2016 H2 J2 Topic L Genetics of Viruses

NANYANG JUNIOR COLLEGE H2 Biology Genetics of Viruses J2/2016 1 GENETICS OF VIRUSES Learning Outcome Candidates should be able to: Core Topic 3 – Genetics of Viruses and Bacteria (a) Discuss whether viruses are living or non -living organisms and explain why viruses are obligate parasites. (b) Describe the structural components of viruses. (c) Describe the reproductive cycles of the following virus types: i. bacteriophages that reproduce via a lytic cycle, e.g. T4 phage; ii. bacteriophages that reproduce via a lysogenic cycle, e.g. lambda phage; iii. an enveloped virus, e.g. influenza; iv. retroviruses, e.g. HIV. (d) Explain how viral infections cause disease in animals, e.g. mammals, through the disruption of host tissue and functions (e.g. HIV and T helper cells [details of the immune system are not required], influenza and epithelial cells of the respiratory tract). Content Outline 1. Introduction 2. Definition of Life – Are Viruses Living or Non-living? 3. Structure of Viruses (a) Genome (b) Capsid (c) Envelope 4. Viral Reproductive Cycles (a) Reproductive cycle of bacteriophages, e.g. T4 phage, lambda phage (b) Reproductive cycle of enveloped viruses, e.g. influenza (c) Reproductive cycle of retroviruses, e.g. HIV 5. Viral Infections and Diseases 6. Course of HIV Infection in Humans References 1. Campbell N. A. & Reece J.B. (200 8). Biology. Chapter 1 9: Viruses. Eighth Edition. Pearson Education, Inc. 2. Brooker R.J. (2008). Biology. Chapter 18 : Genetics of Bacteria and Viruses . International Edition. The McGraw-Hill Companies.

NANYANG JUNIOR COLLEGE H2 Biology Genetics of Viruses J2/2016 2 1. Introduction All living organisms, either eukaryotes or prokaryotes, have nucleic acids which make up their genomes. Viruses possess nucleic acids but require the assistance of living cells to reproduce. As such, it becomes a debate as to whether viruses are living or non-living. Viruses are obligate parasites as they can reproduce only within a host cell as they lack organelles and metabolic enzymes necessary for protein synthesis and replication of the viral genome . Thus, isolated viruses , i.e. virions (infectious viral particles found outside a host cell ), are merely packaged sets of genes in transit from one host cell to another. In this topic, we will explore the structure of viruses, their reproductive cycles as well as the diseases caused by them. 2. Definition of Life – Are Viruses Living or Non-living? It has been an ongoing debate in the scientific world as to whether the virus is a living organism or a non-living particle. The consensus is that life is a characteristic of organisms that exhibit all or most of the following phenomena:  Organisation – Being structurally composed of one or more cells which are the basic units of life.  Metabolism – Consumption of energy by converting chemicals into cellular components (anabolism) and decomposing organic matter (catabolism). Living things requi re energy to produce phenomena associated with life.  Growth – A growing organism increases in size of all of its parts, rather than simply accumulating matter. The particular species begins to multiply and expand as the evolution continues to flourish.  Homeostasis – The ability to regulate and maintain a constant internal environment.  Adaptation – A population of living organisms has t he ability to change over a period of time in response to the environment, an ability that is fundamental to the process of evolution.  Response to stimuli – A response that can take on many forms from contraction of a unicellular organism to external chemicals to complex reactions involving senses of higher animals. A response is often expressed by motion for example the leaves of a plant turning towards the sun, otherwise known as phototropism.  Reproduction – The ability to produce new organisms.

NANYANG JUNIOR COLLEGE H2 Biology Genetics of Viruses J2/2016 3 A virus is considered as a living organism as it is able to:  Reproduce: It takes over the genetic machinery of its host cells to replicate more viral particles.  Adaptable: Viruses have high mutation rates so as to have genetic variation and have a higher chance of survival in unfavourable environments.  Metabolism: Viruses direct its host cells to provide the energy needed to produce more viral particles. Yet, scientists have also argued that virus is not a living organism as it:  Does not grow or increase in size. It merely replicates to produce more viruses in terms of numbers.  Is not a cell or composed of cells, thus does not carry out metabolism on its own.  Does not have the ability to carry out homeostasis since it usually c ontains no more than a genome in a protein coat.  Does not seem to have the ability to response to stimuli, since it does not move on its own. Therefore the answer as to whether viruses are living or non-living remains inconclusive.

NANYANG JUNIOR COLLEGE H2 Biology Genetics of Viruses J2/2016 4 3. Structure of Viruses Viruses are 20 – 400nm in diameter . For comparison, a typical bacterium is 1000 nm in diameter and the diameter of most eukaryotic cells is 10 to 1000 times that of a bacterium. A ribosome has a diameter of about 20nm. Viruses can differ in many aspects from host range (number of species and cell types that they can infect), types of genome and structural features. Thus, viruses have a wide variety of shapes. All viruses have a genome and capsid but can be categorized as enveloped or non- enveloped. (a) Genome The genome of a virus varies according to the type of virus:  A virus is called a DNA virus or an RNA virus, depending on whether the genome consists of DNA or RNA respectively.  For viruses with RNA genome, they may possess either positive-sense RNA (i.e. identical to viral mRNA and thus can be immediately translate d) or negative- sense RNA (i.e. complementary to viral mRNA and thus must be converted to positive-sense RNA by RNA polymerase before translation).  The genome is usually organized as a linear or circular molecule of nucleic acid , depending on the type of virus.  In some viruses, the nucleic acid is single-stranded, whereas in others, it is double- stranded.  Some kinds of viruses may have more than one copy of the genome.  Viral genomes also vary considerably in size, ranging from a few thousand to more than a hundred thousand nucleotides in length. Fewer genes have been related to a less complex viral structure:  The genomes of some simple viruses, such as phage Qβ are only a few thousand nucleotides in length and contain only a few genes.  Other viruses, particu larly those with a complex structure, contain more genes. Phage T4 is an example of a complex virus having many genes. These extra genes are largely involved in the formation of the elaborate protein coat. (b) Capsid  The capsid is a protein coat enclosing the viral genome.  There is a variety of shapes, including helical and polyhedral.  Capsids are built from a large number of protein subunits called capsomeres.  Some viruses carry a few viral enzyme molecules within their capsids.  The most complex capsids are found among viruses that infect bacteria, called bacteriophages / phages.  The capsids of phages have elongated icosahedral heads enclosing their genome.  Attached to the head is a tail shaft with fibres that the phages use to attach to a bacterial cell wall.  Generally, capsids serve to protect the viral genome.

NANYANG JUNIOR COLLEGE H2 Biology Genetics of Viruses J2/2016 5 (c) Envelope  The viral envelope encloses the capsids of many viruses which infect animals.  These viral envelopes comprise of: o host cell phospholipids from the cell surface membrane of the host cell o embedded with virally encoded spike glycoproteins 