Stoker Nucleic Acids Reviewer Finals PDF

lOMoARcPSD|48582454 Stoker Nucleic Acids Reviewer Finals BS Medical Laboratory Science (Holy Angel University) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by itslovespremiums atelier (lareqewe@it...

lOMoARcPSD|48582454 Stoker Nucleic Acids Reviewer Finals BS Medical Laboratory Science (Holy Angel University) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by itslovespremiums atelier ([email protected])  lOMoARcPSD|48582454 CHAPTER 22 NUCLEIC ACIDS Stoker p.798 (818/1065) Nucleic Acid A nucleic acid is an unbranched polymer in which the monomer units are nucleotides Friedrich Miescher (1844–1895) Swiss physiologist Discovered nucleic acids in 1869 while studying the nuclei of white blood cells. Nitrogen-Containing Heterocyclic Bases The fact that they were initially found in cell Only 4 types nuclei and are acidic accounts for the name nucleic acid. Although it is now known that Purine – bicyclic nucleic acids are found throughout a cell, not Adenine – 6-amino purine derivative just in the nucleus, the name is still used for Guanine – 2-amino-6-oxo purine derivative such materials. Pyrimidine – monocyclic TYPES OF NUCLEIC ACIDS Thymine – 5-methyl-2,4-dioxo pyrimidine derivative Deoxyribonucleic Acid (DNA) Cytosine – 4-amino-2-oxo pyrimidine derivative A deoxyribonucleic acid (DNA) is a nucleotide Uracil – 2,4-dioxo pyrimidine derivative polymer in which each of the monomers contains deoxyribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or thymine. 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. DNA is passed from existing cells to new cells during cell division. Ribonucleic Acid (RNA) A ribonucleic acid (RNA) is a nucleotide polymer in which each of the monomers contains ribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or uracil. RNA occurs in all parts of a cell. It functions primarily in synthesis of proteins, the molecules that carry out essential cellular Phosphate functions. Derived from phosphoric acid (H3PO4) Under cellular pH conditions, the phosphoric NUCLEOTIDE BUILDING BLOCKS acid loses two of its hydrogen atoms to give a Nucleotide A three-subunit molecule in which a pentose sugar is bonded to both a phosphate group and a nitrogen-containing heterocyclic base. More complex than monosaccharides of polysaccharides & amino acids of proteins hydrogen phosphate ion (HPO42-) NUCLEOTIDE FORMATION Pentose Sugars 1. First, the pentose sugar and nitrogen-containing base ribose – RNA; Has Oxygen in Carbon 2’ react to form a two-subunit entity called a nucleoside 2’-deoxyribose – DNA; No Oxygen in Carbon 2’ (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. Downloaded by itslovespremiums atelier ([email protected])  lOMoARcPSD|48582454 Nucleoside Formation A nucleoside is a two-subunit molecule in which a pentose sugar is bonded to a nitrogen- containing heterocyclic base. Nucleosides are named as derivatives of the base that they contain; the base’s name is modified using a suffix. 1. For pyrimidine bases, the suffix -idine is used (cytidine, thymidine, uridine). 2. For purine bases, the suffix -osine is used (adenosine, guanosine). 3. The prefix -deoxy is used to indicate that the sugar present is deoxyribose. No prefix is used when the sugar present is ribose. Using these rules, the nucleoside containing ribose and adenine is called adenosine, and the nucleoside containing deoxyribose and thymine is called deoxythymidine. PRIMARY NUCLEIC ACID STRUCTURE Only 4 types of nitrogenous bases Sugar–phosphate Bonds 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. Nucleic Acid Backbone Nucleotide formation Alternating sugar–phosphate chain in a nucleic acid structure Important characteristics of the nucleotide formation Constant process of adding a phosphate group to a nucleoside DNA – alternating deoxyribose sugar and are the following: phosphate units RNA – alternating ribose sugar and phosphate 1. The phosphate group is attached to the sugar at the units C-5' position through a phosphate-ester 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. Table 22.1 summarizes information presented in this section about nucleosides and nucleotides. Downloaded by itslovespremiums atelier ([email protected])  lOMoARcPSD|48582454 Downloaded by itslovespremiums atelier ([email protected])  lOMoARcPSD|48582454 Primary Nucleic Acid Structure Specifying the primary structure for a nucleic acid is Primary nucleic acid structure is the sequence in done by listing nucleotide base components (using which nucleotides are linked together in a their one-letter abbreviations) in sequential order nucleic acid. Because the sugar–phosphate starting with the base at the 5' end of the nucleotide backbone of a given nucleic acid does not vary, strand. The primary structure for the four-nucleotide the primary structure of the nucleic acid DNA segment is depends only on the sequence of bases present. 