Molecular Biology I PDF

Molecular Biology 1 Color Index: Main text (black) Female slides (pink) Male slides (blue) Important (red) Dr’s Notes (green) Editing file Extra Info (grey)  Object...

Molecular Biology 1 Color Index: Main text (black) Female slides (pink) Male slides (blue) Important (red) Dr’s Notes (green) Editing file Extra Info (grey)  Objectives Know the central dogma of molecular biology. Understand the composition, types and structure of DNA and RNA. Describe the organization of DNA in the chromosome and the role of histone proteins.  The central dogma of Molecular Biology A portion of DNA, called a gene is transcribed into RNA RNA is translated into proteins human genome contains about 35,000 genes NOTE: The location of the replication and transcription is in the nucleus while translation in cytoplasm (med439)  Nucleic acids Required for the storage and expression of genetic information Building blocks of nucleic acids are nucleoside triphosphates (nucleotides) -Two types of nucleic acids- DNA Deoxyribonucleic RNA acid Ribonucleic acid  Thymine (T) Only in DNA Nucleotides Cytosine Uracil (C) (U) Only in RNA Ribose (RNA) Pyrimidines (with –OH at C2) (1 ring) A-G-C-U 2 Nucleotides Sugar Nitrogenous are composed (pentose with base of 5 carbon ring) 2 Purines Deoxyribose (2 rings) (DNA) (missing an oxygen Phosphate at C2) group A-G-C-T Adenine Guanine (A) (G) Base formula BASE Nucleosides Nucleotides (X=H) (X=Ribose) (X=Ribose Phosphate) (Base + Sugar) (Base + Sugar + phosphate) Adenine Adenosine Adenylic acid Ade Ado Adenosine monophosphate AMP A A purine Guanine Guanosine Guanylic acid Gue Guo Guanosine monophosphate GMP G G Cytosine Cytidine Cytidylic acid Cyt Cud Cytidine monophosphate CMP C C Uracil Uridine Uridylic Ura Urd Uridine monophosphate pyrimidines UMP U U Thymine Deoxythymidine Deoxythymidylic Acid Deoxythymidine monophosphate Thy dThd dTMP T dT  Nucleotides Structure The sugar carbon numbers are primed (1’ 2’ 3’ etc.), while the nitrogenous base atoms PO4 group are unprimed. The nitrogenous base is bonded to C1’ of sugar Nitrogenous base The PO4 group is bonded to C3’ or C5’ of Sugar carbon sugar. C5 is not part of the ring  Chemical Structure of DNA and RNA Connection: The Backbone: Linkage: The PO4 bridges The PO4 and sugar The linkage between the 3’ and 5’ bonding is the the nucleotides is called positions of backbone of DNA phosphodiester ribose sugar structure bond The direction of the phosphodiester bond is 3’ → 5’ The linkage that form nucleosides (linkage between nitrogen base and ribose) is called glycosidic linkage  Function of Nucleotides Polymers of nucleotides (as DNA or RNA) store and transfer genetic information Free nucleotides and their derivatives perform various metabolic functions not related to genetic information. Other nucleotides: FAD, NAD, CoA (coenzymes)  THE DOUBLE HELIX OF DNA The structure of DNA was first determined by James watson and Francis crick in 1953 (watson-crick structure)  Features of Watson-Crick DNA structure Two polynucleotide chains wind around a common axis The two strands are Each strand is a to form a double helix. anti-parallel (run in right-handed (The two strands are held opposite direction), 1 together by hydrogen bonds 2 5'→3', 3'←5' 3 helix. between the bases) The nitrogenous bases The surface of the Each base is are in the center of the double helix contains hydrogen bonded to double helix and the a base in the opposite 2 grooves, major sugar-phosphate chains strand to form a base 4 are on the sides. 5 and minor. 6 pair (A=T and G≡C) known as Complementary base The helix has 10 base pairs (bp) per turn. ( and 3.6 amino pairing. 