Acellular life

Class 11 Biology, unit 5, book pages 132–147

Practise 66 MCQs Take the unit quiz Review 57 cards

Viruses, prions and viroids are infectious particles that are not cells. They cannot make their own energy or proteins, so a virus must take over a living host cell to multiply. This unit follows the discovery and structure of viruses, the bacteriophage and the HIV life cycles, the viral diseases of humans and cotton, and the even simpler prions and viroids, and it shows why these particles cost lives and money.

Learning outcomes (22)

Justify the status of viruses among living and non-living things.
Trace the history of viruses since their discovery.
Classify viruses on the bases of their hosts and structure.
Describe the structure of a model bacteriophage, and HIV.
Justify that a virus must have a host cell to parasitize in order to complete its life cycle.
Explain how a virus survives inside a host cell, protected from the immune system.
Determine the method a virus employs to survive / pass over unfavourable conditions when it does not have a host to complete the life cycle.
Describe the Lytic and Lysogenic life cycles of a virus.
Outline the usage of bacteriophage in genetic engineering.
Explain the life cycle of HIV.
Justify the name of the virus i.e., "Human Immunodeficiency Virus" by establishing T-helper cells as the basis of immune system.
Reason out the specificity of HIV on its host cells.
List the symptoms of AIDS.
Explain opportunistic diseases that may attack an AIDS victim.
Describe the treatments available for AIDS.
List some common control measures against the transmission of HIV.
Describe the causative agent, symptoms, treatment and prevention of the following viral diseases: hepatitis C, herpes, polio and leaf curl virus disease of cotton.
List the sources of transmission for each of the above-mentioned diseases.
Describe the structure of prions and viroids.
List the diseases caused by prions and viroids.
Interpret how viral infections cause global economic loss.
Describe the limitations of the vaccine for the common cold / flu virus.

5.1Viruses: discovery and structure

This chapter deals with the nature of viruses, prions and viroids. These are acellular (not made of cells) infectious agents. They cause preventable and often fatal infectious diseases, so they also matter for the economy of a country. You met a brief introduction to biodiversity in the IX and X biology course; this unit goes further down to the level below the cell.

You must have heard about influenza, bird flu, polio, swine flu, dengue fever and so on. All these and many other diseases are caused by infectious agents called viruses. Viruses are pathogens, which cause diseases in animals and plants.

Virus: An acellular infectious agent (a pathogen) that causes disease in animals and plants. It is not a cell, it cannot replicate independently, and it is too small to be seen under the light microscope.
Acellular life: The level of organisation below the cell: viruses, prions and viroids.

Three points set viruses apart from every cell you have studied so far:

Viruses are not cells.
They are not capable of independent replication (they cannot copy themselves without a host).
They cannot synthesise their own energy and proteins.
They are too small to be seen under the light microscope.

5.1.1History and discovery of virusOften examined

The word virus comes from a Latin word venom meaning "poison". In the past the term virus was used for any infectious disease whose cause was unknown.

From a filter to a crystal

Timeline of discovery

1884, Charles Chamberland (who worked with Louis Pasteur) found that the causative agent of rabies could pass through a porcelain filter with pores of 100 to 1000 nm. This was the first evidence that viruses exist. The same kind of filter completely removed all the bacteria and other cells known at the time from a liquid, so the rabies agent was something smaller.
1892, Iwanowsky studied tobacco mosaic disease, which was thought to be caused by bacteria. He extracted the juice from diseased tobacco leaves and passed it through a porcelain filter to remove the bacteria. He rubbed the filtered juice on the leaves of healthy plants, expecting no disease, but the healthy leaves soon showed the symptoms.
By 1900 similar disease-producing substances had been found in both plants and animals. They were called filterable viruses.
1935, W. M. Stanley crystallised the infectious particle now known as tobacco mosaic virus (TMV). Later many other viruses were actually seen with the help of the electron microscope.

Timeline of the discovery of viruses.

Iwanowsky's experiment (1892). The filter keeps bacteria back, yet the filtered juice still made healthy leaves ill.

Virology: The study of viruses.
Filterable virus: The name given by 1900 to a disease-producing substance that passes through a porcelain filter.

5.1.2Characteristics of virusesOften examined

Viruses show characteristics of both living and non-living things. This is why their status among living and non-living things is debated.

Living and non-living characteristics of viruses (5.1.2)
Living characteristics	Non-living characteristics
They occur in different varieties or strains.	They lack cellular structure, coenzyme and enzyme system, and have no metabolic activity of their own.
They have their own genetic material, DNA or RNA, that can undergo mutation.	They can be crystallised and stored in bottles.
They reproduce using the metabolic machinery of the host cell they infect.	They do not respire.
They enter the cells of a living organism and cause disease: they are intracellular obligate parasites.	Outside the host they behave as non-living, inert infectious particles.
They are destroyed by ultraviolet rays.

The virus particle: a coat (capsid protein, and an envelope in some viruses) around a core (DNA or RNA and various enzymes).

5.1.3General structure of a virusOften examined

Viruses have a very simple structure. A complete viral particle is called a virion. Primarily it can be divided into two parts: the core and the coat.

Virion: A complete viral particle.
Core: The inner part of the virion. It consists of the viral genome and various proteins (enzymes).
Genome: The genetic material of the virus, either DNA or RNA, which may be single stranded or double stranded.
Core proteins: One or more enzymes that help the virus in its mode of action inside the host body.
Coat: The outer covering of the viral particle. It consists of the capsid and, in some viruses, the envelope.
Capsid: The protective coat of protein surrounding the core. It is composed of identical repeating subunits called capsomeres.
Capsomere: One of the identical repeating protein subunits that make up the capsid.
Envelope: An extra lipoprotein layer around the capsid in a few viruses. It is derived from the cell surface membrane of the host and also contains virally encoded proteins.
Glycoprotein spikes: Spikes of glycoprotein that often cover the viral envelope and help the virus to recognise the host cell.

The core: genome and enzymes

Examples of core enzymes given in the book: all single stranded RNA viruses have an enzyme to convert the single stranded RNA genome into a double stranded RNA genome. Retroviruses and hepatitis B virus contain the enzyme reverse transcriptase, which converts a single stranded RNA genome into a double stranded DNA genome.

The coat: capsid and envelope

The number of capsomeres is specific to a particular kind of virus. The herpes virus has 162 capsomeres in its capsid, while the adenovirus that causes the common cold has 252. There are two forms of symmetry in a virus capsid.

The two forms of capsid symmetry
Symmetry	How the capsomeres are arranged	Appearance
Icosahedral (polyhedral)	In 20 triangles	Spherical or many-sided
Helical	In a hollow coil	Rod shaped

General structure of a virion: (a) icosahedral capsid, (b) helical capsid, (c) a virus with an envelope and glycoprotein spikes. The core (genome) lies inside the capsid.

