Nucleic Acids, Nucleotides, Chromosomes, and Viruses Lecture Notes PDF

Primary structure of The primary structure of nucleic acid DNA/RNA is the linear sequence of nucleotides linked together by phosphodiester bonds. Features Phosphodiester bonds (bridge 3’ and 5’ positions of the sugar moiety) Directionality (5’ to 3’) Oligonucleotide/polynucleotide Bac...

Primary structure of The primary structure of nucleic acid DNA/RNA is the linear sequence of nucleotides linked together by phosphodiester bonds. Features Phosphodiester bonds (bridge 3’ and 5’ positions of the sugar moiety) Directionality (5’ to 3’) Oligonucleotide/polynucleotide Backbone (phosphate and pentoseDNA: 5’-ATGCGGCTATTGTA-3’ sugar) RNA: 5’-UGCGGCUAUUGUA-3’ Underlined sequences are not shown in the Charge illustration Note: The basic building blocks of nucleic acids are nucleoside monophosphates (NMPs). However, nucleoside triphosphates (NTPs) serve as the activated precursors during synthesis. Start from 1.49 https://youtu.be/ min https://youtu.be/RRn8ZzZmcVs  Secondary structure of DNA Erwin Chargaff and colleagues (Late 1940s) gave clues to the DNA secondary structure. Some of their important findings include: 1. The base composition of DNA generally varies from one species to another. 2. DNA specimens isolated from different tissues of the same species have the same base composition. 3. The base composition of DNA in a given species does not change with an organism’s age, nutritional state, or changing environment. 4. The number of adenosine residues is equal to the number of thymidine residues (A = T), and the number of guanosine residues is equal to the number of cytidine residues (G = C). The sum of the purine residues equals the sum of the pyrimidine residues (i.e.) ( A + G = T + C) (Chargaff’s rule).  Secondary structure of DNA The secondary structure of DNA Cont’d5’ 3’ defines the interactions between two DNA chains. In B form 1953, James Watson and DNA 5’ 3’ Francis Crick postulated the 3D structure of DNA. Salient Features: 1. Right-handed Double Helix Structure: The secondary structure of DNA 5’ 3’ consists of two helical DNA Ladderconvertedtohelix chains wound around the same Right-handed twistingof the axis. ladder around a vertical axis 5’ 2. Antiparallel Orientation: 3’ Double-stranded DNA as an The chains exhibit opposite imaginary ladderlike structure orientations, with one reading 5'  Secondary structure of DNA Cont’d 3. Complimentary Base Pairing: Guanine (G) pairs with cytosine (C), and adenine (A) pairs with thymine (T). The base pairing is stabilized by hydrogen bonds, with three bonds forming between G and C, and two bonds forming between A and T. 4. Backbone and Base Orientation: The hydrophilic deoxyribose and phosphate groups form the backbone outside the helix, where it interacts with surrounding water molecules. In contrast, the hydrophobic purine and pyrimidine bases are stacked 5’-C A A T C G T C A-3’ inside the double helix, with their 3’-G T T A G C A G T-5’ nearly planar ring perpendicular to the long axis.  Secondary structure of DNA Cont’d B form 5’DNA 3’ 5. Major and minor grooves: The offset pairing Major of the two strands creates a major groove and a minor groov groove on the surface of the e duplex. Minor groove 3’ 5’ Ladderconvertedtohelix Right-handed twistingof the  Parameter A-DNA B-DNA Z-DNA Forms of s A-DNA DNA B-DNA Z-DNA Helix Right-handed Right- Left-handed DNA B-DNA Z-DNA handed Base-pair Base-pair Rise per 0.26 nm 0.34 nm 0.37 nm spacing Base-pair Base-pair 0.34 nm spacing 0.34nm base pair spacing spacing Helical length 0.34nm Helicallength Helicallength 0.34nm Helicalength 3.4 nm 3.4nm Helical ~ 2.5 nm ~3.4 nm ~ 4.5 nm 3.4nm 3.4nm Major length groove Major groove (Pitch length) Minor Minor groove groove Diameter 2.6 nm 2.0 nm 1.8 nm Base per 11 ~10.5 12 2.0nm 2.0 nm 2.0nm turn 2.0nm Shape Short and Long and Elongated broad thinner and slim (broadest) (intermediat (narrowest) e) Major Extremely Wide and Flattened groove narrow but with out on helix  DNA's secondary structure is sensitive to pH, temperature, DNA Denaturation & ionic strength, and strong H- Renaturation bonding solutes, causing denaturation (separation of strands to individual coils).  