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Informational Macromolecules Biochemistry Finals Informational Macromolecules Page 1 of 92  Types of Nucleic aCID Informational Macromolecules Page 2...

Informational Macromolecules Biochemistry Finals Informational Macromolecules Page 1 of 92  Types of Nucleic aCID Informational Macromolecules Page 2 of 92  TYPES OF NUCLEIC ACIDS deoxyribonucleic acid (DNA) - Nearly all the DNA is found within the cell nucleus. Its primary function is the storage and transfer of genetic information. ◀ This information is used (indirectly) to control many functions of a living cell. In addition, DNA is passed from existing cells to new cells during cell division ribonucleic acid (RNA)- occurs in all parts of a cell. It functions primarily in synthesis of proteins, the molecules that carry out essential cellular functions. Two types of nucleic acids are found within cells of higher organisms: deoxyribonucleic acid (DNAH and ribonucleic acid (RNAH. Informational Macromolecules Page 3 of 92  Nucleotides: Structural Building Blocks for Nucleic Acids Informational Macromolecules Page 4 of 92  NUCLEIC ACID Nucleic acid is an unbranched polymer containing monomer units called nucleotides. A given nucleic acid molecule can contain in excess of one million nucleotide units. The Swiss physiologist Friedrich Miescher (1844–1895H discovered nucleic acids in 1869 while studying the nuclei of white blood cells. The fact that they were initially found in cell nuclei and are acidic accounts for the name nucleic acid. Amost remarkable property of living cells is their ability to produce exact replicas of themselves. Furthermore, cells contain all the instructions needed for making the complete organism of which they are a part. The molecules within a cell that are responsible for these amazing capabilities are nucleic acids Informational Macromolecules Page 5 of 92  NUCLEIC ACID A nucleotide is a three-subunit molecule in which a pentose sugar is bonded to both a phosphate group and a nitrogen- containing heterocyclic base. With a three-subunit structure, nucleotides are more complex monomers than the monosaccharides of polysaccharides or the amino acids of proteins Informational Macromolecules Page 6 of 92  PENTOSE SUGARS Structurally, the only difference between these two sugars occurs at carbon 2′. The -OH group present on this carbon in ribose becomes an -H atom in 2′- deoxyribose. (The prefix deoxy- means “without oxygen.”) RNA and DNA differ in the identity of the sugar unit in their nucleotides. In RNA, the sugar unit is ribose—hence the R in RNA. In DNA, the sugar unit is 2′-deoxyribose—hence the D in DNA. Informational Macromolecules Page 7 of 92  NITROGEN-CONTAINING HETEROCYCLIC BASES Five nitrogen-containing heterocyclic bases are nucleotide components Pyrimidine- , a monocyclic base with a six-membered ring Purine- a bicyclic base with fused fiveand six-membered rings Informational Macromolecules Page 8 of 92  NITROGEN-CONTAINING HETEROCYCLIC BASES The three pyrimidine derivatives found in nucleotides are thymine (T)- the 5-methyl-2,4-dioxo derivative cytosine (C),- 4-amino-2-oxo derivative and uracil (U)- 2,4-dioxo derivative A pyrimidine derivative that was encountered previously is the B vitamin thiami Informational Macromolecules Page 9 of 92  NITROGEN-CONTAINING HETEROCYCLIC BASES The two purine derivatives found in nucleotides are adenine (A) - 6-amino derivative guanine (G) - 2-amino-6-oxo purine derivative Caffeine, the most widely used nonprescription central nervous system stimulant, is the 1,3,7-trimethyl-2,6- dioxo derivative of purine Adenine, guanine, and cytosine are found in both DNA and RNA. Uracil is found only in RNA, and thymine usually occurs only in DNA. Informational Macromolecules Page 10 of 92  PHOSPHATE Phosphate, the third component of a nucleotide, is derived from phosphoric acid (H3PO4). Under cellular pH conditions, the phosphoric acid loses two of its hydrogen atoms to give a hydrogen phosphate ion Informational Macromolecules Page 11 of 92  NUCLEOTIDE FORMATION The formation of a nucleotide from a sugar, a base, and a phosphate can be visualized as a two-step process. 1. First, the pentose sugar and nitrogen-containing base react to form a two-subunit entity called a nucleoside (not nucleotide, s versus t). 2. The nucleoside reacts with a phosphate group to form the three-subunit entity called a nucleotide. It is nucleotides that become the building blocks for nucleic acids Informational Macromolecules Page 12 of 92  NUCLEOTIDE FORMATION Informational Macromolecules Page 13 of 92  NUCLEOSIDE FORMATION A nucleoside is a two-subunit molecule in which a pentose sugar is bonded to a nitrogen-containing heterocyclic base. Important characteristics of the nucleoside formation process of combining two molecules into one are: 1. The base is always attached to C1′ of the sugar (the anomeric carbon atom), which is always in a b-configuration. For purine bases, attachment is through N9 for pyrimidine bases, attachment is through N1 The bond connecting the sugar and base is a b-N-glycosidic linkage. 2. A molecule of water is formed as the two molecules bond together; a condensation reaction occurs. Informational Macromolecules Page 14 of 92  NUCLEOSIDE FORMATION Eight nucleosides are associated with nucleic acid chemistry—four involve ribose (RNA nucleosides) and four involve deoxyribose (DNA nucleosides). RNA Nucleosides DNA Nucleosides ribose–adenine deoxyribose–adenine ribose–cytosine deoxyribose–cytosine ribose–guanine deoxyribose–guanine ribose–uracil deoxyribose–thymine Informational Macromolecules Page 15 of 92  NUCLEOSIDE FORMATION Informational Macromolecules Page 16 of 92  NUCLEOSIDE FORMATION Important characteristics of the nucleotide formation process of adding a phosphate group to a nucleoside are the following: 1. The phosphate group is attached to the sugar at the C5′ position through a phosphoester linkage. 