5.1.4Classification of virusOften examined

Virus classification is based either on the host organisms or on other structural characters such as morphology (shape), genome type and mode of action in the host. The internationally agreed system classifies viruses by the structure and composition of the virion. In some cases the mode of replication is also important.

Classification based upon host

Viruses are classified on the basis of their hosts into bacteriophage viruses, plant viruses and animal viruses.

Classification of viruses based upon host
Group	Host	Facts and examples from the book
Bacteriophage virus	Bacteria	A DNA virus with a polyhedral head and a tail.
Plant viruses	Plants	More than 2,000 viral plant diseases are known. Most plant viruses, including tobacco mosaic virus (TMV), have an RNA genome. Many have a rod shaped capsid like TMV, for example potato yellow dwarf virus.
Animal viruses	Animals	Occur as parasites in animals. Foot and mouth disease of livestock; Rous sarcoma virus causes cancer; many infections destroy certain cells of the human body. Papovirus causes warts, poxvirus causes small pox, picornavirus causes polio and hepatitis A, paramyxovirus causes measles and mumps.

Classification based upon structure

(i) On the bases of capsid

Classification on the bases of capsid
Capsid type	Example
Helical capsid	Tobacco mosaic virus
Polyhedral capsid	Adenoviruses
Enveloped viruses	Influenza viruses
Complex capsid	Bacteriophage

(ii) On the bases of genomes

Classification on the bases of genomes
Genome type	Example
(a) Double-stranded DNA (dsDNA)	Smallpox virus
(b) Single-stranded DNA (ssDNA)	Mild rash virus
(c) Double-stranded RNA (dsRNA)	Diarrhoea virus
(d) Single-stranded RNA (ssRNA) that serves as mRNA	Rubella virus
(e) ssRNA that is a template for mRNA synthesis	Influenza virus
(f) ssRNA that is a template for DNA synthesis	HIV

Worked example: placing viruses in a genome group

Using the book's list, state the genome group of (i) smallpox virus, (ii) rubella virus, (iii) influenza virus, (iv) HIV, and say what the genome does in the groups (iii) and (iv).

Match each virus with its example in the genome list.
Smallpox virus has a double-stranded DNA genome, group (a). Nothing is copied into RNA first: it already has DNA.
Rubella virus is an ssRNA virus whose RNA serves directly as mRNA, group (d).
Influenza virus has ssRNA that is a template for mRNA synthesis, group (e): the RNA is copied to make mRNA.
HIV has ssRNA that is a template for DNA synthesis, group (f): reverse transcriptase copies the RNA into DNA. This is why HIV is a retrovirus.

Virus	Genome group	Role of the genome
Smallpox virus	(a) dsDNA	Stored as DNA
Rubella virus	(d) ssRNA	Works as mRNA
Influenza virus	(e) ssRNA	Template for mRNA
HIV	(f) ssRNA	Template for DNA

5.2Parasitic nature of virusOften examined

Viruses are parasitic in nature. They are highly specific to their host. A bacteriophage infects only bacteria, the tobacco mosaic virus infects only tobacco plants, and rabies virus infects only mammals. Some human viruses even specialise in a particular tissue.

Host specificity of viruses (5.2)
Virus	Cells or host it infects
Bacteriophage	Bacteria only
Tobacco mosaic virus	Tobacco plants only
Rabies virus	Mammals only (all mammalian cells)
HIV	Only certain types of white blood cells
Poliovirus	Spinal nerve cells (humans and other primates)
Hepatitis viruses	Liver cells only
Human cold viruses	Cells lining the upper respiratory tract

Viruses have protein spikes on their surfaces which help them to attach to specific receptors on the host cells. The specificity of attachment determines the host range of the virus.

Specificity of attachment. Protein spikes on the virus bind only to matching receptors on the host cell. The match decides the host range.

Host range: The range of hosts a virus can infect, decided by the specificity of attachment between its surface protein spikes and the receptors of the host cell.

Some viruses have a narrow host range, whereas others have quite a broad range. For example, poliovirus can enter the cells of only humans and other primates (narrow), whereas rabies virus can enter all mammalian cells (broad).

5.2.1Viruses must require host cell to complete life cycleOften examined

A virus must have a host cell to parasitise in order to complete its life cycle because viruses are obligate intracellular parasites. This means they cannot multiply outside a living cell.

Obligate intracellular parasite: An organism or particle that can multiply only inside a living cell of a host. It cannot multiply outside it.

Viruses infect all sorts of cells, from bacterial cells to human cells. An isolated virus is unable to reproduce or do anything else except infect an appropriate host cell. Viruses lack metabolic enzymes, ribosomes and so on for making proteins. Therefore they need a host cell to complete their life cycles.

Why a virus needs a host cell
What is needed to multiply	Has the virus got it?	Where it comes from
Genetic material (DNA or RNA)	Yes	The virus itself
Metabolic enzymes	No	Host cell
Ribosomes to make proteins	No	Host cell (host ribosomes)
Energy	The virus cannot make its own	Host cell

5.2.2Survival of viruses inside a host cellOften examined

When a virus infects an organism it enters inside the host cell. The cell is not only a factory for the virus but also its hiding place. Two things let the virus survive inside the host.

It hides from the immune system. The host immune system is unable to find the virus inside the cell.
It changes quickly. The virus rapidly changes its own genetic constitution, so the vaccines or antibodies of the host against it become ineffective.
The capsid protects the genome. When the virus enters a cell the capsid protects the viral genome from the nucleases of the host cell. Nucleases are the enzymes found in all cells that break down DNA or RNA.

The capsid protects the viral genome from host nucleases. A naked genome would be broken down; the genome inside the capsid is not reached.

5.2.3Viruses can pass unfavourable conditions outside the host

Unlike other "living" organisms, viruses do not need food to survive. Outside the host body they remain dormant (inactive). Being tiny, they are not threatened by other microorganisms. Their only concern is the pH and temperature of the medium, because these would denature the protein.

The virulence of the virus outside the host is maintained for a certain period of time. The period depends on which virus it is and on the pH and temperature of the medium.
Viruses outside the host are non-living: they have no metabolic activity outside a living host, so they pass through a dormant period.
The genome of the virus remains viable for a long time, in inactive form, outside the host.

Enveloped and non-enveloped viruses

Non-enveloped viruses can in fact survive for long periods outside the host (up to several days), whereas enveloped viruses survive for shorter periods. This is because many enveloped viruses rely on the proteins on the surface of the membrane to attach to the host cell. The envelope is generally sensitive to degradation by sunlight and normal cleaning procedures.

Survival of non-enveloped and enveloped viruses outside the host
Point	Non-enveloped virus	Enveloped virus
Survival outside the host	Long, up to several days	Shorter
Surface proteins for attachment	Capsid proteins	Proteins of the envelope membrane
Effect of sunlight and cleaning	Resist better	Envelope is degraded easily

Worked example: which virus stays infectious longer on a surface?

