Structure of Nucleic Acids I H&N PDF

Structure of Nucleic AcidS i H&N ❖ The central dogma or Genetic coding has these main processes: ❖ Nucleic acids We have two chemically distinct types of nucleic acids: 1) DNA (DeoxyriboNucleic Acid) or cel...

Structure of Nucleic AcidS i H&N ❖ The central dogma or Genetic coding has these main processes: ❖ Nucleic acids We have two chemically distinct types of nucleic acids: 1) DNA (DeoxyriboNucleic Acid) or cellular genetic material ✓ has two main tasks: ▪ storing genetic information & transmitting it to progeny (offspring) ✓ DNA is well-suited for these functions due to: 1. It’s high chemical stability because of strong covalent bonds 2. It’s ability to hold a vast amount of info by 4-letter code (A, C, G, & T) Replication: DNA → DNA: copying ✓ makes two identical copies of DNA ✓ takes place before a cell divides, ensuring that genetic information is 2) RNA (RiboNucleic Acid) transmitted from one generation to the next ✓ It has 3 major types: mRNA, rRNA & tRNA ✓ it stores genetic information of some viruses ✓ RNA sequence is also made of a 4-letter code (A, C, G & U). ❖ Expression of Genetic Information: Protein Production from a DNA Gene: ✓ RNA can act as a catalyst (ribozyme) ✓ serve as a template for DNA synthesis, an exception to the usual flow of Transcription: DNA → RNA information in the central dogma (reverse transcription RNA → DNA) o genetic information from DNA is transferred to RNA o We create RNA based on the DNA’s genetic instructions Proteins equally crucial as they’re required in almost every cellular process. Translation: RNA → Protein ❖ The central dogma of molecular biology (central dogma of life) o genetic information in mRNA is converted into a sequence of amino acids, forming the primary structure of a protein ✓ how genetic information flows within a cell, linking DNA, RNA, & proteins. o undergoes further folding to achieve its final 3D shape. DNA guides the production of RNA through transcription RNA then determines the structure & function of proteins during translation. ❖ Human genome: entire genetic information (blueprint) for given organism. Proteins are formed based on the information originally encoded in DNA. Human genome: 3 billion base pairs of DNA. Human genome: codes for approx. 25,000 genes Approx. 3% of the human genome codes for protein (expressible portion) Structure of Nucleic AcidS i H&N ❖ Purines ❖ Structural Components of DNA ✓ Bicyclic: two fused rings (a 6-membered & a 5-membered [imadazole]). ✓ DNA & RNA are polymers made of smaller units called nucleotides which has: ✓ Main purines: Adenine (A) and Guanine (G) (in both DNA and RNA). i. Nitrogenous Base (nucleobases): ✓ Less common purines: Xanthine (X) and Hypoxanthine (Hx). o Divided into two groups: purines & pyrimidines. ✓ Despite the shorter name, purines have a larger structure ‫الصورة تحت‬ o Adenine (A), Guanine (G), and Cytosine (C) are found in both DNA and RNA. o Thymine (T) is mainly in DNA, while Uracil (U) is in RNA. ❖ Pyrimidines o Uracil is the demethylated form of thymine ✓ Monocyclic (6-membered ring [pyramidine]). ii. Sugar (Pentose Monosaccharide): ✓ Main pyrimidines: Cytosine (C), Uracil (U), Thymine (T). o Ribose (in RNA) has OH groups on its 2’, 3’, and 5’ carbon atoms. ✓ Less common: Orotate (O). o Deoxyribose (in DNA) lacks the OH group at the 2’ position. ✓ C in both DNA and RNA; U only in RNA; T only in DNA. iii. Phosphate Group: ✓ Simpler structure despite the longer name. ‫الصورة تحت‬ o Attached to the sugar at the 5’ carbon through an ester bond. o The phosphate gives DNA and RNA a negative charge due to its low pKa, meaning it is deprotonated (negatively charged) at physiological pH. sugar in nucleotide is connected to nitrogenous base by β-N-glycosidic bond: This bond links N1 of pyrimidines (C, T, U) to C1’ of the sugar. Nucleotides can have one, two, or three phosphate groups: It links N9 of purines (A, G) to C1’ of the sugar ✓ Monophosphate (1 p), Diphosphate (2 p), Triphosphate (3 p). #Under normal conditions Cellular DNAs are typically double-stranded polymers of ^ 2 ' -deoxyribonucleoside 5' monophosphate ^ Cellular RNA are single-stranded polymers of ^ ribonucleoside 5' monophosphates^ Structure of Nucleic AcidS i H&N ❖ DNA/RNA Chain Representation: ✓ The pentose sugar is shown as a vertical line with the 5’-OH at the bottom. ❖ Primary structure of DNA ✓ The nitrogenous base is shown as a letter at the top. The primary structure is the linear sequence of deoxynucleotides joined by 3’-5’ ✓ The 3’-OH is placed in the middle of the line. phosphodiester bonds (PDB) → strong covalent bond → 200 million year stable ✓ A line between the 3’-OH of one sugar and the 5’-OH of the next shows PDB ✓ RNA, the 2’-OH is shown on the line. ✓ A phosphate group connects C3’ OH of one nucleotide to C5’ OH of the next. ✓ Since the phosphate forms two ester bonds, it’s called a diester, linking 3’ OH to 5’ OH, establishing the 3’-5’ direction. ▪ The sequence typically starts at 5’ on the left and 3’ on the right, sometim d(ACGT) for deoxy forms. Features: ▪ Writing pACGU shows the free phosphate at the 5’ end 1) Polarity: ✓ DNA has two distinct ends: ✓ 5’ end: has a free 5’ phosphate group. ✓ 3’ end: has a free 3’ hydroxyl group. ✓ DNA is read in 5’ to 3’ direction during most biological processes →→→ 2) Negativity ✓ DNA carries a negative charge because of the phosphates in its backbone. 3) Sugar-phosphate backbone ✓ The backbone consists of alternating sugars & phosphates. ✓ It is hydrophilic due to the negative charges from the phosphates, which pushes it outward towards the surrounding water. Structure of Nucleic AcidS i H&N ▪ Erwin Chargaff: Found Chargaff’s rules (explained later). ✓ the nitrogen (N) atoms in the bases donate hydrogen atoms, while the ▪ Rosalind Franklin & Maurice Wilkins: Used X-ray diffraction to reveal that carbonyl oxygen (=O) and nitrogen (=N) atoms accept them. DNA is double-stranded and antiparallel. ✓ This precise bonding → stabilize the DNA structure. ❖ Base Pairs: ✓ The pairings of A with T and G with C are referred to as base pairs (bp). ✓ Bp are fundamental to DNA structure & has crucial role in storing genetic info ▪ Watson & Crick : earlier research to propose accepted DNA model: DNA consists of two helical strands coiled around a central axis. It has a double-stranded, helical shape. ❖ Chargaff’s Rules for percentages ❖ Features of the Watson-Crick DNA Model: ✓ The percentage of Adenine (A) = the percentage of Thymine (T). ❖ Anti-parallel Strands: ✓ The percentage of Guanine (G) = the percentage of Cytosine (C). ✓ The two strands of DNA run in opposite directions. ✓ The total number of purines (A + G) = total number of pyrimidines (C + T). ✓ If one strand goes from 5’ to 3’, the other must go from 3’ to 5’. If these rules are not observed, the molecule is likely not double-stranded ✓ This orientation is important because it affects how strands interacts DNA, which is crucial for maintaining genetic integrity. ❖ Complementarity: ❖ Hydrophobic Bases: ✓ The bases on one strand are complementary to those on the opposite strand ✓ N-bases are hydrophobic, meaning they do not interact well with water. Adenine (A) pairs only with Thymine (T). ✓ They located in the interior of the DNA helix to avoid contact with H20 Cytosine (C) pairs only with Guanine (G). ✓ In contrast, the sugar-phosphate backbone is hydrophilic (water-attracting) The specific pairing is due to the shapes of the bases and their ability to form and faces outward, interacting with the watery environment inside cells. hydrogen bonds, ensuring accurate copying of genetic information. ❖ Major and Minor Grooves (aiding in compaction) ❖ Hydrogen Bonds: Major Groove: This groove is wider and provides more space for proteins to The bonds between paired bases are called hydrogen bonds: bind and interact with the DNA. Minor Groove: This groove is narrower, providing less access to base pairs. A and T are connected by 2 hydrogen bonds. N7 of purines is always projecting to the major groove: it can serve as a G and C are connected by 3 hydrogen bonds. hydrogen bond acceptor in interactions with proteins The hydrogen bonds form between specific atoms in the bases: Structure of Nucleic AcidS i H&N ❖ Purine-Pyrimidine Pairing: ✓ The pairing of a purine (A or G) on one strand with a pyrimidine (C or T) on More crucial for stability, occur between N-bases & Includes: the other strand keeps the DNA molecule at a consistent width. Hydrophobic Interactions ✓ This helps maintain the stability and structure of the DNA double helix. Van der Waals Forces These interactions, though relatively weak, are additive & limit the space between bases, keeping water away. ▪ Note: There