YIJC [H2] CI2.10 Genetics of Viruses (N)(S) vetted (wo checkpoint answers)

2024 JC1 BIOLOGY LECTURE NOTES CORE IDEA 2: GENETICS AND INHERITANCE TOPIC 2.10: Genetics of Virus Learning Outcomes: You should be able to: Core Idea 1 (e) describe the structural components of viruses, including enveloped viruses and bacteriophages, and interpret drawings and photographs of them (f) discuss how viruses challenge the cell theory and concepts of what is considered living Core Idea 2 (d) [modifed] describe the structure and organisation of viral genomes (including DNA/RNA, single- /double-stranded, number of nucleotides, packing of DNA, linearity/circularity and presence/absence of introns) (e) describe how the genomes of viruses are inherited through outlining the reproductive cycles of: i. bacteriophages that reproduce via a lytic cycle only, including T4 phage ii. bacteriophages that reproduce via lytic and lysogenic cycles, including lambda phage iii. enveloped viruses, including influenza virus iv. retroviruses, including HIV (f) describe how variation in viral genomes arises, including antigenic shift and antigenic drift LECTURE OUTLINE 1 Nature of a virus particle ................................ ................................ ................................ ............ 2 2 Structure of a virus particle ................................ ................................ ................................ ........ 4 3 General features of viral reproductive cycle ……………………………………………………….. 10 4 Structure and Reproductive cycle of virulent bacteriophages e.g. T4 phage ............................ 11 5 Structure & Reproductive cycle of temperate bacteriophages e.g. Lambda phage................... 14 6 Structure & Reproductive cycle of enveloped viruses e.g. Influenza virus ................................ 18 7 Structure & Reproductive cycle of retroviruses e.g. HIV virus (HIV) ................................ ......... 22 8 Mechanisms for Variation in Viral Genomes ................................ ................................ ............ 28 H2

2 1 Nature of a virus particle 1.1 Are viruses alive?  Viruses are small infectious particles that can only replicate in their host cells.  These particles have a simple acellular organisation, consisting of viral genetic material (either DNA or RNA) enclosed in a protein coat called capsid (and a membranous envelope in some viruses).  Viruses are considered to exist at the border between chemistry and life, because they posses both living and non-living characteristics.  They display properties of living organisms only inside their host cells (intracellular phase) and are non-living outside their host cells (extracellular phase).  Living characteristics of viruses: o They are able to reproduce (though not independently). o They possess nucleic acids e.g. DNA or RNA that encode information for the reproduction of new viruses with the same characteristics as themselves. o They are able to obtain and use energy from host, but cannot generate or store energy in the form of ATP. o They are able to respond to the environment such as radiation, chemicals and heat when inside the host cell. o They are able to evolve and mutate. It was deduced that since viruses can reproduce only within cells, they probably evolved as bits of cellular nucleic acid.  Non-living characteristics of viruses: o Viruses are acellular. They lack cytoplasm, all metabolic machinery (e.g enzymes required for metabolism) and cellular organelles (eg. nucleus, mitochondria, ribosomes, etc.) hence o cannot undergo metabolism (eg. cellular respiration, synthesis of organic compounds). o cannot replicate independently. Viruses are dependent on a compatible host cell’s metabolic machinery to synthesise new viral components for replication. Learning Outcome 1(f): discuss how viruses challenge the cell theory and concepts of what is considered living

3 1.2 Viruses are obligate intracellular parasites A virus is a sub-microscopic infectious agent that cannot replicate independently of a living cell, which is called a host cell. Viruses are therefore obligate intracellular parasites that must rely on entering a suitable living cell i.e. infecting a host cell, to carry out their replication cycle and thus multiply.  Upon infecting a host cell, the virus exploits the energy resources, raw materials and metabolic machinery of the host cell.  The virus redirects host metabolic functions towards supporting its replication cycle via the assembly of new viral particles.  Eventually, the new viral particles are released, and the process can repeat itself as the infection spreads. Although viruses can only replicate after infecting a host cell, they have an extracellular form, known as the viral particle or virion that enables them to exist outside the host for long periods, and that facilitates their transmission from one host cell to another. Viral particles can be passed from host to host either through direct contact (e.g. body fluids) or through a vector or carrier (e.g. dengue is transmitted by Aedes mosquito) 1.3 Are viruses cells? Viruses were neither considered cells nor organisms as many characteristics of viruses are in contradiction with the cell theory. Characteristics of viruses that defy the cell theory Cell theory How viruses defy the cell theory 1. Cells are the smallest unit of life. Viruses are much smaller than cells and once thought to be the most basic unit of life. However, whether viruses can be considered living is questionable, as they do not fulfil ALL characteristics of life. 2. All cells come from pre-existing cells. Viruses do not originate from pre -existing viruses ; they cannot replicate independently outside a host cell. 3. All living organisms are composed of cells. The basic structure of viruses consists of the viral genome enclosed in a capsid. Viruses do not possess metabolic machinery or cellular organelles, hence are considered acellular. 1.4 Conclusion on whether viruses are living The general consensus of the scientific community is that viruses are non-living, best described as obligate intracellular parasites. Viruses exhibit host specificity. They infect specific host cells by a “lock and key” fit between viral surface proteins and specific receptor molecules on the host cell surface. They can be classified based on the hosts they infect.  Viruses that infect only bacteria are called bacteriophages.  Viruses that infect only animals are called animal viruses

4 2 Structure of a Virus particle All viruses contain the following two components: i) a nucleic acid genome and ii) a protein coat called a capsid that encloses the genome. Nucleocapsid compromises of both the viral genome and capsid. An infectious viral particle, a virion, will contain a nucleocapsid at least. There are two main classifications of viruses Naked Virus / Non-enveloped viruses Enveloped Viruses Viruses without an envelope are known as naked viruses or non-enveloped viruses. Viruses with a membranous envelope surrounding the nucleocapsid are known as enveloped viruses. Viral genome + Capsid = Nucleocapsid = Naked viruses Viral genome + Capsid + Envelope = Enveloped viruses Some viruses may also contain viral enzymes. The structure and composition of these components can vary widely among different viruses. Learning Outcome 1(e): describe the structural components of viruses, including enveloped viruses and bacteriophages, and interpret drawings and photographs of them

5 Fig. 2: Diverse structures of viruses

6 2.1 Genome Viral genomes vary among different viruses and may be: 1. DNA or RNA but never at the same time. Hence, viruses can be classified as DNA viruses or RNA viruses according to the type of nucleic acid that makes up its genome.