Biochemistry Lecture 5: Nucleic Acid Structures, 2024, MHS

BIOCHEMISTRY / BIOKIMIA Lecture 5 NUCLEIC ACID STRUCTURES: DNA AND RNA W. Donald R. Pokatong, Ph.D. Ir. W. Donald R. Pokatong, M.Sc., Ph.D. Riwayat PENDIDIKAN/EDUCATION  Dr. (Ph.D.) Department of Applied Microbiology and (1994-2001) Food...

BIOCHEMISTRY / BIOKIMIA Lecture 5 NUCLEIC ACID STRUCTURES: DNA AND RNA W. Donald R. Pokatong, Ph.D. Ir. W. Donald R. Pokatong, M.Sc., Ph.D. Riwayat PENDIDIKAN/EDUCATION  Dr. (Ph.D.) Department of Applied Microbiology and (1994-2001) Food Science, College Of Agriculture / Graduate Studies and Research, Univ. Of Saskatchewan, Saskatoon, SK, Canada.  M.Sc. Department of Applied Microbiology and (1990-1994) Food Science, College Of Agriculture / Graduate Studies and Research, Univ. Of Saskatchewan, Saskatoon, SK, Canada.  Ir. Pengolahan Hasil Pertanian, Jurusan (1983-1987) Teknologi Pertanian, Fak. Pertanian, Univ. Sam Ratulangi Manado. 1. Nucleic Acids Nucleic acid: a biopolymer containing three molecular types in one monomer unit. a base derived from purine or pyrimidine (nucleobases) a monosaccharide, either D-ribose or 2-deoxy-D-ribose phosphoric acid Two types of monomer unit: RNA (Ribonucleic Acid) DNA (Deoxyribonucleic Acid) Monomer of RNA Monomer of DNA 1.1 Pyrimidine & Purine Bases The structures of pyrimidine and purine are shown here for comparison Other Bases Less common bases can occur Principally but not exclusively, in transfer RNAs (tRNAs) 1.2 Nucleosides Nucleoside: a compound that consists of D-ribose or 2-deoxy-D-ribose covalently bonded to a nucleobase by a -N-glycosidic bond Lacks (without) phosphate group 1.3 Nucleotides Nucleotide: a nucleoside in which a molecule of phosphoric acid is esterified with an -OH of the monosaccharide, most commonly either the 3’-OH or the 5’-OH Name based on parent nucleoside with a suffix “monophosphate” Polymerization leads to nucleic acids. Linkage is repeated (3’,5’- phosphodiester bond) (Biochemical Connections p. 240) 2. Nucleic Acid Structures Levels of structure 1°structure: the order of bases on the polynucleotide sequence; the order of bases specifies the genetic code 2°structure: the three-dimensional conformation of the polynucleotide backbone 3°structure: supercoiling 4°structure: interaction between DNA and proteins DNA - 1° Structure Deoxyribonucleic acids, DNA: a biopolymer that consists of a backbone of alternating units of 2-deoxy-D-ribose and phosphate the 3’-OH of one 2-deoxy-D-ribose is joined to the 5’- OH of the next 2-deoxy-D-ribose by a phosphodiester bond Primary Structure: the sequence of bases along the pentose-phosphodiester backbone of a DNA molecule base sequence is read from the 5’ end to the 3’ end System of notation single letter (A,G,C,U and T) DNA differs from RNA Sugar is 2’-deoxyribose, not ribose. Sometimes “d” used to designate “deoxy” Writing a DNA strand – an abbreviated notation – even more abbreviated notations d(GACAT) pdApdCpdGpdT pdACGT DNA - 2° Structure Secondary structure: the ordered arrangement of nucleic acid strands the double helix model of DNA 2°structure was proposed by James Watson and Francis Crick in 1953 Double helix: a type of 2° structure of DNA molecules in which two antiparallel polynucleotide strands are coiled in a right-handed manner about the same axis structure based on X-Ray crystallography Base Pairing: T-A Base pairing is complimentary A major factor stabilizing the double helix is base pairing by hydrogen bonding between T-A and between C-G T-A base pair comprised of 2 hydrogen bonds Base Pair: G-C G-C base pair comprised of 3 hydrogen bonds Other Forms of DNA A-DNA a right-handed helix, but thicker than B-DNA 11 base pairs per turn of the helix has not been found in vivo B-DNA considered the physiological form a right-handed helix, diameter 11Å 10 base pairs per turn (34Å) of the helix Z-DNA a left-handed double helix may play a role in gene expression Comparison of A,B, and Z forms of DNA Both A- and B-DNA are right-handed helices Z-DNA is left handed Z-DNA occurs in nature, usually consists of alternating purine- pyrimidine bases Methylated cytosine found also in Z-DNA DNA - 3° Structure Tertiary structure: the three-dimensional arrangement of all atoms of a nucleic acid; commonly referred to as