are no direct covalent bonds between bases within the same strand or between opposite strands. ❖ DNA Denaturation (Melting or Unwinding) converting dsDNA into ssDNA by breaking stacking forces & hydrogen bonds. Denaturation of dsDNA by heat or increased pH leading to strand separation Begins in AT-rich regions (weaker Hydrogen bonds). Gradual & cooperative unwinding until complete denaturation into single strands PDB remain intact during denaturation. ❖ Base Stacking in DNA or RNA ‫من الكتاب‬ ❖ Light Absorbance and Hyperchromicity ‫من الكتاب بالكامل‬ Bases → hydrophobic → positioning in interior → stay away from water. planar structure allows them to stack on top of one another, similar to coins. Nitrogen Bases: These are aromatic heterocycles that absorb light, most Support stability in both single-stranded & double-stranded by: efficiently at a wavelength of 260 nm. Facilitates interactions between bases through hydrophobic forces. ▪ Therefore, the maximum absorbance (Amax) for DNA is at 260 nm Reduces the hydrophobic surface area exposed to water  In dsDNA, nitrogen bases are stacked, which limits the surface area exposed If bases are unstacked, DNA or RNA often adopts a random coil configuration. to light, resulting in lower absorbance.  When dsDNA is denatured, the nitrogen bases are unstacked, exposing more surface area to light, and absorbance increases by 40%. ❖ Forces Affecting the Stability of DNA Double Helix  This increase in absorbance during denaturation is called hyperchromicity. Forces that Stabilize DNA Structure: 1) Hydrogen Bonding: ✓ Although individually weak, these bonds are additive & collectively provide significant stability to double-stranded DNA (dsDNA). 2) Stacking Interactions: Structure of Nucleic AcidS i H&N ❖ Features of Helical Structures ✓ Helical structures, such as dsDNA, have key features: A. Helix Handedness (Direction of Helix Twist): This can be determined in two ways: Rotation direction: o If helix rotates counterclockwise when viewed from above, it is right-handed. o If it rotates clockwise, it is left-handed. ❖ DNA Melting Curve (Denaturation Curve) The melting curve is sigmoidal, representing the relationship between ❖ Conformations (Forms) of dsDNA in the Body temperature (T⁰) & hyperchromicity (light absorbance). It helps track the DNA denaturation process experimentally. B-DNA (Discovered by Watson and Crick): ✓ The most common form of DNA in living cells (>95%). ▪ Key features: i. Initial Temperature Increase: Right-handed Helix o AT-rich regions start to separate, leading to a rise in absorbance. 10 NT per turn , making it long and thin. ii. Further Heating: Found in high humidity & low salt conditions (like the nucleus) o More denaturation occurs, causing a continued rise in absorbance. The base pairs are nearly perpendicular to the helix axis. iii. Plateau: o Once the entire DNA is denatured, absorbance reaches a plateau (100% hyperchromicity), with no further increase. iv. Tm (Melting Temperature): is temperature at 50% of DNA is denatured & there is a 50% ↑in absorbance. DNA with more GC pairs requires higher temperatures for denaturation due to stronger hydrogen bonding, shifting the melting curve to the right & ↑ Tm. ▪ Reversibility: ✓ Denaturation is reversible DNA renature when denaturing agent is removed Chain A: 5’-ATCGATTA-3’ Chain B: 5’-GCGCGCGC-3’ ‫ممكن ييجي زي هيك باالمتحان زي ما قال الدكتور‬ Chain C: 5’-AATTCCGG-3’ Chain D: 5’-TATATATA-3’ Question Example: Which DNA chain has the lowest melting temperature? Structure of Nucleic AcidS i H&N A-DNA (Discovered by Rosalind Franklin): ✓ Right-handed helix. I. Linear DNA: ✓ 11 NT per turn:, making it shorter and thicker. ✓ Typically found in the nuclei of eukaryotic cells. ✓ Occurs in low humidity and high salt environments. ✓ Example: The 46 chromosomes in a diploid human cell are linear double- ✓ It’s a major groove is narrower and much deeper than B form stranded DNA complexed with proteins. ✓ and its minor groove is broader and shallower. ✓ Found In solutions with higher salt concentrations or with alcohol added II. Circular DNA: ✓ Formed by joining the 3’- and 5’-ends of linear DNA A DNA ✓ Most bacterial DNA, DNA of small viruses & free plasmids all have it ✓ Some DNA molecules are sometimes linear & sometimes circular e.g. phage λ ✓ Formed by joining (ligation) of ends of a linear DNA to