Temperature: Double-stranded DNA is denatured at high temperatures. This is called melting or thermal denaturation. The temperature at which half of the double-stranded DNA in a solution is denatured is called melting temperature (Tm).  DNA Denaturation &  pH: pH extremes Renaturation Cont’d DNA. < 2.3 and > 10 denature  Ionic Strength: The double-stranded form of DNA is more stable in dilute salt solutions. DNA in pure water melts even at room temperature.  Denatured DNA will renature to re-form the duplex structure if the denaturing conditions are removed (if the solution is cooled, the pH is returned to neutrality, or the denaturants are diluted out).  Replicatio  DNA can replicate itself in a semi- n conservative way. The preexisting parent strands become separated, and each serves as a template for the biosynthesis of a new complementary strand  DNA encodes the Roles of DNA genetic information that enables living replicatio things to grow, n function and transcriptio translatio reproduce. n n Reverse  The amino acid transcriptio sequence of every n protein in a cell, and the nucleotide sequence of every RNA, is specified by the nucleotide sequence in the cell’s DNA.  Double helical DNA  DNA Size/Organization Nucleus  A cell's DNA is condensed Chromatin Cell into a compact structure called a chromosome, allowing this large molecule to fit within the cell. Histone Nucleosomes Chromatin: Fibers of proteins and DNA, with a very small amount of RNA, constitute the chromosome. Chromatin contains long supercoiled DNA associated with proteins, Basepair mainly histones.  DNA Size/Organization The DNA with itsCont’d tightly associated histones is referred to as a nucleosome. Non-histone proteins either assist in the maintenance of chromosome structure or regulate gene expression. Nucleus Chromatin Cell Histone Nucleosomes  Gen e A Segment of DNA that codes for a protein or RNA is known as a gene. Prokaryotic genes are often continuous.  Gene Cont’d Eukaryotic genes are interrupted by non-coding sequences called introns (Intervening regions) The coding sequences of the eukaryotic genes are called exons (Expressed regions) Thus, in Eukaryotes, a larger portion of cellular DNA contains nucleotide segments that do not code for a functional product (protein or RNA). The gene for ovalbumin has seven introns (A to G) splitting the coding sequence into eight exons (L, 1-7). The gene for the beta subunit of hemoglobin has two introns and three exons, including one intron that alone contains more than half the  Types of RNA (Classical) RNA mediates DNA expression to produce proteins  Messenger RNA: Carries genetic information from DNA in the nucleus to the ribosomes in the cytoplasm, where it serves as a template for protein synthesis. Nucleu s mRN A  Types of RNA (Classical)  Transfer RNA: Cont’d Carries amino acids to the ribosomes during protein synthesis, matching the sequence of the mRNA to the correct sequence of amino acids. (tRNA brings amino acids to ribosomes, matching mRNA sequence).  Ribosomal RNA: Along with proteins, rRNA makes up the ribosomes, which are the cellular structures responsible for protein synthesis. Lys Phe tRNA Met Ribosome mRNA Start codon  Secondary structure of RNA  Single-stranded RNA folds back through complementary base pairing, Singleloops, forming secondary structures like: Stems (stem-loop), nucleotide bulge bulges, and junctions. Single nucleotide bulge Three-nucleotide Hairpin loop bulge Hairpin Mismatch pair Single Single nucleotide bulge Three-nucleotide loop or Three-nucleotide Mismatch pair or Hairpin lo Asymmetric ucleotide bulge nucleotide Mismatch bulge pair or Three-nucleotide Hairpin symmetric loop internal symmetric internal loop bulge internal loop inte Symmetric bulge symmetric internal bulge loop Symmetric loop of internal two nucleotides loop gleSingle nucleotide nucleotide bulge bulge of two nucleotides Three-nucleotide Three-nucleotide bulge of two Hairpin Hairpin loop nucleotides loop Asymmetric internal bulge Symmetric internal loop  Secondary structure of RNA Cont’d Coaxial stacking of stems Junctions (coaxial stacking of stems 1 on stem-loop  Secondary structure of tRNA and 233 rRNA 23s rRNA tRN A