
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