Two viruses are left on a table. Virus X is enveloped and attaches by spikes in its envelope. Virus Y has only a capsid. The table is cleaned with a normal cleaner and left in sunlight. Which virus is more likely to remain infectious, and why?

Decide what each virus needs to stay infectious: an intact structure that can attach to a host cell later. Both have their genome kept safe (viable but dormant).
Virus X depends on the proteins of its envelope for attachment. The envelope is sensitive to sunlight and to normal cleaning, so it is degraded and the virus can no longer attach.
Virus Y has no envelope to lose. Its protein capsid is only threatened by extreme pH and temperature, which the table does not provide.

	Virus X (enveloped)	Virus Y (non-enveloped)
Damaged by sunlight and cleaning?	Yes, envelope degraded	Little
Likely survival	Short	Long (up to several days)

5.3.1Structure of bacteriophageOften examined

The bacteriophage, or simply phage, is the virus that attacks bacteria. It is generally a tadpole shaped virus and consists of a head, a neck and a tail.

Parts of a bacteriophage and their functions
Part	Structure and function (from the book)
Head	Icosahedral in shape. Its inner core consists of a single stranded DNA genome.
Neck (collar)	A narrow part below the head that separates the head from the tail.
Tail	A hollow tube made up of proteins through which the nucleic acid passes during infection. It is surrounded by a contractile sheath, which contracts during infection of the bacterium.
Base plate	Present at the end of the tail. It possesses about six tail fibres around it and several tail pins (spikes) at its lower surface.
Tail fibres and tail pins	Involved in the binding of the phage to the bacterial cell.
Lysozyme	An enzyme present at the bottom of the core tube of the tail. It is released upon contraction of the tail and digests the portion of the host cell wall so that the core tube can penetrate into the host cell during infection.

Figure 5.1: Structure of bacteriophage. The head holds the DNA, the contractile sheath surrounds the hollow tail, and the base plate carries the tail pins and tail fibres that bind to the bacterium.

Worked example: identify the parts A to F of a bacteriophage

Name the parts A to F of the bacteriophage drawn below and give one function of each.

Bacteriophage with lettered parts.

Work from the top down. A is the many-sided structure at the top: the head. It holds the DNA genome.
B is the narrow ring between head and tail: the neck (collar). It separates the head from the tail.
C is the long striped tube: the tail with its contractile sheath. The sheath contracts and pushes the hollow core tube through the cell wall.
D is the flat plate at the bottom of the tail: the base plate. It carries the pins and fibres.
E are the short spikes under the plate: the tail pins. F are the long bent legs: the tail fibres. Both bind the phage to receptors on the bacterial cell.

Letter	Part	Function
A	Head	Contains the DNA genome
B	Neck (collar)	Separates head and tail
C	Tail with contractile sheath	Hollow tube for the DNA; sheath contracts in infection
D	Base plate	Bears tail pins and tail fibres
E	Tail pins	Bind the phage to the bacterium
F	Tail fibres	Bind the phage to the bacterium

5.3.2Life cycle of bacteriophageOften examined

Bacteriophages show two types of life cycles: the lytic cycle and the lysogenic cycle. The life cycle of a bacteriophage has two main steps: the infection process and the replication within the host cells.

The initial steps of the infection process, namely adsorption, penetration and genome injection, are quite similar in both cycles. The mode of replication is much different in the lytic cycle and the lysogenic cycle.

Both life cycles begin with the same infection process. They differ in what the phage DNA does afterwards.

5.3.3Infection processOften examined

The common steps of the infection process of bacteriophages to their host are adsorption, penetration and genome injection.

The three common steps

Adsorption. This is the first step. The phage attaches to the bacterial cell. It is mediated by the tail fibres and tail pins (spikes), which attach to specific receptors on the bacterial cell.
Penetration. The binding of the phage to the bacterium results in the contraction of the sheath and the release of lysozyme that digests the portion of the bacterial envelope. As a result the hollow core tube is pushed through the bacterial envelope. This insertion of the core tube is called penetration.
Genome injection. The penetration of the core results in the injection of viral DNA into the bacterial cytoplasm, whereas the remainder of the phage stays on the outside of the bacterium.

Figure 5.2: Insertion of core into the bacterium. (1) The phage binds to the cell, (2) the sheath contracts and the core tube passes through the wall, (3) the DNA enters the cytoplasm and the empty phage remains outside.

5.3.4Replication of bacteriophage in lytic cycleOften examined

A bacteriophage that performs the lytic cycle is called a lytic or virulent phage, because it immediately causes lysis (breakdown) of its host cell after its own multiplication.

It develops a master-slave relationship with the host cell. The host genomic DNA is immediately disintegrated by a virally encoded DNA digesting enzyme (DNAase). Since the viral DNA is already chemically modified, these enzymes do not affect it. The disintegration of host DNA enables the viral DNA to take over the control of the whole metabolic machinery of its host.

Lytic (virulent) phage: A bacteriophage that multiplies at once inside its host and then lyses (breaks down) the host cell.
Master-slave relationship: The relationship in the lytic cycle: the viral DNA takes over the host cell completely, after the host DNA has been broken down.

After the common infection steps (adsorption, penetration and genome injection) the subsequent steps of the lytic cycle are synthesis of phage components, assembly, maturation, lysis and release.

Lytic cycle after the infection process

Disintegration of host DNA. The viral DNAase breaks down the host DNA. The viral DNA, which is chemically modified, is not affected, and it controls the cell.
Synthesis of phage components. Soon after the disintegration of host DNA, phage specified mRNAs and proteins begin to be produced. The structural proteins (head, tail) that make up the phage, and the proteins needed for lysis of the bacterial cell, are synthesised separately.
Assembly. The nucleic acid is packaged inside the head and then the tail is added to the head.
Maturation. The assembly of phage components into a mature infective phage particle is known as maturation. Within 20 to 25 minutes approximately 200 phage particles are produced.
Lysis and release. In this phase the bacteria begin to lyse because of the accumulation of the phage lysis protein (lysozyme). The intracellular phage particles are released into the medium.

The lytic cycle of a bacteriophage in order: 1 adsorption, 2 penetration and injection of DNA, 3 breakdown of host DNA, 4 synthesis of phage parts, 5 assembly and maturation, 6 lysis and release of about 200 new phages.

5.3.5Replication of bacteriophage in lysogenic cycleOften examined

The bacteriophages that perform the lysogenic cycle are called lysogenic or temperate phages. These phages can either multiply through the lytic cycle or enter a dormant state in the cell.

Such phages develop a host-guest relationship, because in this case the phage DNA actually integrates into the host chromosome. It is replicated along with the host chromosome and passed on to the daughter cells.