create a closed loop ✓ DNA of bacteriophage exists in linear & circular → interconvertible. ✓ Circularization of λ DNA is possible because the 5'-overhangs of the linear form are complementary sequences. Z-DNA (Zigzag Backbone) ✓ The only left-handed helix in DNA ✓ 12 NT per turn, making it thin and elongated. ✓ Found in DNA with alternating purine-pyrimidine sequences (like poly dGC). ✓ Has role in gene expression & regulation by altering chromatin conformation ✓ Present at short sections of DNA ✓ Major groove very shallow (doesn’t exist approximately ) ✓ Deep narrow minor groove ❖ Genomic DNA refers to entire DNA content of a cell & comes in 2 main forms: Structure of Nucleic AcidS i H&N 2. RNA Types and Roles: RNA Structure mRNA: Carries the genetic code from DNA to the ribosome for protein synthesis. ❖ Primary Structure of RNA: rRNA: Forms part of the ribosome, essential for protein synthesis. ✓ RNA is a linear polymer of ribonucleotides (polyribonucleotide) held together tRNA: Brings amino acids to the ribosome, matching codons on mRNA. snRNA: Helps in splicing pre-mRNA, removing introns to create mature mRNA. by 3’-5’ Phosphodiester Bonds (PDB). snoRNA: Assists in processing & modification of pre-rRNA into functional rRNA. ▪ Nucleotides of RNA: 3. Gene Expression Process: o Contains purines A and G, and pyrimidines C and U (T is not usually found). o Rich in modified bases (e.g., methylated bases, acetylation,) imp for stability. rRNA is processed with help from snoRNA to become part of the ribosome. o The pentose sugar in RNA is ribose with a 2’-OH group. pre-mRNA undergoes splicing by snRNA, which removes introns and joins exons, forming mature mRNA with a 5’ cap and poly-A tail. This joining of exons o Doesn’t Follow Chargaff’s Rule:Purines are not equal to pyrimidines. creates a continuous coding sequence (codons) for translation. During translation, tRNA delivers amino acids to the ribosome, which uses mRNA as a template to synthesize proteins. 1. Transcription: DNA is transcribed into RNA. The resulting RNA includes mRNA, rRNA, tRNA, snRNA, & snoRNA. m = messengerr = ribosomal / t= transfer /sn = small nuclear / sno = small nucleolar Structure of Nucleic AcidS i H&N The Signal Recognition Particle (SRP) binds to the Signal Peptide (SP) of a Stability Enhanced by Base-Stacking in the Loop: nascent protein, halting translation. The SRP-Receptor (SR) attaches to the ✓ Base stacking interactions, such as in sequences like UUCG, provide SRP-ribosome complex in the membrane, allowing the nascent protein to additional stability to the RNA structure by allowing bases to stack closely pass through the Opening Translocon (OT) into the Endoplasmic Reticulum together, minimizing exposure to the solvent (ER) lumen, where it will undergo modifications. This process includes the SRP binding to the SP, the complex linking to the SR, and the protein entering the OT into the ER lumen for further processing.. ❖ Secondary Structure of RNA: ✓ arise from short regions of intramolecular base pairing (complementarity). Follow Watson-Crick Pairing: ✓ Standard base pairing between adenine (A) and uracil (U), and guanine (G) and cytosine (C), contributing to the overall stability of RNA. ❖ Tertiary RNA Structure Non-Canonical Pairing: ▪ Rotational Freedom: ✓ Unconventional base pairings that can occur between bases, adding ✓ RNA has significant flexibility in regions where bases are not paired, allowing variability and flexibility to the RNA structure.(e.g A with C) for complex folding and shaping. ✓ The most common secondary structure in RNA is the stem-loop (hairpins), ❖ Formation of Tertiary Structure with stems forming at base-paired areas and loops at non-base-paired areas 1) Hydrogen Bonding: ✓ Involves interactions like triplet base pairing, where three bases pair Stem-Loop Types together, e.g., U:A:U or AGC or ACG. ❖ Hairpin: A common structure where a sequence of RNA folds back on itself, creating a double-stranded stem and a loop at the top. 2. Stem Interactions: ❖ Bulge: ✓ Stems in RNA interact with each other through base stacking, where bases An irregular loop formed when one strand of the RNA has extra unpaired align in a stacked arrangement, stabilizing the structure. nucleotides, creating a bulge in the structure. 