2. As with nucleoside formation, a molecule of water is produced in nucleotide formation. Thus, overall, two molecules of water are produced in combining a sugar, base, and phosphate into a nucleotide. Nucleotides are named by appending the term 5′-monophosphate to the name of the nucleoside from which they are derived. Addition of a phosphate group to the nucleoside adenosine produces the nucleotide adenosine 5′-monophosphate. Abbreviations for nucleotides exist, which are used in a manner similar to that for amino acids (Section 20-2). The abbreviations use the one-letter symbols for the base (A, C, G, T, and U), MP for monophosphate, and a lowercase d at the start of the abbreviation when deoxyribose is the sugar. The abbreviation for adenosine 5′-monophosphate is AMP and that for deoxyadenosine 5′-monophosphate is dAMP. Informational Macromolecules Page 17 of 92  Primary Nucleic Acid Structure Informational Macromolecules Page 18 of 92  NUCLEIC ACID Nucleic acids are polymers in which the repeating units, the monomers, are nucleotides. The nucleotide units within a nucleic acid molecule are linked to each other through sugar–phosphate bonds. The resulting molecular structure involves a chain of alternating sugar and phosphate groups with a base group protruding from the chain at regular intervals. Informational Macromolecules Page 19 of 92 (a) The NUCLEIC ACID generalized backbone structure of a nucleic acid. (b) The specific backbone structure for a deoxyribonucleic acid (DNA). (c) The specific backbone structure for a ribonucleic acid (RNA). Informational Macromolecules Page 20 of 92  NUCLEIC ACID A deoxyribonucleic acid (DNA) is a nucleotide polymer in which each of the monomers contains deoxyribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or thymine The alternating sugar–phosphate chain in a nucleic acid structure is often called the nucleic acid backbone. DNA-deoxyribose RNA- Ribose Informational Macromolecules Page 21 of 92  sequence of bases NUCLEIC ACID -Variable portion attached to the sugar units of the backbone. The sequence of these base side chains distinguishes various DNAs from each other and various RNAs from each other. -Only four types of bases are found in any given nucleic acid structure. In both RNA and DNA, adenine, guanine, and cytosine are encountered as side-chain components; thymine is found mainly in DNA, and uracil is found only in RNA Informational Macromolecules Page 22 of 92  NUCLEIC ACID Primary nucleic acid structure is the sequence in which nucleotides are linked together in a nucleic acid. Because the sugar–phosphate backbone of a given nucleic acid does not vary, the primary structure of the nucleic acid depends only on the sequence of bases present PRIMARY STRUCTURE: 5′ T–G–C–A 3′ P. Each nonterminal phosphate group of the sugar–phosphate backbone is bonded to two sugar molecules through a 3′,5′-phosphodiester linkage. There is a phosphoester bond to the 5′ carbon of one sugar unit and a phosphoester bond to the 3′ carbon of the other sugar. 2. A nucleotide chain has directionality. One end of the nucleotide chain, the 5′ end, normally carries a free phosphate group attached to the 5′ carbon atom. The other end of the nucleotide chain, the 3′ end, normally has a free hydroxyl group attached to the 3′ carbon atom. By convention, the sequence of bases in a nucleic acid strand is read from the 5′ end to the 3′ end. ◀ 3. Each nonterminal phosphate group in the backbone of a nucleic acid carries a P– charge. The parent phosphoric acid molecule from which the phosphate was derived originally had three !OH groups (Section 22-2H. Two of these become involved in the 3′,5′-phosphodiester linkage. The remaining !OH group is free to exhibit acidic behavior—that is, to produce an H+ ion. Informational Macromolecules Page 23 of 92 This behavior by the many phosphate groups in a nucleic acid backbone gives nucleic acids their acidic properties. Specifying the primary structure for a nucleic acid is done by listing nucleotide base components (using their one-letter abbreviations) in sequential order starting with the base at the 5′ end of the nucleotide strand. Informational Macromolecules Page 24 of 92 Three parallels between primary nucleic acid structure and primary protein structure are worth noting: 1. DNAs, RNAs, and proteins all have backbones that do not vary in structure 2. The sequence of attachments to the backbones (nitrogen bases in nucleic acids and amino acid R groups in proteins) distinguishes one DNA from another, one RNA from another, and one protein from another 3. Both nucleic acid polymer chains and protein polymer chains have directionality; for nucleic acids, there is a 5′ end and a 3′ end, and for proteins, there is an N-terminal end and a C-terminal end. Informational Macromolecules Page 25 of 92  The DNA Double Helix and Replication Informational Macromolecules Page 26 of 92  DNA DOUBLE HELIX Like proteins, nucleic acids have secondary, or three-dimensional, structure as well as primary structure. The amounts of A and T were always equal, the amounts of C and G were always equal, as were the amounts of total purines and total pyrimidines. %A = %T