Lysogenic (temperate) phage: A bacteriophage that can either multiply by the lytic cycle or stay dormant inside the host cell.
Prophage: The integrated state of the phage DNA in the host chromosome.
Lysogeny: The process in which the phage DNA is integrated in the host chromosome as a prophage.
Lysogenic bacteria: Bacteria harbouring a prophage.
Induction: The termination of the lysogenic state of a bacterium at any time when it is exposed to adverse conditions.

Figure 5.3: Lytic and lysogenic life cycles of bacteriophage. After infection the phage DNA either takes over the cell (lytic cycle) or becomes a prophage in the bacterial chromosome (lysogenic cycle). Induction sends a lysogenic cell into the lytic cycle.

Lysogenic cycle (steps of the book's Figure 5.3)

The phage DNA enters the bacterium (adsorption, penetration and genome injection, as in every phage infection).
The phage DNA inserts itself, as a prophage, into the bacterial chromosome.
The prophage is replicated along with the bacterial DNA before binary fission.
Binary fission is completed and each cell has the phage DNA incorporated. The cells carry the phage without being destroyed.

Induction

The lysogenic state of a bacterium can be terminated at any time when it is exposed to adverse conditions. This process is called induction. Conditions that favour the termination of the lysogenic state include desiccation, exposure to UV or ionizing radiation, and exposure to mutagenic chemicals. The separated phage DNA then starts the lytic cycle, resulting in cell lysis and release of phages. Such phages are then capable of infecting new susceptible cells and rendering them lysogenic.

Lytic and lysogenic cycles compared
Point	Lytic cycle	Lysogenic cycle
Type of phage	Lytic or virulent phage	Lysogenic or temperate phage
Relationship with the host	Master-slave relationship	Host-guest relationship
Fate of host DNA	Disintegrated at once by the viral DNAase	Phage DNA integrates into the host chromosome and is replicated with it
Fate of the host cell	Lysed immediately after the phage multiplies	Survives and divides; the prophage passes to the daughter cells
Release of new phages	At the end of the cycle (about 200 phages in 20 to 25 minutes)	Only after induction, when the lytic cycle starts

Worked example: a lysogenic bacterium is exposed to UV radiation

A culture of bacteria carrying a prophage is exposed to ultraviolet radiation. Describe what happens to the prophage and to the cells.

Say what the cells are like before the radiation: the phage DNA is a prophage, part of the bacterial chromosome, copied with it at every cell division. The cells live normally.
UV radiation is an adverse condition (like desiccation or mutagenic chemicals). It brings about induction: the lysogenic state ends.
The phage DNA separates from the bacterial chromosome and begins the lytic cycle: phage components are made, assembled and matured.
The cells lyse and release phages. These can infect new susceptible cells and make them lysogenic.

	Before UV	After UV (induction)
Phage DNA	Prophage in the host chromosome	Separated; directs the cell
Bacterial cell	Alive, divides	Lysed
Cycle	Lysogenic	Lytic

5.3.6Usage of bacteriophages in genetic engineering

Genetic engineering is the field of biotechnology in which alteration in the genetic material of an organism is carried out, such as the transfer of a gene from one organism to another. Several biological tools have been used in genetic engineering to accomplish the required task. Bacteriophages have also been used in a number of ways in different approaches of genetic engineering. Some of them are outlined below.

Genetic engineering: The field of biotechnology in which the genetic material of an organism is altered, for example by transferring a gene from one organism to another.
Vector: A carrier of DNA used in genetic engineering. Besides bacterial plasmids, phage DNA is also used as a vector.
Genomic library: A collection of bacteria or bacteriophage clones which contains multiple copies of all the genes of an individual's genome.
Phage therapy: The application of genetically engineered phages that can kill pathogenic bacteria.

Usage of bacteriophages in genetic engineering (5.3.6)
Use	What the book says
(a) Phage DNA as a vector	Besides bacterial plasmids, phage DNA is used as a vector in genetic engineering techniques, such as the development of a genomic library.
(b) Phage therapy	Genetically engineered phages kill pathogenic bacteria. Phages are fairly narrow in their spectrum of activity, so with phage treatment it is possible to kill the bacterial pathogens while avoiding harm to the normal bacterial flora, our good bacteria.
(c) Antibacterial nano medicines	Recently discovered: bacteriophages can be formulated as targeted drug-delivery vehicles.

5.4.1Structure of human immunodeficiency virusOften examined

Human immunodeficiency virus (HIV) is the causative agent of acquired immune-deficiency syndrome (AIDS). It was identified in 1984 by a research team from the Pasteur Institute in France and the National Institute of Health in USA. The virus was named HIV in 1986.

HIV is a retrovirus and is spherical in shape.

Parts of HIV
Part	Structure and function (from the book)
Envelope	The outer covering: a lipoprotein envelope of two layers of lipids. The lipid membrane is borrowed from the host cell during the budding process (formation of new particles).
Spikes (glycoproteins)	Different proteins embedded in the viral envelope form spikes made of the outer glycoprotein gp 120 and the transmembrane gp 41. gp 120 is needed to attach to the host cell and gp 41 is critical for the cell fusion process.
Matrix proteins	A protein shell beneath the envelope. It lies between the envelope and the capsid.
Capsid	Somewhat conical in shape, composed of capsomeres.
Viral core	Contains two single strands of HIV RNA and the enzymes needed for HIV replication: reverse transcriptase, integrase and protease.

Enzymes in the HIV core
Enzyme	Job
Reverse transcriptase	Converts the viral RNA genome into a viral DNA genome
Integrase	Incorporates the viral DNA into the host DNA
Protease	Breaks large structural proteins into smaller units

The structural proteins are encoded by three out of the nine virus genes.

Figure 5.4: Human immunodeficiency virus (HIV), cross section. The envelope carries glycoprotein spikes (gp 120 and gp 41); inside lie the matrix proteins, the conical capsid, two RNA strands and the enzymes.

Bacteriophage and HIV compared
Point	Bacteriophage	HIV
Host	Bacteria	Helper T cells (CD4 cells)
Genome	DNA	Two single strands of RNA
Shape	Tadpole: head, neck and tail	Spherical, with a conical capsid
Envelope	None	Lipoprotein envelope borrowed from the host cell
Attachment	Tail fibres and tail pins	Glycoprotein gp 120 binds the CD4 receptor
Entry	Core tube injects DNA; the phage coat stays outside	Envelope fuses with the cell membrane and the virion enters by endocytosis, then sheds its coat

5.4.2Life cycle of HIVOften examined

HIV attacks only specific cells of the host called CD4 cells. Helper T cells, macrophages and certain brain cells have CD4 receptors and are called CD4 cells. HIV recognises the CD4 receptors for attachment. Since HIV attaches only to CD4 cells, it has host cell specificity.

