Nucleic Acids 1 - Deconstructing nucleic acids PDF

Nucleic acids 1 Deconstructing nucleic acids… Dr Linda Percy  By the end of this lecture you should be able to: Name and describe the components of nucleotides and deoxyribonucleotides Name and describe the different purines and pyrimidines and how they are used for t...

Nucleic acids 1 Deconstructing nucleic acids… Dr Linda Percy  By the end of this lecture you should be able to: Name and describe the components of nucleotides and deoxyribonucleotides Name and describe the different purines and pyrimidines and how they are used for the formation of nucleosides and nucleotides Describe the polymerisation of nucleotides Describe how the chemical components of nucleic acids are important for their function  Nucleic acids are Macromolecules Polymer – built by linking monomers Monomer – small, similar chemical subunits TABLE 1 Macromolecules Macromolecule Subunit Example Function Example functioning structure NUCLEIC ACIDS DNA Nucleotides (deoxyribonucleotides) Encodes genes Chromosomes (material is chromatin) RNA Nucleotides (ribonucleotides) Needed for gene expression Messenger RNA © McGraw Hill, LLC 4  Electron micrograph of chromatin from chicken erythrocyte nuclei From: Allan et al., (1982). Allan, J., Harborne, N., Rau, D. C., & Gould, H. (1982). Participation of core histone "tails" in the stabilization of the chromatin solenoid. The Journal of Cell Biology, 93(2), 285–297.Available at: https://doi.org/10.1083/jcb.93.2.285 Chromatin packing in a eukaryotic chromosome  DNA (Deoxyribonucleic acid) What are the main functions of DNA? To store genetic information To transmit genetic information What properties does DNA require to achieve these functions? It must be chemically stable, to reduce the possibility of damage DNA must be capable of copying the information it contains  RNA (Ribonucleic acid) What are the main functions of RNA? In general RNA transmits genetic information by carrying out the instructions encoded in DNA, it carries this information, deciphers this information and is used in the formation of proteins What properties does RNA require to achieve these functions? It must be capable of ‘transcribing’ the information from DNA It must be capable of folding into particular shapes In general, it must be capable of having a limited life in the cell  It is the molecular components of DNA and RNA that allow for the properties of these macromolecules 5′ 3′ Sugar-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding 3′ 5′ Base pair joined by hydrogen bonding (a) DNA (b) Transfer RNA  Sugar-phosphate backbone 5′ end Nitrogenous bases Pyrimidines 5′C 3′C Nucleoside Nitrogenous base Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) 5′C Purines 1′C Phosphate 3′C group Sugar 5′C (pentose) Adenine (A) Guanine (G) 3′C (b) Nucleotide Sugars 3′ end (a) Polynucleotide, or nucleic acid Deoxyribose (in DNA) Ribose (in RNA) (c) Nucleoside components  Nucleotides Purines (A and G) Pyrimidines (C and T) T is replaced by U in RNA The difference in nucleotides is in the base structure There is a difference between the sugar in DNA and RNA Heterocyclic bases  Functional Groups Functional groups are specific molecular groups that bond to carbon-hydrogen cores Each group has unique chemical properties. Properties of functional groups are retained wherever they attach and influence behaviour of entire molecule in reactions. 18 Examples of Functional Groups 19  Purines Basic structure or purine The purines are composed of two rings that are fused, with each ring containing two nitrogen (N) atoms. The structure is known as bicyclic because of the two interlocking rings. The chemist Emil Fischer discovered that all members of the purine family were variations of the parent substance purine containing the same basic structure with differing functional groups attached. purine caffeine  Pyrimidines Compounds of the pyrimidine family are composed of only a single ring (known as monocylic). The simplest member of the family is pyrimidine with the general structure of all the members of this family based on this structure. Youtube video (0-3.05 mins https://youtu.be/-6SPqgyji7U In the nucelotide bases a conjugated electron system is found. A "double bond" doesn't really exist. Instead, a group of adjacent, overlapping p orbitals results in a conjugated system. This results in a stable molecule.  Properties of Nucleotide Bases Affect the Structure of Nucleic Acids: The resonance involving many atoms in the ring, provides stability The shape of Pyrimidines is planar & Purines are nearly so, allows stacking The purines and pyrimidines are also hydrophobic and relatively insoluble in water at the near neutral pH of the cell. Hydrophobic stacking interactions with the planes of their rings parallel (similar to a stack of coins) is important in DNA. Using the first commercial ultraviolet spectrophotometer, Chargaff's lab precisely measured the amount of UV absorption in a DNA sample. 