and %C = %G The secondary structures of DNAs and RNAs differ, so they will be discussed separately The relative amounts of these base pairs in DNA vary depending on the life form from which the DNA is obtained. (Each animal or plant has a unique base composition.) For example, human DNA contains 30% adenine, 30% thymine, 20% guanine, and 20% cytosine. Informational Macromolecules Page 27 of 92  DNA DOUBLE HELIX In 1953, an explanation for the base composition patterns associated with DNA molecules was proposed by the American microbiologist James Watson and the English biophysicist Francis Crick. Their model, which has now been validated in numerous ways, involves a double-helix structure that accounts for the equality of bases present, as well as for other known DNA structural data. The secondary structures of DNAs and RNAs differ, so they will be discussed separately The relative amounts of these base pairs in DNA vary depending on the life form from which the DNA is obtained. (Each animal or plant has a unique base composition.) For example, human DNA contains 30% adenine, 30% thymine, 20% guanine, and 20% cytosine. Informational Macromolecules Page 28 of 92  DNA DOUBLE HELIX The DNA double helix involves two polynucleotide strands coiled around each other in a manner somewhat like a spiral staircase. The bases (side chains) of each backbone extend inward toward the bases of the other strand. The two strands are connected by hydrogen bonds (between their bases. Additionally, the two strands of the double helix are antiparallel—that is, they run in opposite directions. One strand runs in the 5′-to-3′ direction, and the other is oriented in the 3′-to-5′ direction. The sugar–phosphate backbones of the two polynucleotide strands can be thought of as being the outside banisters of the spiral staircase Informational Macromolecules Page 29 of 92  DNA DOUBLE HELIX The secondary structures of DNAs and RNAs differ, so they will be discussed separately The relative amounts of these base pairs in DNA vary depending on the life form from which the DNA is obtained. (Each animal or plant has a unique base composition.) For example, human DNA contains 30% adenine, 30% thymine, 20% guanine, and 20% cytosine. Informational Macromolecules Page 30 of 92  BASE PAIRING A physical restriction, the size of the interior of the DNA double helix, limits the base pairs that can hydrogen-bond to one another. Only pairs involving one small base (a pyrimidine) and one large base (a purine) correctly “fit” within the helix interior. Of the four possible purine–pyrimidine combinations (A–T, A–C, G–T, and G–C), hydrogen-bonding possibilities are most favorable for the A–T and G–C pairings, and these two combinations are the only two that normally occur in DNA. There is not enough room for two large purine bases to fit opposite each other (they overlapH, and two small pyrimidine bases are too far apart to hydrogen-bond to one another effectively Informational Macromolecules Page 31 of 92  BASE PAIRING Informational Macromolecules Page 32 of 92  BASE PAIRING The pairing of A with T and that of G with C are said to be complementary. A and T are complementary bases, as are G and C. Complementary bases are pairs of bases in a nucleic acid structure that hydrogen-bond to each other. The two strands of DNA in a double helix are not identical—they are complementary. Complementary DNA strands are strands of DNA in a double helix with base pairing such that each base is located opposite its complementary base The fact that complementary base pairing occurs in DNA molecules explains, very simply, why the amounts of the bases A and T present are always equal, as are the amounts of G and C. Wherever G occurs in one strand, there is a C in the other strand; wherever T occurs in one strand, there is an A in the other strand. An important ramification of this complementary relationship is that knowing the base sequence of one strand of DNA enables prediction of the base sequence of the complementary strand. Informational Macromolecules Page 33 of 92  BASE PAIRING The base sequence of a single strand of a DNA molecule segment is always written in the direction from the 5′ end to the 3′ end of the segment. 5′ A–A–G–C–T–A–G–C–T–T–A–C–T 3′ If the end designations for a base sequence (5′ and 3′H are not specified for a sequence of bases, it is assumed that the sequence starts with the 5′ end base. In the base sequence A–C–G–T–T–C it is assumed that A is the 5′ end base The fact that complementary base pairing occurs in DNA molecules explains, very simply, why the amounts of the bases A and T present are always equal, as are the amounts of G and C. Wherever G occurs in one strand, there is a C in the other strand; wherever T occurs in one strand, there is an A in the other strand. An important ramification of this complementary relationship is that knowing the base sequence of one strand of DNA enables prediction of the base sequence of the complementary strand. Informational Macromolecules Page 34 of 92  BASE PAIRING When generating a complementary base sequence from a given 5′-to-3′ base sequence, the complementary base sequence obtained runs in the 3′-to-5′ direction because of the antiparallel relationship that exists between paired base sequences. The following two base sequence notations are entirely equivalent to each other. 