The 12 steps of the HIV life cycle

Attachment (adsorption). The gp 120 envelope proteins of the virion bind to the CD4 proteins (the receptor) on the surface of the T cell.
Penetration. The viral envelope fuses with the cell membrane by using gp 41, and the virion enters the cell by endocytosis. Inside the host cell the HIV particle sheds its protective coat: this is uncoating. It leaves the single stranded viral RNA in the cytoplasm along with viral enzymes.
Reverse transcription. The enzyme reverse transcriptase synthesises a single stranded DNA complementary to the virus RNA, called complementary DNA (cDNA).
Breakdown of viral genomic RNA. After reverse transcription the viral genomic RNA is disintegrated by the enzyme ribonuclease (RNAase).
Replication. The single stranded cDNA is replicated to form double stranded cDNA.
Integration. The double stranded cDNA integrates into the host cell DNA. Integration is mediated by the virus encoded enzyme integrase.
Provirus. The integrated DNA is now called the provirus.
Transcription (steps 8 and 9). Viral mRNA is transcribed from the proviral DNA by the host cell RNA polymerase. During transcription not only viral mRNAs for different proteins are formed, but viral genomic RNA is also produced.
Biosynthesis of protein (step 10). The viral mRNAs are translated by host ribosomes into several large proteins, which are then cleaved by the virus encoded protease to form the virion structural proteins.
Maturation (step 11). The viral components are assembled and mature virions are produced.
Release (step 12). The mature virions are gradually released by budding off from the host cell, enclosing a portion of host cell membrane around them. In this way the host cell size is decreased enough that it becomes non-functional.

Figure 5.5: Life cycle of HIV. 1 Attachment (adsorption), 2 Penetration, 3 Reverse transcription, 4 Breakdown of viral genomic RNA, 5 Replication, 6 Integration, 7 Provirus, 8 and 9 Transcription, 10 Biosynthesis of protein, 11 Maturation, 12 Release.

Worked example: which enzyme acts at which step?

List the enzymes named in the HIV life cycle, give the step at which each acts and say whether it is carried in the virion or supplied by the host.

Go through the 12 steps and pick out each enzyme the book names.
Step 3: reverse transcriptase makes cDNA from the viral RNA. It is part of the viral core (carried by the virion).
Step 4: ribonuclease (RNAase) breaks down the viral genomic RNA after reverse transcription.
Step 6: integrase joins the double stranded cDNA to the host DNA. It is a virus encoded enzyme from the core.
Steps 8 and 9: RNA polymerase transcribes the proviral DNA into viral mRNA and genomic RNA. This one belongs to the host cell.
Step 10: protease cuts the large proteins made by host ribosomes into the structural proteins of the virion. It is virus encoded.

Step	Enzyme	Action	Source
3	Reverse transcriptase	Viral RNA to cDNA	Virion core
4	Ribonuclease	Breaks down viral RNA	Named in the book as the RNAase enzyme
6	Integrase	Joins viral DNA to host DNA	Virion core, virus encoded
8, 9	RNA polymerase	Transcribes proviral DNA	Host cell
10	Protease	Cleaves large proteins	Virus encoded

5.4.2HIV AIDS namingOften examined

Helper T cells are the most important cells of the immune system. They help and activate other cells of the immune system.

Helper T cells activate B cells to secrete antibodies.
They also activate cytotoxic T cells to kill virus-infected and cancerous cells.
Since helper T cells regulate immunity by enhancing the response of other immune cells, a decrease in their number causes a deficiency of the human immune system.

This is why the virus has been named Human Immunodeficiency Virus (HIV): it attacks the helper T cells and leaves the human immune system deficient.

Helper T cells switch on B cells and cytotoxic T cells. HIV destroys helper T cells, so neither can be activated and immunity falls.

Why HIV has its name
Part of the name	Reason (from the book)
Human	The virus infects human cells (it attaches to CD4 cells).
Immunodeficiency	The number of helper T cells, which regulate the other immune cells, decreases, so the immune system becomes deficient.
Virus	An acellular infectious particle with RNA as its genome.

5.4.3Symptoms of AIDSOften examined

An HIV infection can be divided into three stages: asymptomatic carrier, AIDS related complex (ARC) and full blown AIDS.

The three stages of HIV infection
Stage	Symptoms and features (from the book)
Asymptomatic carrier	Symptoms that may include fever, chills, aches (continued pain), swollen lymph glands and an itchy rash. These symptoms disappear and there are no other symptoms for nine months or longer. Although the individual exhibits no symptoms during this stage, he or she is highly infectious. The standard HIV blood test for the presence of antibody becomes positive during this stage.
AIDS related complex (ARC)	The most common symptoms are swollen lymph glands in the neck, armpit or groin that persist for months. Other symptoms include night sweats, persistent cough, flu, persistent diarrhoea, loss of memory and depression.
Full blown AIDS	The final stage. There is severe weight loss and weakness due to persistent diarrhoea, and usually one of several opportunistic infections.

The three stages of an HIV infection, in order.

5.4.4Opportunistic diseasesOften examined

HIV does not cause any disease nor kill any person. It only destroys the T cells of the immune system. The decrease in the human immune system results in the inability of the body to fight diseases. Due to the weak defence system, a person suffering from AIDS is attacked by diseases called opportunistic diseases.

Opportunistic disease: A disease that attacks a person whose defence (immune) system has become weak, as in a person with AIDS.

How HIV leads to opportunistic diseases.

Examples of opportunistic diseases given in the book:

skin cancer
fungal infection
viral infection
gastrointestinal diseases
respiratory diseases
nervous system diseases
eye diseases

5.4.5Treatment of AIDSOften examined

HIV is treated using a combination of medicines to fight the HIV infection. This is called antiretroviral therapy (ART).

Antiretroviral therapy (ART)
What ART can do	Limitations of ART
It is not a cure, but it can control the virus so that an HIV positive person can live a longer, healthier life.	It can have toxicities.
It reduces the risk of transmitting HIV to others.	It is often costly.
It is a highly effective treatment for HIV infection, preventing progression of the disease in the vast majority of recipients.	It requires strict daily pill taking that can lessen the quality of life.
When ART is accessible and started early in the course of infection, the lifespan of HIV-positive people is typically very close to that of comparable HIV-negative people.	Because of these limitations, a cure for HIV infection remains a vital goal for research.

5.4.6Control measures against the transmission of HIVOften examined

AIDS can be controlled by preventing the transfer of body fluid (blood, serum, semen and so on) from a patient to an unaffected person. The following precautionary behaviour will prevent AIDS:

Do not use used syringes and needles.
For blood transfusion, blood must be used only after proper screening for HIV.
Do not share toothbrushes, blades and towels with anyone. Special care must be taken at a barber's shop or hair cutting saloons and beauty salons.
Surgical instruments must be properly sterilised.
AIDS is primarily a sexually transmitted disease. Refrain from immoral sexual activities and follow Islamic teachings to pass a healthy, neat and clean life.
A mother having HIV should not feed her babies.

