BHS016-1 Molecular Genetics Lecture 01 - Nucleic Acids PDF

Molecular Genetics (BHS016-1) Dr Taiwo Shittu 1 Nucleic Acids BHS016-1 Topic 1 2 Learning Outcomes ◼ After this topic you should be able to: ❑ Recall the chemical structures and key elements of nucleotides. ❑ Explai...

Molecular Genetics (BHS016-1) Dr Taiwo Shittu 1 Nucleic Acids BHS016-1 Topic 1 2 Learning Outcomes ◼ After this topic you should be able to: ❑ Recall the chemical structures and key elements of nucleotides. ❑ Explain the formation of nucleic acids from individual nucleotides. ❑ Describe in detail the 3D structure of DNA. ❑ Understand the various functions of nucleic acids and nucleotides. 3 What Is Genetics? ◼ Genetics is the study of heredity. ◼ Heredity is controlled by genes. ◼ Genes are units of biological information. ◼ Genes are units of inheritance. 4 Why Is Genetics Important? Examples of google results for “Genetics” in a typical week. ◼ Heart damage from cancer drugs linked to faulty genes. BIOMEDICAL SCIENCE ◼ Scientists extract oldest ever genetic information from rhino tooth.BIOLOGICAL SCIENCE ◼ Genetic evidence snares man over unsolved rape. FORENSIC SCIENCE 5 Basic Structure Of The DNA Molecule 6 How To Identify Genetic Material? ◼ Was unknown before 1950s. ◼ But before this, it was realised that: ❑ Genetic material must contain complex information. ❑ Genetic material must replicate faithfully. ❑ Genetic material must encode the phenotype. ◼ Definition: PHENOTYPE 7 How Do We Know It Is DNA? ◼ 1869 – Nucleic acid found in nucleus. ◼ 1884 – Histone proteins found in nucleus. ◼ 1887 – Nucleus shown to carry genetic material. ◼ Definition: CHROMATIN ◼ Which component of chromatin is the genetic material, DNA or proteins? ◼ Conclusion misled by tetranucleotide theory (Levene 1910). ◼ Truth first realised in 1944 (Avery et al.). 8 Timeline Of DNA As Genetic Code 9 How Do We Know It Is DNA? ◼ Avery et al. were working with two types of S. pneumoniae bacteria. ◼ One form (S) caused disease in mice, the other (R) did not. ◼ Avery noticed that: ❑ If you killed the S bacteria by heating, they could no longer cause disease in mice. ❑ But, if you mixed the dead S bacteria with living R bacteria, the R bacteria transformed into a disease causing strain. ◼ Avery et al. experimented to find which type of molecule had transformed the R bacteria.10  How Do We Know It Is DNA? Image taken from https://en.wikipedia.org/wiki/Avery-MacLeod-McCarty_experiment. 11 (2016). Author unknown. 1944 – Avery, Macleod And McCarty 12 1944 – Avery, Macleod And McCarty 13 How Can DNA Carry Information? ◼ Late 1800s – Kossel showed that DNA contained four nitrogenous bases. ◼ Definition: PURINE ◼ Definition: PYRIMIDINE Image taken from Pierce, BA. (2012). Genetics: A Conceptual Approach 4th Edn. 14 How Can DNA Carry Information? ◼ 1910 – Levene demonstrated DNA was a polymer of nucleotides. ◼ Definition: NUCLEOTIDE Image taken from Pierce, BA. (2012). Genetics: A Conceptual Approach 4th Edn 15  How Can DNA Carry Information? ◼ DNA contains four different deoxyribonucleotides joined together in long polymer chains. ❑ Chains can be only a few thousand nucleotides long (e.g. viruses). ❑ Can be hundreds of millions of nucleotides long (e.g. human chromosome 1). Image taken from Pierce, BA. (2012). Genetics: A Conceptual Approach 4th Edn 16 How Can DNA Carry Information? ◼ 1948 – Chargaff demonstrated DNA contained fixed ratios of nucleotides. Image taken from Pierce, BA. (2012). Genetics: A Conceptual Approach 4th Edn 17 How Can DNA Carry Information? ◼ 1948 – Chargaff demonstrated DNA contained fixed ratios of nucleotides. ◼ All the DNA molecules examined had: ❑ The same amount of adenine as it had thymine. ❑ The same amount of guanine as it had cytosine. ❑ Therefore the same amount of purines (A+G) as it had pyrimidines (C+T). ◼ WHY? Image taken from Pierce, BA. (2012). Genetics: A Conceptual Approach 4th Edn 18 How Can DNA Carry Information? ◼ 1953 – Watson and Crick demonstrate that DNA is a double helix. ◼ Human chromosomes are linear molecules consisting of two complementary and antiparallel strands of DNA wound into a helical shape. ❑ Hence “double helix”. 