supercoiling Circular DNA: a type of double-stranded DNA in which the 5’ and 3’ ends of each stand are joined by phosphodiester bonds Supercoiling- Further coiling and twisting of DNA helix. Topoisomerases Class I: cut the phosphodiester backbone of one strand, pass the end through, and reseal Class II: cut both strands, pass some of the remaining DNA helix between the cut strands, and reseal DNA gyrase: a bacterial topoisomerase DNA Supercoiling https://www.youtube.com/watch?v=_y2lZb1k33Q DNA - 3° Structure Tertiary structure: the three-dimensional arrangement of all atoms of a nucleic acid; commonly referred to as supercoiling Circular DNA: a type of double-stranded DNA in which the 5’ and 3’ ends of each stand are joined by phosphodiester bonds Supercoiling- Further coiling and twisting of DNA helix. Topoisomerases Class I: cut the phosphodiester backbone of one strand, pass the end through, and reseal Class II: cut both strands, pass some of the remaining DNA helix between the cut strands, and reseal DNA gyrase: a bacterial topoisomerase Supercoiling in Eukaryotic DNA Histone: a protein, particularly rich in the basic amino acids Lys and Arg; found associated with eukaryotic DNA five main types: H1, H2A, H2B, H3, H4 Chromatin: DNA molecules wound around particles of histones in a beadlike structure Topological changes induced by supercoiling accommodated by histone-protein component of chromatin. Chromatin The structure of chromatin Each “Bead” is a nucleosome Nucleosome consists of: DNA wrapped around histone core Denaturation of DNA Denaturation: disruption of 2° structure most commonly by heat denaturation (melting) as strands separate, absorbance at 260 nm increases increase is called hyperchromicity midpoint of transition (melting) curve = Tm the higher the % G-C, the higher the Tm renaturation is possible on slow cooling Class schedules of Biokimia onward September 19 (today) September 26 (+ a make-up class for Oct. 3) October 3 (on-leave: internasional seminar until Oct. 4) October 7 – 11 (mid term) Make-up class  Mon, Sept 23 or 30 (after lunch) Tue, Sept 24 or Oct, 1 (any time) Wed, Sept 25 (after lunch) Thu, Sept 26 (after lunch) Fri, Sept 27 (any time) Denaturation of DNA Double helix unwinds when DNA is denatured Can be re-formed with slow cooling and annealing 3. Principal Types of RNA RNA consist of long, unbranched chains of nucleotides joined by phosphodiester bonds between the 3’-OH of one pentose and the 5’-OH of the next the pentose unit is -D-ribose (it is 2-deoxy-D-ribose in DNA) the pyrimidine bases are uracil and cytosine (they are thymine and cytosine in DNA) in general, RNA is single stranded (DNA is double stranded) Information Transfer in Cells Information encoded in the nucleotide sequence of DNA is transcribed through RNA synthesis Sequence then dictated by DNA sequence Central dogma of biology RNA RNA molecules are classified according to their structure and function 1. tRNA Transfer RNA, tRNA: the smallest kind of the three RNAs a single-stranded polynucleotide chain between 73-94 nucleotide residues carries an amino acid at its 3’ end intramolecular hydrogen bonding occurs in tRNA 2. rRNA Ribosomal RNA, rRNA: a ribonucleic acid found in ribosomes, the site of protein synthesis only a few types of rRNA exist in cells ribosomes consist of 60 to 65% rRNA and 35 to 40% protein in both prokaryotes and eukaryotes, ribosomes consist of two subunits, one larger than the other analyzed by analytical ultracentrifugation particles characterized by sedimentation coefficients, expressed in Svedberg units (S) 3. mRNA Messenger RNA, mRNA: a ribonucleic acid that carries coded genetic information from DNA to ribosomes for the synthesis of proteins present in cells in relatively small amounts and very short-lived single stranded biosynthesis is directed by information encoded on DNA a complementary strand of mRNA is synthesized along one strand of an unwound DNA, starting from the 3’ end 4. snRNA Small nuclear RNA (snRNA) is a recently discovered RNA Found in nucleus of eukaryotes Small (100-200 nucleotides long) Forms complexes with protein and form small nuclear ribonucleoprotein particles (snRNPs) snRNPs help with processing of initial mRNA transcribed from DNA Biosynthesis of Nucleic Acids: Replication