3. Base Modification: ❖ Loop: A region in RNA where bases are unpaired, often found at the end of a ✓ Chemical modificationsinfluence the overall folding and stability of the RNA stem structure, allowing for flexibility & interaction with other molecules. structure like methylation & acetylation Structure of Nucleic AcidS ii H&N Some notes from the doctor about NA1: ❖Chromatin The length of DNA inside the cell = 2 meter or 6 feet ❖Base Stacking The length of DNA inside the human= 10 billion miles ✓ Base stacking is a typical structural arrangement of nucleobases in the 3D DNA packaged in nucleus 0.0000 1 m in diameter structure of nucleic acids (like DNA and RNA). So DNA is roughly compacted in the cell ✓ The bases are planar in shape, and they align in a stacked configuration, ▪ This because DNA is complexed with about an equivalent mass of protein to positioned at contact distances of approximately 3.4 Å (angstroms). form a structure known as chromatin ✓ This stacking helps exclude water molecules from between the bases, ▪ DNA: Protein ratio is approximately 1:1. stabilizing the structure. ✓ Van der Waals interactions play a key role in maintaining this stable ▪ Chromatin is a periodic structure made up of repeating, regularly spaced configuration. subunits called nucleosomes ▪ Within the nucleosomes the major part of DNA is wrapped around histone Coaxially Stacked Arms (tertiary structure) ✓ Main protein family around which DNA is wrapped. ✓ Helical regions of RNA align in a continuous stack, creating a more stable ▪ DNA joining each nucleosome is known as linker DNA conformation, important for complex RNA structures ▪ Characteristics of Histones o Small proteins with highly conserved amino acid sequences across species. o Basic + proteins rich in lysine & arginine, + charged (highly cationic) physiological pH. o Histones bind to - charged phosphate in the DNA backbone via electrostatic attraction, stabilizing the chromatin structure. ❖ Importance of DNA Packaging ✓ Compaction allows for efficient storage of DNA within the nucleus. ✓ Enables access to genetic information during processes like transcription and replication while maintaining structural integrity Structure of Nucleic AcidS ii H&N ❖ Formation of Chromatin and Metaphase Chromosome Naked DNA (dsDNA) ✓ dsDNA existing without any proteins bound to it. Nucleosome Formation 146 ✓ dsDNA wraps around histones to form nucleosomes. ✓ 146 (bp) of DNA wrap around a histone octamer, completing 1 ¾ turns. ✓ Histone Octamer (8) Composition: Consists of two H2A, two H2B, two H3, and two H4 histones. Chromatosome Formation 166 + H1 chromatin unit formed by a nucleosome (146 bp) plus an additional 20 bp of linker DNA bound by the H1 histone, stabilizing the structure and allowing 2 full turns of DNA around the histones. Polynucleosome Formation ✓ A group of linked nucleosomes forms a polynucleosome (or 100 Å nucleofilament), which looks like “beads on a string” under a microscope. Solenoid Formation (300 Å Nucleofilaments) ✓ Groups of 6–7 chromatosomes interact through their H1 histones to form a helical structure called a solenoid. Scaffold and Chromatin Formation ✓ The solenoid loops & coils around scaffold proteins (non-histone proteins), organizing into a higher-order structure. Metaphase Chromosome ✓ In preparation for cell division, chromatin undergoes further condensation to form metaphase chromosomes, the most compacted state of DNA. Structure of Nucleic AcidS ii H&N ❖ ‫أشياء رح تتكرر لقدام بس بدنا نؤخذ عنهم فكرة‬ ❖ Centromere: ✓ Present in each chromosome. ✓ Serves as the attachment site for kinetochore proteins, which link the chromosome to the mitotic spindle during mitosis and meiosis. ✓ Holds the sister chromatids together, ensuring proper chromosome alignment and separation during cell division. ❖ Telomere: ✓ The protective structure located at each end of a eukaryotic chromosome. ✓ Composed of tandemly repetitive DNA sequences at the ends of the chromosome’s DNA molecule. ✓ Functions to prevent the loss of important genetic information by protecting the chromosome from shortening during DNA replication. ❖ Palindromes & Repeated Sequences: ✓ A region of double-stranded DNA where each strand has the same sequence when read in the same direction. ✓ Also known as symmetrical inverted repeats. ✓ These sequences play important roles in DNA structure, replication, & regulation. ✓ Example: they will be the same when we read the from 5 end