TMJC Viruses Notes

Page 1 of 42 Tampines Meridian Junior College JC2 H2/9744 Biology 2024 Core Idea 2B 9. Genetics & Inheritance (VI) Organization & Inheritance of Viral Genomes SYLLABUS OVERVIEW No. Overarching Idea Topics 1 Core Idea 1 The Cell and Biomolecules of Life Cell – The Basic Unit of Life 2 Biomolecules of Life and Cellular Transport 3 Core Idea 3 Energy and Equilibrium Transformation of Energy – Photosynthesis and Cellular Respiration 4 Core Idea 2 Genetics and Inheritance Genetics and Inheritance (I) – The Cell Cycle 5 Genetics and Inheritance (II) – DNA Replication and Gene Expression 6 Genetics and Inheritance (III) – DNA Mutations and their Consequences 7 Genetics and Inheritance (IV) – Molecular Techniques in DNA Analysis 8 Genetics and Inheritance (V) – Organization of Genome & Control of Gene Expression in Eukaryotes [Includes Core Idea 1D: Stem Cells] 9 Genetics and Inheritance (VI) – Organization and Inheritance of Viral Genomes 10 Genetics and Inheritance (VII) – Organization of Genome & Control of Gene Expression in Prokaryotes 11 Genetics and Inheritance (VIII) - Inheritance 12 Core Idea 3 Energy and Equilibrium Communication and Equilibrium in Multicellular Organisms 13 Core Idea 4 Biological Evolution Biological Evolution 14 Extension Topic A Infectious Diseases Immunity and Infectious Diseases 15 Extension Topic B Impact of Climate Change on Animals & Plants Climate Change – Causes and Impacts on Animals and Plants

Page 2 of 42 NARRATIVE An understanding of Genetics and Inheritance that would help make sense of the transition from molecular to organismal level. Genetics and Inheritance provides the molecular basis to the understanding of how variations in populations arise and this is important in the study of biological evolution. At the cellular level, expression of genes involves cellular structures such as the nucleus, endoplasmic r eticulum and ribosome. Many essential products of gene expression are enzymes involved in biochemical path ways which control physiological functions. As such, mutation of genes may give rise to dysfunctional proteins which in turn could result in diseases. Sickle cell anemia and cancer are raised as examples of a monogenic and a mul ti-genic disease respectively. The following questions should help students frame their learning: • How does the genetic make-up of an organism influence its appearance, behavior and survival? • How can we ensure continuity of human as a species? Heritable information, in the form of DNA (and in some cases RNA), provides for continuity of life Genetic information is stored in an organism’s DNA; expression of genes results in the synthesis of functional products, such as rRNA, tRNA and proteins. These products play a role in intra- and extra-cellular biochemical pathways and influence the physiological processes in organisms. Genomes contain heritable information necessary for continuity of life at all levels: cell, organism and system. This information is stored and passed on to subsequent generations via DNA. Reproduction can occur at the cellular or organismal level; each progeny needs to receive heritable genetic information from its parents. An understanding of how eukaryotic, prokaryotic and viral genomes are organised has implications on how gene expression in organisms is controlled. Unlike prokaryotes and eukaryotes, the genome of viruses varies greatly; they can be DNA or RNA in nature, single or double-stranded, depending on the type of virus. Viruses undergo different reproductive cycles: some bacteriophages, e.g. T4 phage, reprodu ce via lytic cycle while others, e.g. lambda phage, reproduce via lytic and/or lysogenic cycles; animal viruses, such as influenza virus and HIV, reproduce through other mechanisms. Again, unlike their prokaryotes or eukaryotes counterparts, viruses do not photosynthesize or respire, and they require host cells (bacteria, plants or animals) to reproduce. As such, debate ensues as to whether viruses are considered living or non -living. LEARNING OUTCOMES Core Idea 2B: Organization of Genomes In contrast to eukaryotic and prokaryotic genomes, the viral genome varies according to the type of virus; the genome may be DNA or RNA in nature and single or double-stranded. For RNA viruses, they may possess either positive-sense RNA (i.e. identical to viral mRNA and thus can be immediately translated) or negative - sense RNA (i.e. complementary to viral mRNA and thus must be converted to positive -sense RNA by RNA polymerase before translation). Candidates should be able to: a) Describe the structure and organization of viral, prokaryotic and eukaryotic genomes (including DNA/RNA, single-/double-stranded, number of nucleotides, packing of DNA, linearity/circularity and presence/absence of introns) b) Describe how the genomes of viruses are inherited through outlining the reproductive cycles of: i) Bacteriophages that reproduce via lytic cycle only, e.g. T4 phage; ii) Bacteriophages that reproduce via lytic and lysogenic cycles, e.g. lambda phage; iii) enveloped viruses, e.g. influenza; and iv) retroviruses, e.g. HIV c) Describe how variation in viral genomes arises, including antigenic shift and antigenic drift.

Page 3 of 42 LECTURE OUTLINE 1. Overview of viruses 1.1 Characteristics of viruses 1.2 General features of viral reproductive cycle 2. Structure and Organization of Viral Genome 2.1 Structure of Viral Genome 2.2 Organisation of Viral Genome 3. Bacterial Viruses (Bacteriophages) 3.1 T4 bacteriophage 3.1.1 Structure 3.1.2 Reproductive cycle (lytic) 3.2 Lambda bacteriophage 3.2.1 Structure 3.2.2 Reproductive cycle (lytic and lysogenic) 4. Animal Viruses 4.1 Influenza Viruses 4.1.1 Structure 4.1.2 Reproductive cycle 4.2 Human Immunodeficiency Virus (HIV) 4.2.1 Structure 4.2.2 Reproductive cycle 4.3 Treatment of viral diseases 4.3.1 How viral infections cause disease 4.3.2 Overview of treatment strategies 5. Variation in viral genome (e.g. influenza virus) 5.1 Antigenic shift 5.2 Antigenic drift TEXTBOOK REFERENCES Biology, Campbell and Reece, 9th Edition, pgs 427 - 441

Page 4 of 42 INTERNET ANIMATIONS 1. Entry of Virus into Host Cell 2. Mechanism for Releasing Enveloped Viruses 3. T4 phage reproductive cycle 4. Lambda phage reproductive cycle 5. Influenza virus reproductive cycle 6. HIV reproductive cycle 7. HIV treatment (protease and reverse transcriptase inhibitors) 8. Antigenic drift 9. Antigenic shift

Page 5 of 42 1. Introduction 1.1 Characteristics of Viruses 1. Nucleic acid (viral genome) (details in Section 2.1) 2. Capsid (protein coat) ➢ It is a protein coat, built from a large number of protein subunits called capsomeres. ➢ There are many capsid shapes (eg. helical, icosahedral, complex) (Fig. 1.1b). ➢ The viral nucleic acid plus its surrounding protein capsid is known as a nucleocapsid. ➢ Functions of the capsid: i. Encloses the viral genome and protects it from digestion by enzymes. ii. Aids in the attachment to and penetration of the host cell. iii. Carries viral enzymes involved in viral replication. 3. Viral envelope (only in some viruses i.e. enveloped viruses) ➢ Consists of a phospholipid bilayer (derived from the host’s plasma membrane during budding) which surrounds the capsid. ➢ Some contain glycoproteins that project from the viral envelope as spikes. These glycoproteins are encoded by the viral genome. Examples of enveloped viruses with glycoproteins are influenza viruses and HIV. ➢ Functions i. Glycoproteins on the viral envelope are complementary in shape to and can therefore bind to the receptor proteins on the host cell membrane. This determines the specific host range (i.e. specific cell types or species/organisms that a virus can infect). Some viru