Nucleic Acids Biochemistry Notes

LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken  I. Structure of Nucleic Acids  A nucleotide is made up of 3 compone...

LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken  I. Structure of Nucleic Acids  A nucleotide is made up of 3 components that are covalently (Part 1) bonded together  Nucleic acids come in two principal 1. A nitrogenous base types: deoxyribonucleic acid (nucleobase) (DNA) and ribonucleic acid  A nitrogenous base can (RNA) have 2 general structures: - DNA is found in the chromosomal form in the cell’s nucleus. It serves as N N N the repository of genetic information NH - RNA is present in 3 major N N types: Pyrimidine Purine  Ribosomal RNA (rRNA) – combines  Nitrogenous bases arise from with proteins to form these general structures thus ribosomes they are derivatives of the  Messenger RNA purines and pyrimidines (mRNA) – directs the  For Purines: amino acid sequence of proteins  Transfer RNA (tRNA) – transports amino acids to the site of NH2 protein synthesis  Nucleic acids are polymers of N N nucleotides. - Polymer: a typically large unit or molecule N NH - Monomer: single unit; Adenine (in RNA and DNA) makes up polymers - Think of polymer as the house and the monomer as the materials used to make that house. O  In this case, the “house” is a nucleic N acid and the HN “materials” are the nucleotides - This means nucleotides are H2N N NH monomers of nucleic acids Guanine (in RNA and DNA) LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken   For Pyrimidines: NH2 N 2. Pentose sugar O N  Another component of H H H nucleotides is a sugar, especially pentose. Cytosine (in RNA and DNA)  The pentose is also known as ribose. - For RNA, the sugar is O ribose - For DNA, the sugar is deoxyribose HN  Quick background info: - Ribose is a five-carbon sugar (pentose) O N - Its structure is H H H H HO CH2 OH Uracil (in RNA only) O H H O H H CH3 OH OH HN Ribose (a pentose sugar) - Ribose’s specific (name is O N β-D-Ribose H H H H - Deoxyribose is simply ribose but the OH in Thymine (in DNA only) carbon 2 is replaced with H  Carbon 2 in the  Structure of some of less structure is the next common nucleobases: carbon to the left of the heterocyclic oxygen. 5 HO CH1 2 O OH 4 ( H H 1 1H H 3 2 ( ( OH 1 Hq 1 Deoxyribose ( (a pentose sugar) ( (  LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken   A nucleobase bonds with the 3. A phosphate group ribose or deoxyribose in the 1st  The phosphate (or phosphoryl atom of pyrimidine and the 9th group) is bonded to the atom of purine and the 1st hydroxyl group of the fifth carbon of the sugar carbon of the sugar ribose (or deoxyribose). NH2 - This phosphate is N specifically called a N phosphate ester N HO N O O – 5 H H O P O CH 1 2 OH H H – O O (4 OH OH (H) 1 H H 1 A purine-pentose complex A phosphoryl group (PO42-) H( 3 2 H( 1 1 NH2 OH OH ( ( N  In pyrimidines, numbering starts from the bottom nitrogen HO O N then proceeds clockwise up to O the 6th carbon. H H  For purines, numbering starts first on the 6-atom ring, from H H the right nitrogen proceeding OH OH (H) counterclockwise to the north A pyrimidine-pentose complex carbon. Then the number seven starts from the nitrogen  The bond (or linkage) between at the top right of the 5-atom the nucleobase and the sugar ring proceeding clockwise to up is called a β-glycosidic to the next nitrogen. linkage.  The bond happens when a 4 6 7 condensation reaction 3 N 1 5 1 N 1 5 N 1 occurs wherein the OH of the 1 1 1 ( ( ( 8 1st carbon of the sugar and the 6 ( 2 2 1 H of the N of the nucleobase ( ( 4( NH 1 N 1 1 1 N 1 9 are dehydrated or removed. 3 ( ( ( ( 1 1 ( (  Numbering applies ( on the ( derivatives as well LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken  NH2 N O NH HO O + OH H H H H OH OH NH2 N H2O HO O N  Conformation of nucleosides a β-glycosidic O linkage can be syn or anti. H H o Syn – if the nucleobase H H and sugar are on the OH OH same side o Anti – if the nucleobase II. Nomenclature of Nucleic Acids and sugar are on  We already know that a opposite sides. nucleic acid is a polymer of o The anti-conformation is nucleotides more stable because there is less  Nucleotides are made up of electrochemical three components: repulsion of same - Pentose sugar charges when placed (deoxyribose or ribose) on opposite sides. - Nucleobase derivative (or simply nucleobase) - Phosphate group  When only a nucleobase and a sugar are bonded together, the whole complex is called a nucleoside. - The name of the nucleoside depends on what type of nucleobase is bonded to the sugar.  