19 Primary Structure Of DNA 20 How Can DNA Carry Information? ◼ Nucleotides can join together into polymers by making phosphodiester bonds. ❑ -C-O-P-O-C- ◼ Nucleotide forms covalent bond between its 5’-PO4 group and the 3’-OH group on another nucleotide. An example of a condensation reaction. ◼ Definition: COVALENT ◼ Definition: 5’ (“5 prime”) and 3’ (“3 prime”) 21  Phosphodiester Bond Formation Image from Pearson Education. 22  Phosphodiester Bonds = Backbone ◼ This covalent bonding of nucleotides produces a polymer with a sugar-phosphate backbone. Sugar Phosphate 5’ end 3’ end ◼ Bases protrude out from this linear molecule. Image from Bowen, R. http://www.vivo.colostate.edu/hbooks/genetics/biotech/basics/nastruct.html. 23 Secondary Structure Of DNA 24  Base Pairing ◼ Chargaff’s rules = base pairing. ◼ Bases pair by hydrogen bonding. ◼ Two H-bonds link adenine to thymine. ◼ Three H-bonds link guanine to cytosine. ◼ Definition: H-BOND Image from Pearson Education. 25  Base Pairing = Interior ◼ Linear polynucleotide strands can therefore pair to give a double stranded molecule. ◼ Pairing of A with T, or C with G, is called COMPLEMENTARY BASE PAIRING. ◼ Complementary strands are ANTIPARALLEL. Image taken from Pierce, BA. (2012). Genetics: A Conceptual Approach 4th Edn 26 Summary Of Basic DNA Structure ◼ DNA consists of two polynucleotide strands. ◼ Each strand has a sugar phosphate backbone on outside of molecule. ◼ Nitrogenous bases on interior of molecule. ◼ Hydrogen bonding joins bases of two strands. ◼ Adenine pairs with thymine. ◼ Guanine pairs with cytosine. ◼ The two polynucleotide strands are complementary and antiparallel. https://www.youtube.com/watch?v=o_-6JXLYS-k http://www.youtube.com/watch?v=qy8dk5iS1f0 27 How Can DNA Carry Information? ◼ Genetic material must contain complex information. ❑ Extremely long sequence of nucleotide “letters” in a single DNA strand, spelling coded instructions. ◼ Genetic material must replicate faithfully. ❑ Complementary base pairing means that each strand can act as a template for new complementary DNA strand production. ◼ Genetic material must encode the phenotype. ❑ Breaking the DNA code took much longer. 28 Tertiary Structure Of DNA 29 DNA Structure ◼ Definition: PRIMARY STRUCTURE. ◼ Definition: SECONDARY STRUCTURE. ◼ Definition: TERTIARY STRUCTURE. 30 DNA Is A Double Helix ◼ 5’3’ phosphodiester bonds cause some torsional force that twists the double stranded DNA molecule. ◼ Forms an ALPHA HELIX. ◼ DNA is a double helix: ❑ of - TWO ANTI-PARALLEL CHAINS ❑ helix is - RIGHT HANDED (Clockwise) ❑ has a - MAJOR and a MINOR GROOVE 31 B-DNA Structure Image taken from Pierce, BA. (2012). Genetics: A Conceptual Approach 4th Edn 32 DNA Requires Further Packing ◼ In cells, each double strand DNA molecule forms a structure called a chromosome. ◼ Bacterial chromosome in E. coli is 4.6 million base pairs (Mbp) long. ❑ 1000 times longer than the bacterial cell. ◼ Human nuclei contain 3.2 billion base pairs (3,230 Mbp) of DNA. ❑ Smallest human chromosome is 14,000 times the length of the nucleus. 33 Prokaryote DNA Simple Structure ◼ Prokaryotes (e.g. bacteria) usually have a single chromosome with a simple structure. ◼ The DNA is folded into long loops. ◼ The ends of each loop are attached to structural proteins that hold the DNA in place. ◼ This structure can be seen when prokaryote cells are lysed (broken open). 