3′ A–T–C–G 5′ and 5′ G–C–T–A 3′ When needed, a 3′-to-5′ base sequence can be converted to a 5′-to-3′ base sequence by simply reversing the order of the bases listed. Informational Macromolecules Page 35 of 92  HYDROGEN BONDING INTERACTIONS Hydrogen bonding between base pairs is an important factor in stabilizing the DNA double-helix structure. Although hydrogen bonds are relatively weak forces, each DNA molecule has so many base pairs that, collectively, these hydrogen bonds are a force of significant strength. In addition to hydrogen bonding, base-stacking interactions contribute to DNA double-helix stabilization. Informational Macromolecules Page 36 of 92  STACKING INTERACTIONS Stacking interactions involving a given base and the parallel bases directly above and below it also contribute to the stabilization of the DNA double helix. These stacking interactions are as important in their stabilization effects as is the hydrogen bonding associated with base pairing Purine and pyrimidine bases are hydrophobic in nature, so their stack ing interactions are those associated with hydrophobic molecules— mainly London forces The concept of hydrophobic interactions has been encountered twice previously. Hydrophobic interactions involving the nonpolar tails of membrane lipids contribute to the structural stability of cell membranes, and hydrophobic interactions involving nonpolar R groups of amino acids contribute to protein tertiary structure stability Informational Macromolecules Page 37 of 92  HYDROGEN BONDING INTERACTIONS Informational Macromolecules Page 38 of 92  DNA REPLICATION The process by which new DNA molecules are generated is DNA replication. DNA replication is the biochemical process by which DNA molecules produce exact duplicates of themselves. In DNA replication, the two strands of the DNA double helix are regarded as a pair of templates, or patterns. During replication, the strands separate. Each can then act as a template for the synthesis of a new, complementary strand. The result is two daughter DNA molecules with base sequences identical to those of the parent double helix. Each time a cell divides, an exact copy of the DNA of the parent cell is needed for the new daughter cell. The process by which new DNA molecules are generated is DNA replication Informational Macromolecules Page 39 of 92  DNA REPLICATION Under the influence of the enzyme DNA helicase, the DNA double helix unwinds, and the hydrogen bonds between complementary bases are broken. This unwinding process, is somewhat like opening a zipper. The point at which the DNA double helix is unwinding, which is constantly changing (moving), is called the replication fork Informational Macromolecules Page 40 of 92  DNA REPLICATION Informational Macromolecules Page 41 of 92  DNA REPLICATION The pairing process occurs one nucleotide at a time. After a free nucleotide has formed hydrogen bonds with a base of the old strand (the template), the enzyme DNA polymerase verifies that the base pairing is correct and then catalyzes the formation of a new phosphodiester linkage between the nucleotide and the growing strand The net result of DNA replication is the production of two daughter DNA mol ecules, both of which are identical to the one parent DNA molecule from which they were formed Informational Macromolecules Page 42 of 92  DNA REPLICATION The net result of DNA replication is the production of two daughter DNA molecules, both of which are identical to the one parent DNA molecule from which they were formed The bases of the separated strands are no longer connected by hydrogen bonds. They can pair with free individual nucleotides present in the cell’s nucleus Informational Macromolecules Page 43 of 92  DNA REPLICATION The enzyme DNA polymerase can operate on a forming DNA daughter strand only in the 5′-to-3′ direction. Because the two strands of parent DNA run in opposite directions (one is 5′ to 3′ (LEADING STRAND) and the other 3′ to 5′ (LAGGING STRAND), only one strand can grow continuously in the 5′-to-3′ direction. The other strand must be formed in short segments, called Okazaki fragments (Reiji Okazaki). The breaks or gaps in this daughter strand are called nicks. Okazaki fragments are connected by action of the enzyme DNA ligase Informational Macromolecules Page 44 of 92  DNA REPLICATION The process of DNA unwinding does not have to begin at an end of the DNA molecule. It may occur at any location within the molecule. Indeed, studies show that unwinding usually occurs at several interior locations simultaneously and that DNA replication is bidirectional for these locations; that is, it proceeds in both directions from the unwinding sites. the result of this multiple-site replication process is the formation of “bubbles” of newly Informational Macromolecules Page 45 of 92  DNA REPLICATION The process of DNA unwinding does not have to begin at an end of the DNA molecule. It may occur at any location within the molecule. Indeed, studies show that unwinding usually occurs at several interior locations simultaneously and that DNA replication is bidirectional for these locations; the result of this multiple-site replication process is the formation of “bubbles” of newly synthesized DNA. The bubbles grow larger and eventually coalesce, giving rise to two complete daughter DNAs. Multiple-site replication enables large DNA molecules to be replicated rapidly Informational Macromolecules Page 46 of 92  DNA REPLICATION Based on mode of action, several types of anticancer drugs exist. One large group of such drugs are the antimetabolites, drugs which are DNA-replication inhibitors. The focus on relevancy feature Chemical Connections Antimetabolites: Anticancer Drugs That Inhibit DNA Synthesis—discusses several substances that find use as