For purines: the suffix -osine  Remember: is used Nucleotide = base + sugar + o guanosine and phosphate adenosine Nucleoside = base + sugar  For pyrimidines: the suffix –  A nucleotide is named from the idine is used parent nucleoside with the o Cytidine, thymidine, suffix –monophosphate uridine added. o The suffix is accompanied by the position of the LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken  phosphate ester, meaning the number of the carbon atom where the phosphate group is esterified with the hydroxyl group of the carbon.  When numbering a nucleoside, treat the molecule as its components, the nucleobase and sugar. Numbering of sugars include an apostrophe to signify the numbers belong to the sugar and are different III. Properties of Purines and from that of the nucleobase. Pyrimidines o Example: Adenosine 3’ monophosphate 1. Strong UV absorbance indicates that the position of the esterified  Indicative of aromaticity phosphate is at the 3rd  Strong UV absorbance due to the carbon of the pentose aromaticity of heterocyclic bases sugar. 2. Acid/base dissociation  Splitting (dissociation) of molecules into their ion components o Example: NaCl → Na+ + Cl- o The smaller the pKa value, the more acidic the molecule is. The more acidic a molecule, the more readily a proton (H+) is released or dissociated o The higher the pKa value, the molecule becomes a weak acid. Weak acids can still dissociate into H+ but in very small amounts.  In purines and pyrimidines, the nitrogen components express acid/base dissociation: LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken  3. Tautomerism  Structural isomers differing in the location of their hydrogen atoms and double bonds  The transfer of a hydrogen atom from one side of the same molecule to the other side. A. Keto-enol tautomerism  Tautomerism between a C=C bond and hydroxyl (-OH) group on the same molecule  Conversion of a keto (-C=O) group to its enol form (-OH).  Determines whether the oxygens (O) serve as donors or acceptor of H-bonds in base pairing. IV. Structure of Nucleic Acids (Part 2)  Nucleic acids have a covalent backbone made up of alternating deoxyribose or ribose and phosphate groups.  The heterocyclic bases (nucleobases) are linked to the B. Lactam-lactim tautomerism covalent backbone via N- glycosidic bonds and protrude  Heterocyclic rings of from the structural backbone. nitrogenous bases (purines and  The nucleotide residues of nucleic pyrimidines) with oxo (oxygen) acids are numbered from the 5’ groups exhibit lactam-lactim end, which carries a free tautomerism phosphate group, to the 3’ end,  Important in determining whether which has a free –OH group the N’s (nitrogen) serve as H- o Polymerization (bonding) of bond donor or acceptor in base nucleotides always occurs pairing at one of the oxygens of  Involves amides (N-C=O) shifting the phosphate group and between a carbonyl form (called the –OH group found at lactam) and an imine-like form the 3rd carbon of the sugar (lactim) component. o 5’ end indicates the fifth carbon of the sugar.  In a chain of nucleotides, the first nucleotide in the sequence always ends with 5’ carbon phosphate group. LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken  o The last nucleotide in the A.1: The Primary Structure (1°) of sequence always ends with Nucleic Acids the 3’ carbon –OH group.  The individual nucleotides that comprise the sequence of nucleic acids determine the genetic information that leads to the sequence of RNA and protein.  The order of nucleotides in DNA is used as basis for RNA to produce specific types of proteins.  