How HIV is and is not transmitted (5.4.6)
HIV can spread by	HIV is not spread by
Used syringes and needles	Shaking hands, hugging, coughing or sneezing
Unscreened blood in blood transfusion	Swimming in the same pool
Shared toothbrushes, blades and towels	Inanimate objects such as toilets, door knobs, telephones, office machines and household furniture
Unsterilised surgical instruments	Mosquitoes and other insects
Sexual contact; an infected mother feeding her baby

5.5Viral diseasesOften examined

This section describes the causative agent, symptoms, treatment, transmission and prevention of hepatitis, herpes, polio and cotton leaf curl disease.

Overview of the viral diseases in the unit (5.5)
Disease	Causative agent	Main route of transmission	Affects
Hepatitis A	Hepatitis A virus (HAV)	Faecal-oral route	Liver
Hepatitis B	Hepatitis B virus (HBV)	Blood, sexual contact, mother to newborn	Liver
Hepatitis C	Hepatitis C virus	Blood only	Liver
Hepatitis D	Hepatitis D viroid	Blood or serum transfusion (needs the hepatitis B virus)	Liver
Hepatitis E	Hepatitis E virus (HEV)	Faecal-oral route	Liver
Oral herpes	Herpes simplex virus type-1	Saliva, contact with sores, shared objects	Lips, mouth, face, tongue
Genital herpes	Herpes simplex virus type-2	Sexual contact	Genital area, buttocks, anus
Poliomyelitis	Polio virus (an enterovirus)	Faecal-oral route	Motor neurones of the spinal cord
Cotton leaf curl disease	Begomoviruses	Whitefly (insect vector)	Cotton plants

5.5.1HepatitisOften examined

Hepatitis is generally characterised as inflammation of the liver, including other symptoms. It is generally caused by viral infection, or rarely due to toxicity of drugs and certain other causes. It may present in acute (recent infection, relatively rapid onset) or chronic (slowly progressing) forms. The most common causes of viral hepatitis are hepatitis A, B, C, D and E.

The five types of hepatitis (5.5.1)
Type	Cause	Transmission	Symptoms	Treatment	Prevention
Hepatitis A (infectious hepatitis)	HAV	Faecal-oral route	Typical symptoms: fever, loss of appetite, nausea, vomiting and jaundice. Dark urine and pale faeces are also seen.	No antiviral therapy is available.	Active immunisation with a vaccine containing inactivated HAV. Observation of proper hygiene.
Hepatitis B (serum hepatitis)	HBV	Blood, sexual contact and prenatally from mother to newborn	Similar to hepatitis A.	Alpha interferon is effective against HBV.	The vaccine is highly effective. All blood transfusion should be screened.
Hepatitis C	Hepatitis C virus	Only via blood	Just like hepatitis B.	A combination of alpha interferon and ribavirin is the treatment of choice for chronic hepatitis C.	No vaccine is available. Blood transfusion should be screened.
Hepatitis D	Hepatitis D viroid	Blood or serum transfusions; the viroid can enter a liver cell only inside a capsid with a binding protein, obtained from the hepatitis B virus	As in hepatitis B but more severe.	Same as HBV.	Same as HBV.
Hepatitis E	HEV	Faecal-oral route, like HAV	(not listed in the book)	No antiviral treatment.	No vaccine. Observation of proper hygiene.

Hepatitis D: the viroid enters a human liver cell only when it is enclosed in a capsid that carries a binding protein taken from the hepatitis B virus.

Worked example: which type of hepatitis?

A patient has fever, nausea, vomiting, jaundice, dark urine and pale faeces. Several people who shared the same contaminated drinking water fell ill at the same time. Which types of hepatitis are likely, how is the disease spread, and what protects against it?

The symptoms (fever, loss of appetite, nausea, vomiting, jaundice, dark urine, pale faeces) are the typical symptoms of hepatitis A.
A group of people sharing contaminated water points to the faecal-oral route. The types spread by that route are A and E.
Hepatitis B, C and D spread through blood or body fluids, not through water, so they do not fit.
Protection: hepatitis A has an inactivated-virus vaccine and proper hygiene helps; hepatitis E has no vaccine and no antiviral treatment, so hygiene is the only prevention.

Clue	Points to
Typical symptoms with dark urine and pale faeces	Hepatitis A
Shared contaminated water	Faecal-oral route: A or E
Protection	Vaccine (A) and hygiene (A and E)

5.5.2Herpes simplex

Herpes simplex is a superficial viral infection characterised by one or more painful, fluid-filled sores or blisters on the skin or on the epithelium of the outer openings of the body. Tingling, itching or burning may be felt on the skin before the blisters appear. The blisters break open, often ooze fluid and form a crust, before healing. The sores can last from 7 to 10 days. There are two primary types of herpes: oral herpes and genital herpes.

Oral and genital herpes
Point	Oral herpes	Genital herpes
Cause	Herpes simplex virus type-1 (HSV-1)	Herpes simplex virus type-2 (HSV-2)
Transmission	Primarily through oral secretions (saliva) or physical contact with sores on the skin. Also by sharing objects such as toothbrushes or eating utensils.	During sexual contact with someone who has a genital HSV-2 infection.
Symptoms	Most blisters appear on the lips or around the mouth. Sometimes blisters form on the face or on the tongue.	Sores typically occur on the penis, vagina, buttocks or anus.
Treatment	Antiviral drugs are used to treat herpes.	Antiviral drugs are used to treat herpes.
Prevention	Avoid contact with the affected area of the patient.	Avoid contact with the affected area of the patient.

5.5.3Poliomyelitis

Cause: polio virus, which is also an enterovirus. Transmission: faecal-oral route.

Symptoms: the virus replicates in the oropharynx and the intestinal tract and spreads to the blood and the central nervous system, where it replicates in the motor neurones located in the spinal cord. Death of these cells results in paralysis of the muscles innervated by these neurones. The motor nerve damage is permanent.

How poliovirus causes paralysis.

Treatment and prevention of poliomyelitis
Treatment	Prevention
There is no antiviral therapy. Physiotherapy for the affected muscles is important.	Polio can be prevented by the killed (Salk) vaccine, also called the injectable polio vaccine (IPV), and the live attenuated (weakened) Sabin vaccine, also called the oral polio vaccine (OPV).

Salk vaccine (IPV): A killed, injectable polio vaccine.
Sabin vaccine (OPV): A live, attenuated (weakened) oral polio vaccine.

5.5.4Cotton leaf curl disease

Cotton leaf curl disease (CLCuD) is a serious disease of cotton. Cause: begomoviruses. Transmission: this disease is transmitted by the whitefly. Symptoms: the symptoms are initially characterised by a deep downward cupping of the youngest leaves. This is followed by the development of cup-shaped, leaf-like structures. Treatment and prevention: control of CLCuD is mainly based on insecticide treatments against the insect vector.