34 Bacterial DNA Folded In Twisted Loops Image taken from Pierce, BA. (2012). Genetics: A Conceptual Approach 4th Edn 35 Eukaryotic DNA Shows Complex Packing 2 nm wide double helix 11 nm nucleosome 30 nm chromatin fibre 300 nm coiled fibre 700 nm coiled coil 1400 nm chromosome 36 Double Helix Packed Into Nucleosomes ◼ Definition: NUCLEOSOME. ◼ 160-200 bp of DNA helix wrapped around eight core histone proteins. ❑ 2x (H2A, H2B, H3 and H4) ◼ Nucleosomes linked together into solenoid structure by linker histone, H1. 37 Nucleosomes Packed Into 30 nm Fibre “Beads on a string” Solenoid 38 30 nm Fibre Packed Into Larger Coils 300 nm coiled fibre 700 nm coiled coil 39  700 nm Coiled Coil Forms Chromosome Chromosome 700 nm coiled coil 40 Eukaryotic DNA Shows Complex Packing 41 DNA Packing Alters During Cell Cycle ◼ In eukaryotes, chromosomes are made of CHROMATIN (the complex of DNA and proteins e.g. histones). ◼ The structure of chromatin over the whole chromosome changes during cell cycle. ❑ Small local changes in chromatin can also occur during transcription, DNA replication, DNA repair. ◼ Chromatin is tightly packed during M-phase. ❑ Condenses (tightly packs) during prophase. ❑ Decondenses (loosens slightly) at telophase. 42 DNA Packing Alters During Cell Cycle ◼ During interphase, most regions of chromatin are more loosely packed. ❑ Definition: EUCHROMATIN. ❑ Transcriptionally active regions (protein and RNA coding regions). ◼ Some regions of chromatin stay tightly packed, even during interphase. ❑ Definition: HETEROCHROMATIN. ❑ Includes centromeres and telomeres (structural regions, other repetitive elements). 43 Functions Of DNA And Nucleotides 44 Functions Of Genomic DNA ◼ Found in the nucleus of eukaryotic cells. ◼ “Naked” in cytoplasm of prokaryotes. ◼ The “genetic” material of the cell: ◼ Provides instructions: ❑ ⇒ GENES for building proteins. ❑ ⇒ REGULATORY REGIONS for control of “gene expression” ❑ ⇒ NON-CODING DNA structural and “unknown” 45 Functions Of Other DNA ◼ Mitochondrial DNA (in eukaryotes): ❑ 37 genes: enzymes for oxidative phosphorylation, ribosomal RNA and transfer RNA. ◼ Chloroplast DNA (in plants): ❑ Encodes for redox proteins involved in electron transport in photosynthesis. ◼ Plasmid DNA (in some prokaryotes): ❑ Separate circular DNA in some bacterial cells. ❑ May encode for drug resistance, fertility, (conjugation) toxins, virulence genes. 46  Functions Of Nucleotides ◼ In addition to forming DNA or RNA, nucleotides have other important biochemical functions. ◼ Cyclic Nucleotide Monophosphates: ❑ Act as cell signalling molecules (e.g. cAMP). ◼ Coenzymes (coenzyme A, NAD): ❑ Coenzymes in metabolism. 47 Functions Of Nucleotides ◼ Nucleotide Triphosphates (e.g. ATP, GTP): ❑ Provide energy storage and transport. ❑ Cofactors for enzymatic phosphorylation. ❑ They function by conversion to and from diphosphate form (e.g. ADP ATP) 48 Summary – You Should Now Know… ◼ The structure of bases, deoxyribose, nucleotides, and DNA. ◼ The formation of DNA polynucleotides. ◼ The primary, secondary and tertiary structures of the DNA double helix. ◼ The functions of DNA and nucleotides. 49 To-Do List ◼ Review DNA structure: ❑ E.g. Pierce Genetics 6th ed. chapter 1 and 10 ◼ Write your own definitions of: deoxyribose sugar; bases; purines; pyrimidines; nucleotides; nucleosides; DNA; and chromatin. ◼ Show diagrammatically how two deoxynucleotides join into a polynucleotide chain. ◼ Produce further notes and simple drawings on histones, chromosome packing and chromatin (including euchromatin & heterochromatin). ◼ Write a short table summarising the functions of DNA molecules and nucleotides 50 Before Next Week’s Lecture For next lecture: ◼ Read about Chromosome Structure in a suitable textbook. ❑ E.g. Pierce Genetics 6th Ed. Chapter 2 and 11. 51