260 nm UV absorption is a property of the bases, and each base absorbs differently. Purine and pyrimidine bases exist in different forms called tautomers. Tautomerism is a phenomenon in which a set of molecules can interconvert by movement of a hydrogen or group of atoms and/or molecular rearrangement. Keto to enol These nitrogenous bases can have alternate molecular structures based on different locations of a particular hydrogen atom. They can switch from one tautomer to the other Amino to imino In the early 1950s, guanine and thymine were generally portrayed in the enol form. Watson and Crick considered them in their keto form in their discovery of the structure of DNA  Unusual nucleotide bases In DNA the most common of these are methylated forms of the major bases; in some viral DNAs, certain bases may be hydroxymethylated or glucosylated. Altered or unusual bases in DNA molecules often have roles in regulating or protecting the genetic information. In this case methylation does not interfere with the Watson-Crick pairing of DNA - the methyl group is positioned in the major groove of the DNA controlling protein binding to target sites on DNA Xu, T., Gao, H. (2020) Hydroxymethylation and tumors: can 5- hydroxymethylation be used as a marker for tumor diagnosis and treatment?. Human Genomics 14(15) Available at: https://doi.org/10.1186/s40246-020-00265-5  A nucleotide has three parts Heterocyclic base: purines or pyrimidines One to three phosphates DNA - deoxyribose RNA - ribose  Pentose (Monosaccharide) Carbons 5’ numbered 1’ - 5’ 4’ 1’ Bonds through 5’ and 3’ C 2’ form polymer 3’ (DNA or RNA) 2’OH - Ribose 2’H (no OH) deoxyribose  Nucleotide Structure Figure 3.14 Access the text alternative for slide images. © McGraw Hill, LLC 37 A nucleotide has three parts N Glycosidic link  A nucleotide has three parts Heterocyclic base: purines or pyrimidines One to three phosphates DNA - deoxyribose RNA - ribose  Formation of a nucleotide The combination of a nucleoside with a phosphate group results in the formation of a nucleotide. Three compounds are needed HO O OH to make a nucleotide A sugar OH This one is deoxyribose They combine through two condensation NH 2 reactions (condensation N N a base means ‘splitting out’ water, H2O) NH (this one is adenine) N O and HO P OH phosphoric acid OH   Ester bond  Nucleotides are precursors of nucleic acid (polynucleotides) Nucleic acids form by the joining of single nucleotides into a chain. For these nucleotides to exist as together as a chain they must form bonds with one another. Two nucleotides can join together by a condensation reaction between the hydroxyl group (OH) group on carbon 3 (3’) of the sugar molecule of one nucleotide and the phosphate group (attached to the carbon 5 (5’) of the sugar group of another nucleotide Phosphodiester bonds form between the phosphate group attached to the 5ʹ carbon of one nucleotide and the hydroxyl group of the 3ʹ carbon in the next nucleotide, bringing about polymerization of nucleotides in to nucleic acid strands. Note the 5ʹ and 3ʹ ends of this nucleic acid strand. From: https://bio.libretexts.org/Courses/Portland_Community_College/Cascade_Microbiology/22%3A_Appendix_B_- _Molecular_Genetics_Review/22.2%3A_Structure_and_Function_of_DNA  Structure of a single strand of nucleic acid Phosphodiester backbone – repeating sugar and phosphate units joined by phosphodiester bonds A single strand extends in a 5′ to 3′ direction © McGraw Hill, LLC 54  DNA Structure Versus RNA Structure Access the text alternative for slide images. © McGraw Hill, LLC 55 Using the first commercial ultraviolet spectrophotometer, Chargaff's lab precisely measured the amount of UV absorption in a DNA sample. 260 nm UV absorption is a property of the bases, and each base absorbs differently  Chargaff’s Rules RESULTS: The bases were not present in equal quantities (which overturned the tetranucleotide hypothesis) and they varied from organism to organism. Erwin Chargaff determined that: Always an equal proportion of two-ringed purines (A and G) and single-ringed pyrimidines (C and T) Amount of adenine = amount of thymine Amount of cytosine = amount of guanine The ratio of A-T and G-C varies by species © McGraw Hill, LLC 58  Base-pairing in DNA Pattern of base-paring is complementary A forms two hydrogen bonds with T G forms three hydrogen bonds with C © McGraw Hill, LLC 60  The complementary polynucleotide strands held together by H bonding between base pairs A+T 2 H-bonds Purine-pyrimidine pairs G+C 3 H-bonds Base pairing interactive 2D animation Try the base –pairing animation tool to correctly match the nucelotides in DNA ! https://dnalc.cshl.edu/view/15888-Base-pairing-interactive-interactive- 2D-animation.html  Summary The molecular components of nucleic acids are the reason for their physical characteristics The function of nucleic macromolecules is related to structure Understanding the properties of nucleic acids provides the ability for their analysis within the laboratory MCQ quiz for Lecture 11: Deconstructing Nucleic Acids Answers will be given in your Seminar sessions – with further discussion. You must attempt before your seminar session. These quizzes are part of your learning for the Biochemistry module They will aid your on-going studies at the University of Westminster 1) The purine nucleotides in the below diagram are? a) All of the shown nucleotides. b) Nucleotides shaded red and green. c) Nucleotides shaded red and blue. d) Nucleotides shaded yellow and green. e) None. Purine is an amino acid and found in proteins. 2) The sugar shown in the below diagram is_____; thus, this nucleic acid is ______. a) Ribose; DNA b) Deoxyribose; DNA c) Deoxyribose; RNA d) Ribose; RNA e) There are no sugars in the diagram.  3) Match the functional group to the nucleotide. Functional 2 NUCLEO Groups 1 TIDE one amine; one carbonyl 1 one amine; 2 no carbonyl 3 two carbonyl; no amine 4 one carbonyl; 4 one amine 3 4) Which the correct polarity of the two nucleotide strands? a) Yellow and blue are both 3’ ; red and green are both 5’ b) Yellow and red are 5’; blue and green are 3’ c) Yellow and green are 3’ ; blue and red are 5’ d) Yellow and green are 5’ ; blue and red are 3’ e) There is no way of telling from the information given. 5) In the below diagram the indicated bonds (red arrows) are correctly called? a) Phospho-diester bonds b) Hydrogen bonds c) Glycosidic bonds d) Phospho-ester bonds e) Peptide bonds