DNA Structure and Types Lecture Notes PDF

Cell Biology DNA Structure and types Learning Objectives: ØName the different types of purine and pyrimidine bases and sugars present in nucleic acids. ØDefine the nucleoside, nucleotide, and DNA and name the structural components of each one ØDefine nucleosom...

Cell Biology DNA Structure and types Learning Objectives: ØName the different types of purine and pyrimidine bases and sugars present in nucleic acids. ØDefine the nucleoside, nucleotide, and DNA and name the structural components of each one ØDefine nucleosome, mention its structure and list the different stages of chromatin condensation till chromosome ØKnow the different types of DNA Prof. Abdel-Raheim Meki Dr Eman Magdy Radwan  Nucleic acids ØNucleic acid include DNA (deoxyribonucleic acid) or RNA (ribonucleic acid) ØNucleic acids are polymers of monomers called nucleotides, composed of building units called nucleotides linked by phosphodiester linkages. Each nucleotide is formed of 3 components: (1) Nitrogenous base: purines or pyrimidines (2) Pentose (5-carbon) sugar: ribose or deoxyribose (3) Phosphoric acid (Phosphate) molecule : H3PO4  Nitrogenous bases 1. Purines (9 membered ring): These include Adenine (A) and guanine (G), both found in DNA and RNA. DNA & RNA 2. Pyrimidines (6 membered ring): include Cytosine (C) which is present in both DNA and RNA, Thymine (T) is usually found only in DNA and uracil (U) which is found only in RNA. DNA & RNA RNA ONLY DNA ONLY  Sugar in Nucleotides In RNA, The pentose sugar is ribose, oxygen at C2. In DNA, The pentose is deoxyribose, no oxygen at C2.  Nucleosides and Nucleotides Nucleosides are formed by covalently linking a nitrogenous base to the number 1 carbon of a sugar. Nucleoside Þ Base-pentose The attachment of C1 of the pentose sugar to the N1 of pyrimidine or N9 of purine forms Nucleosides. Nucleotides are formed when one or more phosphate groups is attached to the 5ʹ carbon of a nucleoside. Nucleotide Þ Base-pentose-phosphoric acid O NH 2 HN N N O 5’ O 5’ O HO P O CH 2 O N 1 HO P O CH 2 O 9N N OH H H 1’ OH 1’ H H H H H H OH OH OH OH Pyrimidine nucleotide Purine nucleotide  Nucleoside 9 Phosphoester bond 5’ N-glycosidic bond 3’ Nucleotide (dAMP) Note that: nucleotides with di- and triphosphates are high-energy compounds  Deoxyribonucleic acid (DNA) DNA is present in the nuclei as a part of the chromosomal structure and in mitochondria of all cells. Each molecule is formed of millions of nucleotides consists of 2 strands of DNA turning around each other (in a double stranded helix ). DNA functions: 1. DNA carries and transfers the genetic information from one generation to next. It makes copies of itself (replication) and then transfers it to daughter cells during mitosis. 2. Formation of RNAs (Transcription) for protein synthesis (Translation). Genome: is the whole DNA content of the cell. Genes: are certain areas along the genome exerting a specific function (encoding for certain protein) There are many orders of DNA structure: Ø Primary structure: Poly-deoxy-ribo-nucleotides Ø Secondary structure: Double stranded helix Ø Tertiary structure: Double helix wrapped around a histone octamer to form nucleosome (10 nm) Ø Higher orders structure: Formation of chromatin (30 nm fibers), chromosomes.  I. Primary structure of DNA: Primary structure of DNA is the linear O sequence of its building deoxyribonucleotide N gaunine NH 5' units (dAMP, dGMP, dTMP, dCMP). OH N N NH2 O P O O NH2 The nitrogenous bases are adenine and OH H H H H N N adenine O H guanine as purines and thymine and cytosine O P O N N NH2 cytosine as pyrimidines and the sugar is deoxyribose. OH H H H H N O H O N ØPolarity: each strand has 2 ends, one end O P O O thymine OH H H CH 3 (5`end) with free phosphate and the other H H HN O H O (3`end) with free (OH). O P O N OH H H ØThe base sequence of a nucleic acid strand is H OH H H written by convention, in the 5ʹ→3ʹ direction: 3' e.g., 5ʹ-GACT-3ʹ or GACT Nucleic acid strand has a 5'-3' polarity. Ø The nucleotides are covalently bounded by 3`,5`phosphodiester bonds. Ø The hydroxyl group of C3 of the pentose 3’ of a nucleotide forms an ester bond with H3PO4 attached to C5 of the pentose of the subsequent nucleotide.  II. Secondary structure of DNA: DNA is present in the form of double stranded molecule. The two strands are complementary and anti-parallel, i.e., one strand runs in 5’ Þ 3’ direction (i.e., the coding or sense strand) while the other strand runs in 3’ Þ 5’ direction (i.e., the antisense, non- coding strand). The double stranded is held together by Hydrogen bonds Base pairing rule: Adenine in one strand is linked to thymine only (by 2 hydrogen bonds) Guanine is linked to cytosine only (by 3 hydrogen bonds). The two strands are complimentary, If sequence 5’-ACTG-3’ on one chain, the opposite chain MUST have the complementary sequence 3’-TGAC-5’ Because of the specific base pairing, the amount of A equals the amount of T, and the amount of G equals the amount of C. Thus, total purines equals total pyrimidines. These properties are known as Chargaff ’s rules.  Hydrophobic The sugar-phosphate linkages form Hydrophilic the backbone of the polymer (Hydrophilic) Whereas the nitrogenous bases are inside of the stands (Hydrophobic).  