For example: Adenine (A) – Cytosine (C) – Guanine (G) – Uracil (U) results in the formation of a protein different than that of the sequence Thymine (T) – Guanine (G) – Cytosine (C) – Adenine (A) A.2: The Secondary Structure (2°) A. Levels of Structures of Nucleic of Nucleic Acids (DNA) Acids  DNA is viewed as a double helix  Primary structure when observed in its 3-dimensional o The order of bases in the conformation. polynucleotide sequence o It consists of two long from the 5’ → 3’ direction strands of nucleotides o The nucleotides held together by H-bonds themselves between base pairs on  Secondary structure opposite strands. o The 3-dimensional  As part of its double helix structure, conformation of the DNA twists and turns to achieve backbone stability while protecting the o 3D version of primary genetic information stored inside. structure o A complete turn of the helix  Tertiary structure spans ten base pairs, o Refers to the supercoiling covering a distance of 34 Å of the molecule (angstrom) or 3.4 nm  Quaternary structure o The individual base pairs o Interaction of nucleic acids are spaced 3.4 Å (0.34 with other classes of nm) apart macromolecules (e.g., o The inside diameter is 11Å proteins) to form complexes (1.1 nm), and the outside o Combination of nucleic dimeter is 20 Å (2.0 nm) acids and another  Within the cylindrical outline of the biomolecule double helix are two grooves, a o Example: RNA + protein = small one and a large one. ribosomes o Grooves are formed by the twisting of DNA double helix. LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken  o As the two strands twist, bonds (H-bonds) between base the grooves formed are not pairs on opposite (antiparallel) equally spaced because stands when adenine (A) always the base pairs are not pairs with thymine (T) or uracil exactly in the middle (U) and guanine (G) always pairs between the two strands– with cytosine (C). they are a little off to one o Complementary base side. Thus, when DNA pairs: A-T (or U) and G-C twists, the strands do not twist evenly, creating the major and minor grooves.  The negative signs (-) alongside the strands represent the negatively charged phosphate groups along the entire length of each strand.  The two strands of DNA are antiparallel to each other, meaning one end of one strand o For the adenine-thymine (or starts at 5’ and ends at 3’ while uracil) base pairs, 2 one end of the other strand starts hydrogen bonds hold at 3’ and ends at 5’. them together. o This configuration allows o For the guanine-cytosine the DNA strands to form base pairs, 3 hydrogen complementary base bonds hold them together. pairs using hydrogen  Complementary base pairing bonds. occurs along the entire double o If the strands were parallel, helix, thus, the two chains are the nucleotides would not referred to as complementary be complementary to each strands other and, as a result,  With the help from X-ray patterns would not pair. and chemical analyses, the amount of A is always the same as the amount of T, and that the amount of G always equaled the amount of C. o This is called Chargaff’s rule and is true to all species and any organism. o This reached into a conclusion that DNA consists of two complementary polynucleotide chains are wrapped around each other to form a helix.  Hydrogen bonds between bases on opposite chains determine the  In the double helix, the two strands alignment of the helix, with the are held together by hydrogen LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken  paired bases lying in planes weakened due to interactions perpendicular to the helix axis. with water. o The sugar-phosphate o To prevent this, the double backbone is the outer part strand is wound into a of the helix. helix, where the bases are  The double helix structure of DNA inside the helix. was proposed by James Watson o If water would be present and Francis Crick in 1953 based between the base pairs, the on the X-ray crystallography data hydrogen bonding would of Rosalind Franklin and occur between water and a Maurice Wilkins. nucleobase, preventing the o The X-ray crystallography bases to pair with each data for DNA showed a other therefore disrupting regular, repeating 3-D the sequence of genetic structure and defined information. atomic spacing and dimensions of the molecule.  DNA can have 3 different forms depending on the specific sequence of bases. o B-DNA  The most common form of DNA at physiological pH.  