DNA-replication inhibitors. Informational Macromolecules Page 47 of 92  CHROMOSOMES A chromosome is an individual DNA molecule bound to a group of proteins. Once the DNA within a cell has been replicated, it interacts with specific proteins in the cell called histones to form structural units that provide the most stable arrangement for the long DNA molecules. Cells from different kinds of organisms have different numbers of chromosomes. A normal human has 46 chromosomes per cell, a mosquito 6, a frog 26, a dog 78, and a turkey 82. Typically, a chromosome is about 15% by mass DNA 85% by mass protein. Informational Macromolecules Page 48 of 92  CHROMOSOMES Chromosomes occur in matched (homologous) pairs. The 46 chromosomes of a human cell constitute 23 homologous pairs. One member of each homologous pair is derived from a chromosome inherited from the father, and the other is a copy of one of the chromosomes inherited from the mother. Homologous chromosomes have similar, but not identical, DNA Base sequences both code for the same traits but for different forms of the trait (for example, blue eyes versus brown eyes). Offspring are like their parents, but they are different as well; part of their DNA came from one parent and part from the other parent. Occasionally, identical twins are born Such twins have received identical DNA from their parents. Informational Macromolecules Page 49 of 92  DNA REPLICATION The process by which new DNA molecules are generated is DNA replication. DNA replication is the biochemical process by which DNA molecules produce exact duplicates of themselves. In DNA replication, the two strands of the DNA double helix are regarded as a pair of templates, or patterns. During replication, the strands separate. Each can then act as a template for the synthesis of a new, complementary strand. The result is two daughter DNA molecules with base sequences identical to those of the parent double helix. Informational Macromolecules Page 50 of 92  RNA and the Protein synthesis Informational Macromolecules Page 51 of 92  PROTEIN SYNTHESIS The synthesis of proteins (skin, hair, enzymes, hormones, and so on) is under the direction of DNA molecules. It is this role of DNA that establishes the similarities between parent and offspring that are regarded as hereditary characteristics. The overall process of protein synthesis is divided into two phases. The first phase is called transcription and the second translation RNA molecules is needed and involved in transcription, as the end products, and in translation, as the starting materials Informational Macromolecules Page 52 of 92  RIBONUCLEIC ACIDS Four major differences exist between RNA molecules and DNA molecules: 1. The sugar unit in the backbone of RNA is ribose; it is deoxyribose in DNA. 2. The base thymine found in DNA is replaced by uracil in RNA. 3. RNA is a single-stranded molecule; DNA is double-stranded (double helix). Thus RNA, unlike DNA, does not contain equal amounts of specific bases. 4. RNA molecules are much smaller than DNA molecules, ranging from 75 nucleotides to a few thousand nucleotides. Note that the single-stranded nature of RNA does not prevent portions of an RNA molecule from folding back upon itself and forming double-helical regions. If the base sequences along two portions of an RNA strand are complementary, a structure with a hairpin loop results Informational Macromolecules Page 53 of 92  TYPES OF RNA MOLECULES Heterogeneous nuclear RNA (hnRNA) is RNA formed directly by DNA transcription. Post-transcription processing converts the heterogeneous nuclear RNA to messenger RNA. Messenger RNA (mRNA) is RNA that carries instructions for protein synthesis (genetic information) to the sites for protein synthesis. The molecular mass of messenger RNA varies with the length of the protein whose synthesis it will direct. Informational Macromolecules Page 54 of 92  TYPES OF RNA MOLECULES Small nuclear RNA (snRNA) is RNA that facilitates the conversion of heterogeneous nuclear RNA to messenger RNA. It contains from 100 to 200 nucleotides. Ribosomal RNA (rRNA) is RNA that combines with specific proteins to form ribosomes, the physical sites for protein synthesis. Ribosomes have molecular masses on the order of 3 million amu. The rRNA present in ribosomes has no informational function. Transfer RNA (tRNA) is RNA that delivers amino acids to the sites for protein synthesis. Transfer RNAs are the smallest of the RNAs, possessing only 75–90 nucleotide units. Informational Macromolecules Page 55 of 92  TYPES OF RNA MOLECULES At a nondetail level, a cell consists of a nucleus and an extranuclear region called the cytoplasm. The process of DNA transcription occurs in the nucleus, as does the processing of hnRNA to mRNA. (DNA replication [Section 22-5] also occurs in the nucleus.) The mRNA formed in the nucleus travels to the cytoplasm where translation (protein synthesis) occurs. Figure 22-P5 summarizes the transcription and translation processes in terms of the types of RNA involved and the cellular locations where the processes occur. Informational Macromolecules Page 56 of 92  Transcription and Translation Informational Macromolecules Page 57 of 92  TRANSCRIPTION Transcription is the process by which DNA directs the synthesis of hnRNA/mRNA molecules that carry the coded information needed for protein synthesis During transcription, a DNA molecule unwinds, under enzyme influence, at the particular location where the appropriate base sequence is found for the hnRNA/mRNA of concern, and the “exposed” base sequence is