Topic 02-DNA Structure and Function_S2_AY23-24 (1).pdf

Topic 2: DNA Structure and Function 9/19/2024 GRD 101-Molecular Genetics 1 Reading Material Text Book: Campbell, N. A., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., & Reece, J. B. (2017). Biology: A Global Approach, ePub, Global Edition, 11/e (11th Edition). Pearson Intern...

Topic 2: DNA Structure and Function 9/19/2024 GRD 101-Molecular Genetics 1 Reading Material Text Book: Campbell, N. A., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., & Reece, J. B. (2017). Biology: A Global Approach, ePub, Global Edition, 11/e (11th Edition). Pearson International Content. https://bookshelf.vitalsource.com/books/9781292234939 Chapter 16: Nucleic Acids and Inheritance 16.1 DNA is the genetic material p. 365 16.2 Many proteins work together in DNA replication and repair p. 370 16.3 A chromosome consists of a DNA molecule packed together with proteins p. 380 9/19/2024 GRD 101-Molecular Genetics 2 Course Learning Outcomes CLO-6 : structure of DNA and RNA for understanding of central dogma of life Learning Objectives − Basic structure of Nucleic acids − Watson and Crick’s model of DNA structure − Types of RNA − Central dogma of life − Practice 9/19/2024 GRD 101-Molecular Genetics 3 Vocabulary For Vocab Self-Quiz, check the following link : https://media.pearsoncmg.com/intl/ge/2017 /ge_campbell_biology_11/msa/vocab/flash cards.php Select “chapter 16”  Select “Create Deck” 9/19/2024 GRD 101-Molecular Genetics 4 Nucleic Acid  Nucleic acids are polymers of nucleotides  Nucleotides are formed of a phosphate group, a pentose sugar, and a nitrogenous base  There are two types of nucleic acids: 1. DNA (deoxyribonucleic acid) 2. RNA (ribonucleic acid) 9/19/2024 GRD 101-Molecular Genetics 5 Deoxyribonucleic acid (DNA) Purines Pyrimidines DNA is a chain of nucleotides having: (double ring) (single ring) Base NH2 O 1. Phosphate group O– N CH3 H N N O P O CH2 H O 2. Pentose sugar O– N N H N O HH HH H ―Deoxyribose Phosphate Thymine (T) H OH H Adenine (A) 3. Nitrogenous base Deoxyribose O NH2 ―Purines (double ring)– Adenine (A), N H H N N H Guanine(G) N NH2 H O N N H H ―Pyrimidines (single ring) – Cytosine Guanine (G) Cytosine (C) (C), Thymine (T) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 9/19/2024 GRD 101-Molecular Genetics 6 Ribonucleic acid (DNA) RNA is a chain of nucleotides having: Base NH2 O– 1. Phosphate group O P O CH2 N N H H O H O– 2. Pentose sugar N N H H HH H H Phosphate H ―Ribose (ribonucleic Acid) OH OH Adenine (A) Uracil (U) NH2 3. Nitrogenous base Ribose O N H H N ―Purines (double ring)– N H Adenine (A), Guanine (G) N N NH2 H N O H H Guanine (G) Cytosine (C) ―Pyrimidines (single ring) – Cytosine (C), Uracil (U) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 9/19/2024 GRD 101-Molecular Genetics 7 Nucleotide numbering system O 4 H CH3 5  Sugar carbons are 1’ to 5’. N 3 Thymine 6 H 2 O O– 1N  Base attached to 1’ carbon on sugar O P O CH2 5′ O O– 1′ 4′ H H H  Phosphate attached to 5’ carbon on Phosphate H 3′ 2′ sugar OH H Deoxyribose Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 9/19/2024 GRD 101-Molecular Genetics 8 Chain of nucleotides or Strands ― Nucleotides are covalently bonded ― The Backbone has phosphodiester bonds to join phosphate group links to sugar ―Hydrogen bond is formed between two nitrogen bases ― Bases project away from the backbone 9/19/2024 GRD 101-Molecular Genetics 9 DNA is the Genetic Material The Search for the Genetic Material: Scientific Inquiry Early in the 20th century, the identification of the molecules of inheritance was a major challenge to biologists T. H. Morgan’s group showed that genes are located on chromosomes. The two components of chromosomes —DNA and protein—became candidates for the genetic material. Thomas Hunt Morgan 9/19/2024 GRD 101-Molecular Genetics 10 Timeline of the DNA Discovery 9/19/2024 GRD 101-Molecular Genetics 11 Chargaff's Discovery In 1950, Erwin Chargaff reported that DNA composition varies from one species to the next 9/19/2024 GRD 101-Molecular Genetics 12 Chargaff’s rules Chargaff’s rules state the following : 1. The base composition of DNA varies between species 2. In any species the number of A and T bases are equal, and the number of G and C bases are equal. ? ? ? ? 9/19/2024 GRD 101-Molecular Genetics 13 Watson & Crick’s DNA model Watson and Crick combined the studies of Franklin and Chargaff and proposed Watson and Crick DNA Model. The main features of the model are: 1. DNA had two sides or strands with a fixed width, and these strands were twisted together like a twisted ladder - the double helix. 2. The DNA double helix is anti-parallel and elongates in the 5’ to 3’ direction. 3. DNA base pairs (A-T and G-C) on two strands are complementary and are connected via hydrogen bonds. 4. DNA can copy itself by semiconservative mode (which was later proved correct). 