The double helix is stabilized by 3  It is right-handed, types of forces: has a gentle figure and each turn 1. H-bonds between pairs of spans 10 base complementary bases on pairs. opposite strands  Base pairs are 2. Electrostatic force due to perpendicular to polarization of the aromatic the axis of the rings helix 3. van der Waals interactions  Each base pair is between “stacked bases” centered on the inside the double helix helix axis  Hydrogen bonding between bases  The major grow is is important for the formation of wider and more double helices, but its effect is accessible, allowing regulatory LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken  proteins or other  Nearly flat major molecules to gain groove, narrow and access to deep minor groove nucleotide functional groups.  Hydrogen in the 2’ position (2’ carbon of the sugar) allows DNA to readily adopt the B-DNA structure. o A-DNA  Right-handed, short and broad, and each turn spans 11 base pairs.  Major and minor grooves nearly equal in depth  Usually found in DNA- RNA or RNA-RNA hybrids  Major groove is deeper and narrower compared to B-DNA, making the A-form double helices less accessible to proteins than that of B-form DNA. A.3: Tertiary Structure of Nucleic  The minor groove is Acids (DNA) wider and shallower  The DNA molecule is very long o Z-DNA and relatively thin.  Left-handed, o It can fold back on itself longest, and into tertiary structures thinnest and each just like proteins do. turn spans 12 base  In addition to the helical twist of the pairs. double helix, further twisting and  Usually found in coiling of the double helix is segments of DNA possible. that have strictly o This is called supercoiling alternating C and  The DNA helix is in relaxed state G nucleotides if it does a helical turn with the  G (or A) residues normal number of base pairs are in the syn o So, in this state, the two conformation, strands of B-DNA twist  C (or T) residues around the helical axis are in the normal once every 10.4-10.5 base anti conformation pairs of sequence. LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken  o Adding or subtracting Eukaryotic DNA Supercoiling twists on the strand imposes strain (or stress)  More complicated than the supercoiling of the circular DNA of  DNA supercoiling refers to the over- or under-winding of a DNA prokaryotes strand, and is an expression of o Eukaryotic DNA is complexed with proteins. the strain on that strand o This occurs to relieve the o The resulting material is called chromatin, a molecule from helical stress by twisting around complex of DNA and proteins itself. o Overtwisting (overwinding)  DNA wound around principal leads to positive proteins called histones, an supercoiling, while octamer, in an arrangement that undertwisting leads to gives the appearance of beads on negative supercoiling a string. o Each of the “beads” is Prokaryotic DNA Supercoiling called a nucleosome, consisting of DNA wrapped  The sugar-phosphate backbone of around a protein core of a prokaryotic DNA can form a eight histone molecules covalently bonded circle, giving  Further coiling of the DNA spacer rise to circular DNA regions produces the compact  When a segment of a circular DNA form of chromatin found in the is under strain, the circular DNA cell. contorts into a new shape, such as a simple number 8 figure. o Such a contortion is a supercoil LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken  Summary on the Levels of Structures of Nucleic Acids (DNA):  The double helix is the predominant secondary structure of DNA o The sugar-phosphate backbones, which run in antiparallel directions on the two strands, lie on the outside of the helix o Pairs of bases, one on each strand, are held in alignment by hydrogen bonds  The base pairs lie in a plane perpendicular to the helix axis in the most usual form of the double helix, but there are variations in structure.  The tertiary structure of DNA depends on supercoiling. o In prokaryotes, the circular DNA is twisted  Human DNA’s total length is before the circle is approximately 2 meters which sealed, giving rise to must be packaged into a supercoiling. nucleus that is about 5 o In eukaryotes, the micrometers in diameter. supercoiled DNA is o This represents a complexed with compression of more proteins known as than 100,000 histones o It is made possible by wrapping the DNA V. Denaturation (melting) of DNA around protein spools called nucleosome and  The heat denaturation of DNA, then packing these in also called melting, can be helical filaments monitored experimentally by observing the absorption of ultraviolet light at 260 nm. o The amount of light absorbed increases as DNA is heated and the strands separate. o This is called hyperchromicity LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken   Stacked base pairs in native denature DNA rich in G-C DNA absorb less light. DNA base pairs. becomes unstacked as it is denatured, causing it to absorb VI. Structures of RNA more light.  