transcribed. A short segment of a DNA strand so transcribed, which contains instructions for the formation of a particular hnRNA/mRNA, is called a gene. Informational Macromolecules Page 58 of 92  GENE A gene is a segment of a DNA strand that contains the base sequence for the production of a specific hnRNA/mRNA molecule. In humans, most genes are composed of 1000–3500 nucleotide units. Hundreds of genes can exist along a DNA strand. Obtaining detailed information concerning the total number of genes and the total number of nucleotide base pairs present in human DNA was an area of intense research activity during the 1980s and 1990s. Informational Macromolecules Page 59 of 92  GENOME The central project in this research was the Human Genome Project, a decade-long internationally based project to determine the location and base sequence of each of the genes in the human genome. A genome is all of the genetic material (the total DNA) contained in the chromosomes of an organism. Informational Macromolecules Page 60 of 92  FUN FACT Before the Human Genome Project began, current biochemical thought predicted the presence of about 100,000 genes in the human genome. Initial results of the Human Genome Project, announced in 2001, pared this number down to 30,000– 40,000 genes and also indicated that the base pairs present in these genes constitute only a very small percentage (2%) of the 2.9 billion base pairs present in the chromosomes of the human genome. In 2004, based on reanalysis of Human Genome Project information, the human gene count was pared down further to 20,000–25,000 genes. Informational Macromolecules Page 61 of 92  TRANSCRIPTION STEPS 1. A portion of the DNA double helix unwinds, exposing a sequence of bases (a gene). The unwinding process is governed by the enzyme RNA polymerase rather than by DNA helicase (replication enzyme). 2. Free ribonucleotides, one nucleotide at a time, align along one of the exposed strands of DNA bases, the template strand, forming new base pairs. In this process, U rather than T aligns with A in the base-pairing process. Only about 10 base pairs of the DNA template strand are exposed at a time. Because ribonucleotides rather than deoxyribonucleotides are involved in the base pairing, ribose, rather than deoxyribose, becomes incorporated into the new nucleic acid backbone. Informational Macromolecules Page 62 of 92  TRANSCRIPTION STEPS 3. RNA polymerase is involved in the linkage of ribonucleotides, one by one, to the growing hnRNA molecule. 4. Transcription ends when the RNA polymerase enzyme encounters a sequence of bases that is “read” as a stop signal. The newly formed hnRNA molecule and the RNA polymerase enzyme are released, and the DNA then rewinds to re-form the original double helix. Informational Macromolecules Page 63 of 92  TRANSCRIPTION STEPS Informational Macromolecules Page 64 of 92  POST-TRANSCRIPTION PROCESSING: FORMATION OF MRNA The RNA produced from a gene through transcription is hnRNA, the precursor for mRNA. The conversion of hnRNA to mRNA involves post-transcription processing of the hnRNA. In this processing, certain portions of the hnRNA are deleted and the retained parts are then spliced together. This process leads to the concepts of exons and introns. An exon is a gene segment that conveys (codes for) genetic information. Exons are DNA segments that help express a genetic message. An intron is a gene segment that does not convey (code for) genetic information. Introns are DNA segments that interrupt a genetic message. A gene consists of alternating exon and intron segments It is now known that not all bases in a gene convey genetic information. Instead, a gene is segmented; it has portions called exons that contain genetic information and portions called introns that do not convey genetic information. Informational Macromolecules Page 65 of 92  POST-TRANSCRIPTION PROCESSING: FORMATION OF MRNA Both the exons and the introns of a gene are transcribed during production of hnRNA. The hnRNA is then “edited,” under enzyme direction, to remove the introns, and the remaining exons are joined together to form a shortened RNA strand that carries the genetic information of the transcribed gene. The removal of the introns and joining together of the exons takes place simultaneously in a single process Informational Macromolecules Page 66 of 92  POST-TRANSCRIPTION PROCESSING: FORMATION OF MRNA The “edited” RNA so produced is the messenger RNA (mRNAH that serves as a blueprint for protein assembly. Splicing is the process of removing introns from an hnRNA molecule and joining the remaining exons together to form an mRNA molecule. The splicing process involves snRNA molecules, the most recent of the RNA types to be discovered. This type of RNA is never found “free” in a cell. An snRNA molecule is always found complexed with proteins in particles called small nuclear ribonucleoprotein particles, which are usually called snRNPs (pronounced “snurps”). Informational Macromolecules Page 67 of 92  POST-TRANSCRIPTION PROCESSING: FORMATION OF MRNA The “edited” RNA so produced is the messenger RNA (mRNAH that serves as a blueprint for protein assembly. Splicing is the process of removing introns from an hnRNA molecule and joining the remaining exons together to form an mRNA molecule. The splicing process involves snRNA molecules, the most recent of the RNA types to be discovered. This type of RNA is never found “free” in a cell. An snRNA molecule is always found complexed with proteins in particles called small nuclear ribonucleoprotein particles, which