The two strands of a DNA molecule are not simply parallel but are intertwined with each other. The two strands form a "double helix" structure, which was first discovered by James D. Watson and Francis Crick in 1953. Major groove There are 2 grooves, major and minor grooves. The major grooves act as a binding sites for regulatory proteins, while the minor groove is for histone binding. Minor groove Each turn contains 10.5 base pairs (2 nm width) James D. Watson and Francis Crick DNA denaturation: It is process of separation (unwinding) of the two stands. It is used in PCR techniques. ØDenaturation of DNA results in breakage of hydrogen bonds and separation of the base pairs. ØWhen DNA solution is heated above certain temperature, the two strands of the DNA double helix get separated (melted). The melting temperature (Tm): It is temperature at which DNA is half- denatured (50% DNA of is half-denatured). Annealing process: When melted DNA is slowly cooled to temperature below TM, it results in reformation of double helix DNA, i.e. renaturation, due to formation of the complementary base pairs.  III. Tertiary structure of DNA: Chromatin structure ØChromatin is a term designing the 3ry structure in which DNA exists within cells. ØNuclear DNA in eukaryotes is found in chromatin associated with DNA-binding proteins. ØThere are 2 classes of DNA-binding proteins involved in maintaining and stabilizing the compact structure of chromatin: a- Histones b- Non histones Ø Non histone proteins include Transcription factors, Polymerases, Hormone receptors and other nuclear enzymes. In any living cell there are more than 1000 different types of non histone proteins bound to the DNA.  Histones Histones are the major class of DNA-binding proteins. They are rich in basic amino acids lysine and arginine, which confer a positive charge on the proteins. These basic proteins (having positive charges), form ionic bonds with the negatively charged acidic DNA phosphate group facilitating their binding. There are 5 types: H1, H2A, H2B, H3, H4. Functions: ØCondensation of the DNA into more compact chromosomes. ØProtect the DNA from digestion by exonucleases. Note: There are no histones in prokaryotes Ø Condensation of the DNA The double stranded DNA wraps around a, Core H1 histone octamer core (2 molecules of each of H2A H2B H2A, H2B, H3, H4) to form the nucleosome. Nucleosome H3 H4 H1 Nucleosome cores are further linked by DNA Linker linker wrapped around H1 which protects the Nucleosome linker DNA from digestion by exonucleases. DNA The series of nucleosomes is sometimes called “beads on a string” but is more properly referred to as a 10 nm chromatin fiber. Nucleosome: is the basic packaging unit of chromatin results from binding of DNA by the histones generates 10 nm structure.  Higher orders of DNA structure: ØDNA (2 meter) is condensed to occupy a small space. ØThe nucleosomes are supercoiled to form the chromatin filaments of 30 nm. ØFurther condensation occurs to form the 300 nm fibrils, then 700 fibril, then the 1400 nm chromosome. How DNA folds into chromosomes Sections of the chromosome shown here have been coloured in. Each section is a piece of DNA called a gene. A gene acts as a recipe or code for making a protein.  Types of DNA Double stranded linear: Eukaryotic nuclear chromosome. Double stranded circular: Mitochondrial, bacterial chromosome, plasmid, and viral. Single stranded circular DNA: (small viruses)  Mitochondrial DNA It is a circular double stranded DNA of about 16 kb length It codes for few number of genes as enzymes involved in energy production/ respiratory chain. It is maternally inherited because the ovum contains hundreds or thousands of mitochondria compared to the sperm. Example of diseases is the MELAS (myopathy, encephalopathy, lactic acidosis, and stroke-like episodes) is maternally inherited disease due to deficiency of complex I and IV of the electron transport chain. Revise your knowledge MCQs 1. Which of the following compounds contains sugar residue? a.Adenine b. Adenosine c. Guanine d. Cytosine 2. The primary structure of DNA is the: a. Double stranded helix b. Linear sequence of its building deoxyribonucleotide units c. Double helix wrapped around a histone octamer d. 300nm fibril 3. All the following are components of the nucleosides EXCEPT: a. Adenine b. Ribose c. Phosphoric acid d. Guanine 4. According to Chargaff ’s rules: a. The amount of A = G b. Amount of C=T c. Amount of C A=T d. Amount of U=C 5. The backbone of DNA is comprised of: a. Ribose and phosphate b. Ribose c. Nitrogenous bases d. Phosphoric acid 6. Plasmids contain: a. Double stranded linear DNA b. Double stranded circular DNA c. Single stranded circular DNA d. Single stranded linear DNA Short essay questions I. Define the following terms: 1. Nucleosomes 2. Nucleosides 3. Mitochondrial DNA 4. DNA denaturation 5. Genome II. Write the functions of the following: 1. DNA 2. Histones 3. Major groove Ø Sources: A- Lectures notes: Hand out of the lectures will be available as PDF on the college web. B-Textbooks: 1. Harper’s Illustrated Biochemistry (31 ed., 2018 McGraw-Hill Education / Medical). 2. Lippincott Illustrated Reviews: Biochemistry, 8th Edition, Wolters Kluwer, 2017.