RNA molecules are typically single-stranded  The transition (melting)  The principal types of RNA are temperature, Tm, increases as transfer RNA (tRNA), the guanine and cytosine (G- ribosomal RNA (rRNA), and C content) increase. messenger RNA (mRNA) o This is because G and C o These RNAs participate base pairs have three in the synthesis of hydrogen bonds that proteins in a series of contribute to the high reactions directed by melting temperature. the base sequence of the cell’s DNA. o The base sequences of all types of RNA are determined by that of DNA.  The process by which the order of bases is passed from DNA to RNA is called transcription and from RNA to proteins is called translation VI.A: Transfer RNA (tRNA)  A tRNA is a single-stranded polynucleotide chain, between 73 and 94 nucleotide residues Summary: long, that generally has a molecular mass of about  The two strands of the double 25,000 Da (daltons). helix can be separated by  Although single-stranded, RNA heating DNA samples. This molecules are rich in double- process is called denaturation stranded regions that form  DNA denaturation can be when complementary monitored by observing the sequences within the chain rise in ultraviolet absorption come together and join via that accompanies the process. intrastrand base pairing.  The temperature at which DNA - This is in contrast to DNA becomes denatured by heat double strand’s interstrand depends on its base base pairing composition; higher temperatures are needed to LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken   Intrachain hydrogen bonding  A particular tertiary structure in tRNA occurs, forming A-U is necessary for tRNA to and G-C base pairs similar to interact with the enzyme that those that occur in DNA except covalently attaches the amino for the substitution of uracil acid to the 2’ or 3’ end. for thymine. o To produce this tertiary o These interactions create structure, the tRNA folds hairpin stem-loop into an L-shaped structures in which the conformation that has base-paired regions been determined by X- form the stem and the ray diffraction. unpaired regions between base pairs are the loop o The structure can depicted as a cloverleaf, which can be considered the secondary structure of tRNA because it shows the hydrogen bonding between certain bases.  The paired regions of RNA cannot form B-DNA type double helices because the RNA 2’-OH groups are a steric VI.B: Ribosomal RNA (rRNA) hindrance to this conformation. o Instead, these paired  rRNa molecules tend to be regions adopt a quite large. conformation similar to o The RNA portion of a the A-form of DNA. ribosome accounts for 60%-65% of the total weight, and the protein portion constitutes the remaining 35%-40% of the weight.  In both prokaryotes and eukaryotes, a ribosome consists of two subunits, one larger than the other. VI. C: Messenger RNA (mRNA)  The least abundant type of RNA LEC 2A CHEM218: Biochemistry by: Gian Derick Abancio BIO2-A Libre matcha w/ coffee kung mapa tutor kau saken   The sequences of bases in mRNA specify the order of the amino acids in proteins.  In rapidly growing cells, many different proteins are needed within a short time interval o Fast turnover in protein synthesis becomes essential o Consequently, mRNA is formed when it is needed, directs the synthesis of proteins, and then is degraded so that the nucleotides can be recycled. VII. Differences of DNA and RNA DNA RNA Double- Single- stranded stranded Deoxyribose Ribose sugar sugar Uses G, C, A, Uses G, C, T base pairs A, U base pairs T:A, C:G U:A, C:G  Why does DNA contain thymine? o Uracil is derived from cytosine through deamination. o Repair enzymes in DNA recognize uracils as “mutations” thus they replace them with cytosines. o This “mutant U” resulted in using thymine (5-methyl- uracil) in place of uracil in DNA.