DNA Organization Lecture Notes PDF

BMS: 141 Lecture No: 1 Title: DNA organization Instructor Name: Dr Amira Abdel Haleem Medicine and Surgery Program Fall 2024  Intended Learning Outcomes of lecture At the end of this lecture...

BMS: 141 Lecture No: 1 Title: DNA organization Instructor Name: Dr Amira Abdel Haleem Medicine and Surgery Program Fall 2024  Intended Learning Outcomes of lecture At the end of this lecture, the students will be able to: 1- Describe linear structure of DNA with respect to polarity, sugar phosphate backbone and purine and pyrimidine base 2- Describe base complementarily 3- Describe the DNA double helix (Watson and Crick model) 4- Describe the process of DNA packing Deoxyribonucleic acid (DNA) Function: storage and expression of genetic information. Direct its own replication during cell division Direct the synthesis of RNA (Transcription). In human cells, the DNA present mainly in nucleus. Also, small amount present in mitochondria. Polymer of deoxy-ribonucleotides linked by 3'→5'phosphodiester bond. Its shape is like a twisted ladder.  Primary structure of DNA DNA is formed of 2 strands (chains) of polynucleotides. Each strand: -The alternating sugar-phosphate units form the backbone. - Nitrogenous bases are projecting to inside of the 2 stands, with right angle. The sequence of bases determines the coding information of DNA. Polarity: each strand has 2 ends: - One end (5`end) with free phosphate - The other (3`end) with free (OH).  Secondary structure of DNA Commonly known as Watson-Crick structure (B form; the most common form). Two chains paired to each other & wind to form right handed double helix. The two strands run anti-parallel (Run in opposite direction; one from 5`to 3`direction & the other from 3`to 5` direction). Nitrogenous bases are in the center of double helix (Base-pairing rule) & the sugar-phosphate backbone are on the outside. The helix has 10.4 base pairs per turn & 2nm wide.  The spatial relationship between the two strands in the helix creates - Major groove & - Minor groove These two grooves are of unequal size & act as a binding sites for regulatory proteins Complementary base pairing The double helix is stabilized by hydrogen bonds formed between a purine and pyrimidine base. Base pairing role: - Adenine (A) pairs with Thymine (T) (A=T) (By two hydrogen bonds) - Guanine (G) pairs with Cytosine (C) (GΞC) (By three hydrogen bonds)  DNA Organization DNA from 23 pairs of human chromosomes. - (22 autosomes + two sex chromosomes ) have a total length of approximately 1.74 meter. - Packed in the nucleus of about 5-10 μm in diameter. How such large quantities of DNA are packed into a single cell nucleus? (DNA Organization) - All chromosomes inside a nucleus forms the chromatin network which is a complex of: 1. Double stranded DNA molecule. 2. Histones protein.  Histones Five major classes of histones: H1 , H2A , H2B , H3 , H4. Histones are positively charged, due to high content of positively charged amino acids (Arginine and Lysine). These proteins can form ionic bond with the negatively charged DNA (due to phosphate groups) to stabilize the chromatin structure.  Levels of eukaryotic DNA organization Nucleosomes 10-nm chromatin fibril 30-nm chromatin fiber 700-nm chromatid 1400-nm chromosome  Nucleosomes The simplest unit of DNA- protein interaction. A segment of DNA (about 146 bp) wind nearly twice around histone octamer (core histones; 2 molecules of H2A, H2B, H3 & H4) to form a nucleosome (10-nm diameter & 5-nm height). Neighboring nucleosomes are joined by “linker” DNA (about 50 bp). Histone H1; binds to the linker DNA chain between the nucleosome beads. 10-nm fibril Consists of nucleosomes arranged “Beads-on-string shape”. 30-nm fiber The 10-nm fibril is further supercoiled with 6-7 nucleosomes per turn to form the 30-nm chromatin fiber. 700-nm chromatid The 30-nm fibril is further coiled into loops. Looped structures then wrapped → forming rosette. Each rosette contain 6 loops. Rosettes are arranged into coils. About 30 rosettes forms one turn in a coil. 10 such coils forms a chromatid. 1400-nm chromosome Each chromosome is formed of two identical sister chromatids connected at a centromere. The end of each chromatid consists of tandem repeat of 5-TTAGGG-3 sequence (many kilos bp long) called telomere. Centromere: AT- rich region. Position of centromere → forms “arms of chromosome” p: The shorter arm of the two arms q: The longer arm  ……Number of Chromosomes….. # Somatic cell→ Diploid Number Contains two copies of each chromosome (23 pairs of chromosomes) # Germ cell = gamete (Sperm or ovum) → Haploid Number Contains only one copy of each chromosome (23 chromosomes; 22 autosomes + 1 sex chromosome)  Linker DNA is formed What is the simplest unit from of ……. of DNA-protein interaction? a- 50 bp a- Nucleotides b- 146 bp b- Nucleosomes c- 5 bp c- Nucleosides d- 1000 bp d- Nucleic acid Answer: a Answer: b  What is the most common Histone proteins usually form of DNA? have a high proportion of……..amino acids. a- A form a- Positively-charged b- Z form b-Negatively-charged c- B form c-Hydrophobic d- m form d-Aromatic e-Heterocyclic Answer: c Answer: a  What are the components Nucleoside contains: of a nucleotide: a) base-sugar a)Nitrogenous base b) base-phosphate b)Nit. Base + sugar c) base-sugar-phosphate c)Nit. Base + sugar + d) sugar-phosphate phosphate d)Purine base + phosphate Answer: a e)Purine or pyrimidine + sugar Answer: c  The sugar molecule present Purine base found in RNA in nucleotide is is a) triose a) Cytosine b) tetrose b) Thymine c) pentose c) Guanine d) Hexose d) Uracil Answer: C Answer: C  References Lippincott’s illustrated reviews, Biochemistry, 6th edition, 2014. BRS Biochemistry, Molecular Biology and Genetics, 5th edition, 2010. Chatterjea’s Textbook of Medical Biochemistry, 8th edition. Vasudevan's Textbook of Biochemistry For Medical Students, 6th Edition.