are usually called snRNPs (pronounced “snurps”). A small nuclear ribonucleoprotein particle is a complex formed from an snRNA molecule and several proteins. Informational Macromolecules Page 68 of 92  TRANSLATION: PROTEIN SYNTHESIS Translation is the process by which mRNA codons are deciphered and a particular protein molecule is synthesized. The substances needed for the translation phase of protein synthesis are mRNA molecules, tRNA molecules, amino acids, ribosomes, and a number of different enzymes A ribosome is an rRNA–protein complex that serves as the site for the translation phase of protein synthesis. Informational Macromolecules Page 69 of 92  TRANSLATION: PROTEIN SYNTHESIS Translation is the process by which mRNA codons are deciphered and a particular protein molecule is synthesized. The substances needed for the translation phase of protein synthesis are mRNA molecules, tRNA molecules, amino acids, ribosomes, and a number of different enzymes A ribosome is an rRNA–protein complex that serves as the site for the translation phase of protein synthesis. There are five general steps to the translation process: (1) activation of tRNA, (2) initiation, (3) elongation, (4) termination, and (5) post-translation processing. Informational Macromolecules Page 70 of 92  TRANSLATION: PROTEIN SYNTHESIS Activation of tRNA There are two steps involved in tRNA activation. First, an amino acid interacts with an activator molecule (ATP) to form a highly energetic complex. This complex then reacts with the appropriate tRNA molecule to produce an activated tRNA molecule, a tRNA molecule that has an amino acid covalently bonded to it at its 3′ end through an ester linkage. Informational Macromolecules Page 71 of 92  TRANSLATION: PROTEIN SYNTHESIS Informational Macromolecules Page 72 of 92  TRANSLATION: PROTEIN SYNTHESIS Initiation The initiation of protein synthesis in human cells begins when mRNA attaches itself to the surface of a small ribosomal subunit such that its first codon, which is always the initiating codon AUG, occupies a site called the P site An activated tRNA molecule with an anticodon complementary to the codon AUG attaches itself, through complementary base pairing, to the AUG codon. The resulting complex then interacts with a large ribosomal subunit to complete the formation of an initiation complex (Since the initiating codon AUG codes for the amino acid methionine, the first amino acid in a developing human protein chain will always be methionine.) Informational Macromolecules Page 73 of 92  TRANSLATION: PROTEIN SYNTHESIS Informational Macromolecules Page 74 of 92  TRANSLATION: PROTEIN SYNTHESIS Elongation Next to the P site in an mRNA–ribosome complex is a second binding site called the A site (aminoacyl site). At this second site the next mRNA codon is exposed, and a tRNA with the appropriate anticodon binds to it. With amino acids in place at both the P and the A sites, the enzyme peptidyl transferase effects the linking of the P site amino acid to the A site amino acid to form a dipeptide. Such peptide bond formation leaves the tRNA at the P site empty and the tRNA at the A site bearing the dipeptide. Translocation is the part of translation in which a ribosome moves down an mRNA molecule three base positions (one codon) so that a new codon can occupy the ribosomal A site The empty tRNA at the P site now leaves that site and is free to pick up another molecule of its specific amino acid. Simultaneously with the release of tRNA from the P site, the ribosome shifts along the mRNA. This shift puts the newly formed dipeptide at the P site, and the third codon of mRNA is now available, at site A, to accept a tRNA molecule whose anticodon complements this codon Informational Macromolecules Page 75 of 92  TRANSLATION: PROTEIN SYNTHESIS Informational Macromolecules Page 76 of 92  TRANSLATION: PROTEIN SYNTHESIS Informational Macromolecules Page 77 of 92  TRANSLATION: PROTEIN SYNTHESIS Informational Macromolecules Page 78 of 92  TRANSLATION: PROTEIN SYNTHESIS Termination The polypeptide continues to grow by way of translocation until all necessary amino acids are in place and bonded to each other. Appearance in the mRNA codon sequence of one of the three stop codons (UAA, UAG, or UGA) terminates the process. No tRNA has an anticodon that can base pair with these stop codons. The polypeptide is then cleaved from the tRNA through hydrolysis. Informational Macromolecules Page 79 of 92  TRANSLATION: PROTEIN SYNTHESIS Post-Translation Processing Some modification of proteins usually occurs after translation. This post-translation processing gives the protein the final form it needs to be fully functional. Some of the aspects of post-translation processing are the following: 1. In most proteins, the methionine (Met) residue that initiated protein synthesis is removed by a specialized enzyme in a hydrolysis reaction. A second hydrolysis reaction releases the polypeptide chain from its tRNA carrier. Informational Macromolecules Page 80 of 92  TRANSLATION: PROTEIN SYNTHESIS Post-Translation Processing 2. Some covalent modification of a protein can occur, such as the formation of disulfide bridges between cysteine residues 3. Completion of the folding of polypeptides into their active conformations occurs. Protein folding actually begins as the polypeptide chain is elongated on the ribosome. For proteins with quaternary structure, the various components are assembled together. Informational Macromolecules Page 81 of 92  Nucleic Acids and Viruses Informational Macromolecules Page 82 of 92  NUCLEIC