7 acid per turn)  Watson-Crick base pairs Adenine(A) Thymine(T) Guanine(G) Cytosine(C) In RNA, Thymine is replaced by Uracil(U)  Types of DNA structure Types of DNA A-DNA B-DNA Z-DNA Note: Directions , Helix length , Major (watson and crick) and Minor grooves and The number of Direction Right-handed Right-handed Left-handed base pairs per turn for each type are (clockwise) (clockwise) (anti-clockwise) very IMPORTANT. Also, you might be Helix length Short Elongated More elongated asked in the exam to differentiate between two types. Major groove Deep and narrow Wide Not a real groove Minor groove Wide Narrow Narrow Placement of BP Displaced away Centered over the Zig-Zag pattern from the helical axis helical axis (nearly perpendicular to the helical axis) BP per turn 11 10 12 Conformation of C3 C2 G(C2) : C(C3) Deoxyribose Types of DNA structure A-DNA B-DNA Z-DNA DNA supercoiling The chromosomes of many bacteria and viruses contain circular DNA which is supercoiled in order to take a smaller place, and to give it more protection.  Melting temperature (MT) - The temperature at which the double-stranded DNA is separated into two single strands. - Melting point (MT) of DNA depends on nitrogenous base content (A-T and G-C). G-C has 3 hydrogen bonds, so it is stronger than A-T which only has two. Team441 note : Schematic representation of strand separation in duplex DNA resulting from heat denaturation  The types and functions of RNA RNA is a single-stranded polymer of ribonucleotides. Types: Transcription process mRNA (Messenger RNA): (DNA to mRNA) Recognition and transferring, tRNA (transfer RNA): it recognizes amino acids’ codons and transfers the selected amino acids to the growing protein chain. Site of protein synthesis rRNA (ribosomal RNA): (factory)  Organization of DNA in a chromosome The human genome contains 3.5 billion base pairs and more than 95% is non-coding or “junk” DNA. The DNA from single 23 human chromosomes have a length of 1 meter. Each chromosome is a complex of a single linear DNA molecule and protein called chromatin. 50% of chromatin consists of proteins called histones.  HISTONES Histones have These proteins bind five major types: to negatively charged H1, H2A, H2B, H3, H4 PO4 groups of DNA Histones have to stabilize the positively charged chromatin amino acids structure. (arginine and notice that there lysine). isn’t a type of histones called H5  Nucleosomes Nucleosomes are particles consisting of DNA and histones connected by thin strands of naked DNA (like beads on a string; Sibhah in Arabic). Nucleosomes consist of the histone octamer (8 histones) and DNA. Nucleosomes consist of the histone octamer (eight) and DNA (H2A)2, (H2B)2, (H3)2, (H4)2 H1 binds to 2 complete helical turns of DNA. H1 clips the DNA to keep it in place, (it’s not part of the octamer)  Take Home Message The central dogma of molecular biology involves three components: DNA, RNA and protein. There are two chemically distinct types of nucleic acids: DNA and RNA, which perform several crucial functions. To package the long sequence of the genomic DNA, it is highly organized into chromosomes.  MCQs 1 Nitrogenous base is bonded to …… of sugar ? A C1’ B C2’ C C3’ D C5’ 2 How many base pairs per turn are present in the type A-DNA? A 10 B 11 C 12 D 13 Which of the following is true about the structure of the DNA 3 double helix? A The two strands B The two strands are There are 8 base pairs D Bases are on the anti-parallel C per turn outside of the helix are parallel 1- A. 2-B. 3-B  MCQs 4 What holds the two strands of the DNA double helix together? Covalent Hydrogen Van der Waals A B C Ionic bonds D bonds bonds forces 5 Which type of DNA does not have a real groove A-DNA B-DNA RNA A B C Z-DNA D 4- B. 5-C.  Biochemistry Team Saad AlDosari Leaders Nada AlMuhawwis Abdulrahman Turki Members Kadi Jood Alnasser Alanazi Alluhayyan Alqosi Faisal Salman Norah Horia Alnemri Almutairy Alrashid Alotaibi Abdulaziz Rahaf Latifah Mohammed Alotaibi Alshalawi Aldossary Alqahtani Basma Renad Fahad Albahkly Alsanad Almosa Ruba Team MED445 Aldibas