Cotton leaf curl disease passes from plant to plant by the whitefly, so the insect vector is the target of control.

Vector: Here, the insect (the whitefly) that carries the virus from one plant to another.

5.6Economic losses due to viral infections

COVID-19 is considered the most significant threat since World War II and the greatest global health disaster of the century. The coronavirus outbreak has caused a global economic collapse. Most countries implemented full or partial lockdown measures to slow the spread of the disease. The lockdown slowed global economic activity, many companies downsized or closed down, and people lost their jobs.

How a viral outbreak becomes an economic loss, as described in the book for COVID-19.

What viral infections damage in an economy (5.6)
Affected	Examples given in the book
Sectors	Service providers, manufacturers, agriculture, the food industry, education, tourism, airlines, sports and entertainment
Markets and activity	The capital market, the labour market, foreign trade, consumer spending and production
The economy	The GDP of many countries was negatively affected

Costs of pandemics
Outbreak	Cost given in the book
COVID-19 pandemic	Claimed thousands of lives; cost the world more than 8.5 trillion dollars; the GDP was reduced
H1N1 outbreak of 2009 (a weak influenza pandemic)	The World Bank estimates that it could reduce global GDP by half, or about $300 billion

5.7Limitations of flu vaccine

Although we often refer to the causative agent of cold as "the cold virus", there are actually more than 200 viruses that cause cold. Developing a vaccine against the infection is therefore not practical.

Why the cold and flu vaccine is limited
Limitation	Why (from the book)
Too many viruses	More than 200 different viruses cause the common cold, so a single vaccine cannot cover them.
Evolving strains	The strains of the flu virus are constantly evolving.
Changing immune response	Our body's immune response changes over time.

Taken together, the constantly evolving strains and the changing immune response essentially render the previous year's vaccinations useless against new strains.

5.8.1Prions

The idea of an infectious agent that did not use nucleic acids and proteins together was considered impossible, but the pioneering work of the Nobel Prize-winning biologist Stanley Prusiner has convinced the majority of biologists that such agents do exist. Prions and viroids are such agents. They are acellular infectious particles like viruses, but are even simpler and smaller than viruses.

Prion: An infectious protein particle, smaller than a virus, that contains no nucleic acid (neither DNA nor RNA).

Prions are much more resistant to inactivation by ultraviolet light and heat than viruses are.
A prion is composed of a single protein, encoded by a single cellular gene.
Prion proteins on brain cells cause clumping, memory loss, neurodegeneration and permanent damage.

Diseases caused by prions
Point	Prion disease facts (from the book)
Examples	Fatal neurodegenerative diseases: Kuru in humans and mad cow disease in cattle were shown to be transmitted by prions
Spread	Through body fluids, and by direct and indirect contact
Treatment	There is no treatment or cure of prion diseases

5.8.2Viroids

Viroids are pathogens that consist of a short, circular, single-stranded RNA without a protein coat or envelope. The viroid RNA does not code for any protein.

The replication mechanism involves the enzyme RNA polymerase II, which synthesises new RNA using the viroid's RNA as template.
Some viroids are ribozymes, having catalytic properties which allow self-cleavage.
The only human disease known to be caused by a viroid is hepatitis D.
Viroids cause several plant diseases, for example potato spindle tuber disease and cucumber pale fruit disease.
Viroids spread via mechanical damage, seed, pollen or biological vectors.

A virus has its nucleic acid inside a protein coat. A viroid is only a short circle of single stranded RNA, with no coat at all.

Prions and viroids compared
Point	Prions	Viroids
Made of	Protein only	Short, circular, single stranded RNA
Nucleic acid	None (neither DNA nor RNA)	RNA, but it codes for no protein
Resistance	Much more resistant to UV light and heat than viruses	Not stated in the book
Diseases	Kuru in humans, mad cow disease in cattle	Hepatitis D (the only human disease); potato spindle tuber and cucumber pale fruit disease in plants
Replication or spread	Spread through body fluids, direct and indirect contact	RNA polymerase II copies the RNA; spread via mechanical damage, seed, pollen or biological vectors