ACIDS AND VIRUSES Viruses are very small disease-causing agents that are considered the lowest order of life. Indeed, their structure is so simple that some scientists do not consider them truly alive because they are unable to reproduce in the absence of other organisms. A virus is a small particle that contains DNA or RNA (but not both) surrounded by a coat of protein and that cannot reproduce without the aid of a host cell. Viruses do not possess the nucleotides, enzymes, amino acids, and other molecules necessary to replicate their nucleic acid or to synthesize proteins. To reproduce, viruses must invade the cells of another organism and cause these host cells to carry out the reproduction of the virus. Such an invasion disrupts the normal operation of cells, causing diseases within the host organism. The only function of a virus is reproduction; viruses do not generate energy. Informational Macromolecules Page 83 of 92  NUCLEIC ACIDS AND VIRUSES There is no known form of life that is not subject to attack by viruses. Viruses attack bacteria, plants, animals, and humans. Many human diseases are of viral origin. Among them are the common cold, mumps, measles, smallpox, rabies, influenza, infectious mononucleosis, hepatitis, and AIDS. Viruses most often attach themselves to the outside of specific cells in a host organism. An enzyme within the protein overcoat of the virus catalyzes the breakdown of the cell membrane, opening a hole in the membrane. The virus then injects its DNA or RNA into the cell. Once inside, this nucleic acid material is mistaken by the host cell for its own, whereupon that cell begins to translate and/or transcribe the viral nucleic acid. When all the virus components have been synthesized by the host cell, they assemble automatically to form many new virus particles. Within 20 to 30 minutes after a single molecule of viral nucleic acid enters the host cell, hundreds of new virus particles have formed. So many are formed that they eventually burst the host cell and are free to infect other cells. Informational Macromolecules Page 84 of 92  NUCLEIC ACIDS AND VIRUSES If a virus contains DNA, the host cell replicates the viral DNA in a manner similar to the way it replicates its own DNA. The newly produced viral DNA then proceeds to make the proteins needed for the production of protein coats for additional viruses. An RNA-containing virus is called a retrovirus. Once inside a host, such viruses first make viral DNA. This reverse synthesis is governed by the enzyme reverse transcriptase. The template is the viral RNA rather than DNA. The viral DNA so produced then produces additional viral DNA and the proteins necessary for the protein coats. Informational Macromolecules Page 85 of 92  NUCLEIC ACIDS AND VIRUSES A vaccine is a preparation containing an inactive or weakened form of a virus or bacterium. The antibodies produced by the body against these specially modified viruses or bacteria effectively act against the naturally occurring active forms as well. Thanks to vaccination programs, many diseases, such as polio and mumps (caused by RNA-containing viruses) and smallpox and yellow fever (caused by DNA-containing viruses), are now seldom encountered. Informational Macromolecules Page 86 of 92  Recombinant DNA and Genetic Engineering Informational Macromolecules Page 87 of 92  RECOMBINANT DNA AND GENETIC ENGINEERING Genetic engineering is the process whereby an organism is intentionally changed at the molecular (DNA) level so that it exhibits different traits. The first organisms to be genetically engineered were bacteria in 1973 and mice in 1974. Insulin-producing bacteria were commercialized in 1982, and genetically modified food crops have been available since 1994. Genetically modified forms of foods and fibers now dominate several major crops in the United States Informational Macromolecules Page 88 of 92  RECOMBINANT DNA AND GENETIC ENGINEERING Genetic engineering is the process whereby an organism is intentionally changed at the molecular (DNA) level so that it exhibits different traits. The first organisms to be genetically engineered were bacteria in 1973 and mice in 1974. Insulin-producing bacteria were commercialized in 1982, and genetically modified food crops have been available since 1994. Genetically modified forms of foods and fibers now dominate several major crops in the United States Informational Macromolecules Page 89 of 92  RECOMBINANT DNA AND GENETIC ENGINEERING Informational Macromolecules Page 90 of 92  RECOMBINANT DNA AND GENETIC ENGINEERING Genetic engineering procedures involve a type of DNA called recombinant DNA. Recombinant DNA is DNA that contains genetic material from two different organisms. The notation rDNA is often used to designate recombinant DNA. The bacterium E. coli, which is found in the intestinal tract of humans and animals, is the organism most often used in recombinant DNA experiments. Yeast cells are also used, with increasing frequency, in this research. Informational Macromolecules Page 91 of 92  RECOMBINANT DNA AND GENETIC ENGINEERING Genetic engineering procedures involve a type of DNA called recombinant DNA. Recombinant DNA is DNA that contains genetic material from two different organisms. The notation rDNA is often used to designate recombinant DNA. The bacterium E. coli, which is found in the intestinal tract of humans and animals, is the organism most often used in recombinant DNA experiments. Yeast cells are also used, with increasing frequency, in this research. Informational Macromolecules Page 92 of 92