5' T–G–C–A 3' The following list describes some important points Three parallels between primary nucleic acid structure about nucleic acid structure that are illustrated in Figure and primary protein structure are worth noting: 22.5: 1. DNAs, RNAs, and proteins all have backbones 1. Each nonterminal phosphate group of the that do not vary in structure. sugar–phosphate backbone is bonded to two sugar molecules through a 3’,5’-phosphodiester 2. The sequence of attachments to the backbones linkage. There is a phosphoester bond to the 5’ (nitrogen bases in nucleic acids and amino acid R carbon of one sugar unit and a phosphoester groups in proteins) distinguishes one DNA from bond to the 3’ carbon of the other sugar. another, one RNA from another, and one protein from another. 2. A nucleotide chain has directionality. One end of the nucleotide chain, the 5’ end, normally 3. Both nucleic acid polymer chains and protein carries a free phosphate group attached to the polymer chains have directionality; for nucleic 5’ carbon atom. The other end of the nucleotide acids, there is a 5’ end and a 3’ end, and for chain, the 3’ end, normally has a free hydroxyl proteins, there is an N-terminal end and a C- group attached to the 3’ carbon atom. By terminal end. convention, the sequence of bases of a nucleic acid strand is read from the 5’ end to the 3’ end. The DNA Double Helix 3. Each nonterminal phosphate group in the %A = %T and %C = %G backbone of a nucleic acid carries a –1 charge. The parent phosphoric acid molecule from The DNA double helix involves two which the phosphate was derived originally had polynucleotide strands coiled around each other three –OH groups (Section 22.2). Two of these in a manner somewhat like a spiral staircase. become involved in the 3’,5'–phosphodiester Sugar–phosphate backbones of the two linkage. The remaining –OH group is free to polynucleotide strands – can be thought of as exhibit acidic behavior—that is, to produce a H+ being the outside banisters of the spiral ion. staircase Bases (side chains) of each backbone – extend This behavior by the many phosphate groups in a inward toward the bases of the other strand. nucleic acid backbone gives nucleic acids their acidic The two strands are connected by hydrogen properties. 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. 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. Downloaded by itslovespremiums atelier ([email protected])  lOMoARcPSD|48582454 BASE PAIRING DNA single strand is always 5’ to 3’ Complementary strand is 3’ to 5’ (antiparallel) 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. 3’ A-T-C-G 5’ and 5’ G-C-T-A 3’ One small base (pyrimidine) + One large base (purine) A–T (2 H bonds) G–C (3 H bonds) T–G (1 H bond) C–A (1 H bond) Complementary Bases Complementary bases are pairs of bases in a nucleic acid structure that can 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. HYDROGEN BONDING INTERACTIONS Downloaded by itslovespremiums atelier ([email protected])  lOMoARcPSD|48582454 Hydrogen bonding between base pairs is an important factor in stabilizing the DNA double DNA Replication Overview helix structure. Although hydrogen bonds are relatively weak In DNA replication, the two strands of the DNA double forces, each DNA molecule has so many base helix are regarded as a pair of templates, or patterns. pairs that, collectively, these hydrogen bonds During replication, the strands separate. Each can then are a force of significant strength. act as a template for the synthesis of a new, Base-stacking interactions also contribute to complementary strand. The result is two daughter DNA DNA double-helix stabilization. molecules with base sequences identical to those of the parent double helix. Details of this replication are as BASE STACKING INTERACTIONS follows. The bases in a DNA double helix are positioned with the planes of their rings parallel (like a stack Under the influence of the enzyme DNA helicase, the of coins). DNA double helix unwinds, and the hydrogen bonds Stacking interactions involving a given base and between complementary bases are broken. This the parallel bases directly above and below it unwinding process is somewhat like opening a zipper. also contribute to the stabilization of the DNA The point at which the DNA double helix is unwinding, double helix. which is constantly changing (moving), is called the Purine and pyrimidine bases are hydrophobic in replication fork. nature, so their stacking interactions are those associated with hydrophobic molecules—mainly The bases of the separated strands are no longer London forces connected by hydrogen bonds. They can pair with free individual nucleotides present in the cell’s nucleus. Use of the Term