9/19/2024 GRD 101-Molecular Genetics 14 DNA double helix C G 5′ end Watson and Crick C G Hydrogen bond 3′ end G C G C T A 3.4 nm T A G C G C C G A T 1 nm C G T A C G G C C G A T A T 3′ end NOTE: New nucleotides can only be A T added at the 3’ end. 0.34 nm Sugar phosphate Backbone T A 5′ end (b) Partial chemical structure DNA is antiparallel, so the two (a) Key features of Adenine (A) paired only with thymine (T), and strands elongate in opposite DNA structure guanine (G) paired only with cytosine (C)- directions. Justifying Chargaff's rules. 9/19/2024 GRD 101-Molecular Genetics 15 DNA base pairing – Hydrogen bonds! The two strands of DNA are linked and stay in a stable shape because of the many hydrogen bonds linking the base pairs: 2 hydrogen bonds connect A-T 3 hydrogen bonds connect G-C 9/19/2024 GRD 101-Molecular Genetics 16  DNA Replication is Semiconservative The Basic Principle: Base Pairing to a Template Strand The two strands of DNA are The two strands separate and each strand acts as a template for complementary building a new strand in replication 9/19/2024 GRD 101-Molecular Genetics 17 Summary of DNA replication: Overview Leading Origin of strand replication Lagging Leading strand strand 3′ template Leading Single-strand Lagging strand strand 5′ binding proteins Leading strand Overall directions Helicase of replication 5′ DNA pol III 3′ Primer 3′ 5′ Primase 3′ Parenta 5 DNA pol Lagging l 5′ III 3′ strand DNA pol I DNA ligase DNA 4 5′ 3 2 1 3′ Lagging strand 5′ template 9/19/2024 GRD 101-Molecular Genetics 18 9/19/2024 GRD 101-Molecular Genetics 19 9/19/2024 GRD 101-Molecular Genetics 20 DNA Polymerization 9/19/2024 GRD 101-Molecular Genetics 21 Central Dogma: The flow of genetic information, named by Francis Crick in 1956 Transcription: is the synthesis of mRNA under the direction of DNA. Translation: is the synthesis of a protein using the information in the mRNA. Ribosomes are the sites of translation/protein synthesis. 9/19/2024 GRD 101-Molecular Genetics 22  Nucleus DNA Protein synthesis: Transcription and Step 1: Transcription Translation RNA Plasma membrane Cytoplasm RNA Step 2: Ribosome Translation Protein 9/19/2024 GRD 101-Molecular Genetics 23 Types of RNA There are three major classes of RNA, each with specific functions in protein synthesis: 1. Messenger RNA (mRNA) – takes a message from DNA in the nucleus to the ribosomes in the cytoplasm 2. Transfer RNA (tRNA) – transfers amino acids to the ribosomes 3. Ribosomal RNA (rRNA) – along with proteins, makes up the ribosomes, where polypeptides are synthesized 9/19/2024 GRD 101-Molecular Genetics 24 Protein Synthesis: Transcription occurs in the nucleus genetic information encoded in DNA is copied onto a strand of RNA to direct protein synthesis. Information in one DNA strand is converted to messenger RNA (mRNA). mRNA is synthesised in a 5’ 3’ direction. mRNA is complementary to that strand of DNA (Template strand). Copyright ©2021 John Wiley & Sons, Inc. 25 Steps of Transcription 1. Initiation It is the start of transcription The enzyme RNA polymerase binds to the 5’ region of a gene called the promoter. 2. Elongation RNA polymerase reads the unwound DNA strand Synthesizes mRNA molecule using complementary base pairs. 3. Termination Occurs when RNA polymerase crosses a stop (termination) sequence in the gene. The mRNA strand is complete, and it detaches from DNA. 9/19/2024 GRD 101-Molecular Genetics 26 Protein Synthesis: Translation  Process of mRNA converting to a protein  Occurs in the cytoplasm on the ribosome  three sequences of bases on mRNA are called codons, and they determine which amino acid is coded for by the RNA (and DNA).  The translators are tRNA molecules, each with a specific anticodon at one end and a corresponding amino acid at the other. Copyright ©2021 John Wiley & Sons, Inc. 27  Synthesis of Protein 1. Initiation Small subunit binds to mRNA start codon is AUG – which means methionine is the first amino acid attached at the P-site 2. Elongation A site recognizes codon and pairs with the correct tRNA peptide bond forms between the carboxyl end of the polypeptide at the P site and the amino acid at the A site The amino acid in the A site translocate to the P site 3. Termination 1. Stop codon is reached at the A site (UAA, UAG, UGA) 2. Release factors free the polypeptide from the ribosome 9/19/2024 GRD 101-Molecular Genetics 28 Protein Synthesis During Translation 9/19/2024 GRD 101-Molecular Genetics 29 Triplet Code: Codons Codon Chart 3 Nucleotides = 1 amino acid 9/19/2024 GRD 101-Molecular Genetics 30  Protein Synthesis Interactions Animation: Protein Synthesis Copyright ©2021 John Wiley & Sons, Inc. 31 9/19/2024 GRD 101-Molecular Genetics 32 9/19/2024 GRD 101-Molecular Genetics 33 9/19/2024 GRD 101-Molecular Genetics 34 Try to find the amino acid sequence DNA Sequence: GTA CCA GAA CGA RNA Sequence: ___ ___ ___ ___ Amino Acid Sequence: ___ ___ ___ ___ Now change one base (e.g. GTA > ATA) and find the amino acid sequence. What is the change? 9/19/2024 GRD 101-Molecular Genetics 35 Do you want to test your understanding of TOPIC 2 ? Check the following link for multiple-choice questions: https://media.pearsoncmg. com/intl/ge/2017/ge_camp bell_biology_11/msa/conten t/practice-test/practice- test.php Select Chapters 16 and 17 9/19/2024 GRD 101-Molecular Genetics 36