Key terms

Virus: An acellular infectious agent (pathogen) that causes disease in animals and plants. It is not a cell, cannot replicate independently and cannot make its own energy and proteins.
Acellular life: The level of organisation below the cell: viruses, prions and viroids.
Virology: The study of viruses.
Filterable virus: The name given by 1900 to a disease-producing substance that passes through a porcelain filter.
Tobacco mosaic virus (TMV): The virus that causes tobacco mosaic disease. Its particle was crystallised by W. M. Stanley in 1935. It has an RNA genome and a rod shaped capsid.
Virion: A complete viral particle, made of a core and a coat.
Core: The inner part of the virion: the viral genome and various proteins (enzymes).
Genome: The genetic material of a virus, either DNA or RNA, single or double stranded.
Coat: The outer covering of the viral particle, made of the capsid and, in some viruses, the envelope.
Capsid: The protective protein coat that surrounds the core, made of identical repeating subunits called capsomeres.
Capsomere: One of the identical repeating protein subunits of a capsid.
Icosahedral (polyhedral) symmetry: The capsid form in which the capsomeres are arranged in 20 triangles.
Helical symmetry: The capsid form in which the capsomeres are arranged in a hollow coil, giving a rod shape.
Envelope: An extra lipoprotein layer around the capsid of a few viruses, derived from the host cell surface membrane.
Glycoprotein spikes: Spikes on the viral envelope that help the virus recognise the host cell.
Host range: The range of hosts a virus can infect, decided by the specificity of attachment of its spikes to receptors on the host cell.
Obligate intracellular parasite: A parasite that cannot multiply outside a living cell; all viruses are of this kind.
Nuclease: An enzyme found in all cells that breaks down DNA or RNA. The viral capsid protects the genome from it.
Bacteriophage (phage): A virus that attacks bacteria. It is tadpole shaped, with a head, neck and tail.
Lysozyme (of the phage): The enzyme at the bottom of the tail core tube that digests part of the host cell wall so the tube can enter.
Base plate: The plate at the end of the phage tail that carries the tail fibres and tail pins.
Adsorption: The first step of infection: the phage attaches, by its tail fibres and pins, to specific receptors on the bacterial cell.
Penetration: The insertion of the hollow core tube of the phage through the bacterial envelope after the sheath contracts.
Genome injection: The passage of the phage DNA into the bacterial cytoplasm while the rest of the phage stays outside.
Lytic (virulent) phage: A phage that causes lysis of its host cell immediately after its own multiplication.
Master-slave relationship: The relationship of a lytic phage with its host: the viral DNA destroys the host DNA and takes over the cell.
Lysogenic (temperate) phage: A phage that can either multiply by the lytic cycle or stay dormant in the cell with its DNA integrated in the host chromosome.
Host-guest relationship: The relationship of a temperate phage with its host: the phage DNA integrates into the host chromosome and is replicated with it.
Prophage: The integrated state of phage DNA in the host chromosome.
Lysogeny: The process by which phage DNA integrates into the host chromosome as a prophage.
Lysogenic bacteria: Bacteria that harbour a prophage.
Induction: The termination of the lysogenic state when the bacterium is exposed to adverse conditions such as desiccation, UV or ionizing radiation or mutagenic chemicals.
Lysogenic (phage) conversion: The change in the properties of a bacterial cell caused by extra prophage genes being expressed after lysogenization.
Genetic engineering: The field of biotechnology in which the genetic material of an organism is altered, for example by transferring a gene from one organism to another.
Genomic library: A collection of bacteria or bacteriophage clones containing multiple copies of all the genes of an individual's genome.
Phage therapy: The use of genetically engineered phages that kill pathogenic bacteria while sparing normal bacterial flora.
HIV (human immunodeficiency virus): The retrovirus that causes AIDS. It has a lipoprotein envelope with gp 120 and gp 41 spikes and two single strands of RNA in a conical capsid.
AIDS (acquired immune-deficiency syndrome): The disease caused by HIV, in which the immune system is deficient because helper T cells are destroyed.
Retrovirus: A virus (such as HIV) with an RNA genome that is copied into DNA by the enzyme reverse transcriptase.
Reverse transcriptase: The enzyme that converts the single stranded viral RNA genome into DNA.
CD4 cells: Helper T cells, macrophages and certain brain cells that carry CD4 receptors; the only cells HIV attaches to.
Complementary DNA (cDNA): The single stranded DNA made by reverse transcriptase that is complementary to the viral RNA.
Integrase: The virus encoded enzyme that incorporates the viral DNA into the host DNA.
Protease: The virus encoded enzyme that cleaves large proteins into the smaller structural proteins of the virion.
Provirus: The viral DNA integrated into the host cell DNA.
Uncoating: The shedding of the protective coat of the HIV particle inside the host cell.
Helper T cells: Cells of the immune system that activate B cells and cytotoxic T cells; their decrease causes immune deficiency in AIDS.
Asymptomatic carrier: The first stage of HIV infection: no lasting symptoms for nine months or longer, but the person is highly infectious and the antibody test is positive.
AIDS related complex (ARC): The second stage of HIV infection: persistent swollen lymph glands, night sweats, cough, diarrhoea, memory loss and depression.
Opportunistic disease: A disease that attacks a person with a weak defence system, as in AIDS (for example skin cancer or fungal infection).
Antiretroviral therapy (ART): Treatment of HIV with a combination of medicines. It controls the virus but is not a cure.
Hepatitis: Inflammation of the liver, caused by viruses (types A to E) or rarely by drug toxicity.
Herpes simplex: A superficial viral infection with painful fluid-filled blisters: oral herpes (HSV-1) and genital herpes (HSV-2).
Poliomyelitis: A disease caused by the polio virus (an enterovirus) that destroys motor neurones of the spinal cord and causes permanent paralysis.
Cotton leaf curl disease (CLCuD): A serious cotton disease caused by begomoviruses and spread by the whitefly.
Prion: An infectious protein particle with no nucleic acid, smaller than a virus; causes Kuru and mad cow disease.
Viroid: A pathogen made of a short, circular, single-stranded RNA without a protein coat or envelope; causes hepatitis D and some plant diseases.

Multiple choice questionsp. 145–146

Select the correct answer.

Viruses are considered non-living because

Ado not mutate
Bthey do not move
Ccannot reproduce independentlyAnswer
Dhave nucleic acid

Why

Viruses cannot multiply on their own. They reproduce only with the metabolic machinery of the host cell they infect (sections 5.1.2 and 5.2.1).

Option A is false because viruses do mutate, which the book lists among their living characteristics. Option D is not a reason, since living cells also carry nucleic acid.

Which of these are found in all viruses?

Aenvelope, nucleic acid, capsid
BDNA, RNA and proteins
Cproteins and nucleic acidAnswer
Dprotein, carbohydrate, lipids

Why

Every virion has a core of genome (DNA or RNA) and a capsid of protein (section 5.1.3). Together these are the two constants of all viruses.

A is wrong because an envelope is found only in some viruses. B is wrong because a virus has either DNA or RNA, never both. D is wrong because carbohydrate and lipid are not universal (lipid appears only in enveloped viruses).

Which step in the lytic cycle follows attachment of virus and release of DNA into the cell?

Aproduction of lysosome
Bdisintegration of host DNAAnswer
Cassemblage
DDNA replication

Why

In the lytic cycle the viral DNA is injected after penetration, and the host genomic DNA is immediately disintegrated by the viral DNAase (section 5.3.4). This is the step that follows.

A is the trap: the phage makes lysozyme, which is a lysis enzyme, not a lysosome. Assembly (C) and replication of phage DNA (D) happen later, after the host DNA has been broken down and the phage mRNAs and proteins are made.

Which of these is a true statement?

Aviruses carry with them their own ribosome for protein formation
Bnew viral ribosomes form after viral DNA enters the cell
Cviruses use the host ribosomes for their own needsAnswer
Dviruses do not need ribosomes for protein formation

Why

Viruses lack ribosomes and the other protein-making machinery, so the virus uses the host cell's ribosomes to translate its mRNA into proteins (sections 5.2.1 and 5.4.2, step 10).

A and B are false because no viral ribosome exists. D is false because viruses do need ribosomes to make protein; they simply borrow them from the host.

Which part of an animal virus is not reproduced in multiple copies?

AenvelopeAnswer
Bprotein
Ccapsid
Dribosome

Why

The capsid and the other viral proteins are made again and again, once for every new virion, from the viral genome. Each capsid is built from many identical capsomeres (section 5.1.3).

The envelope is a piece of host cell membrane borrowed during budding (section 5.4.1), so the virus does not reproduce it from its own genome. D is not a viral part at all: viruses have no ribosomes and use the host's.

Note. The book prints no key. A is taken as the answer because the envelope is host-derived and is not made from viral genetic information; D is also not reproduced, but a ribosome is not a part of a virus, so it cannot be the intended answer. The question is loosely worded.

RNA retroviruses have a special enzyme that

Adisintegrates host DNA
Bpolymerises host DNA
Ctranscribe viral RNA to DNAAnswer
Dtranslates host DNA

Why

Retroviruses carry reverse transcriptase, which makes DNA from the viral RNA genome (sections 5.1.3 and 5.4.2, step 3). This is the reverse of normal transcription, which is why the virus is a retrovirus.

A describes the viral DNAase of the lytic bacteriophage cycle (section 5.3.4), not a retrovirus enzyme. B and D are not functions of a retroviral enzyme: translation is done by ribosomes, not by an enzyme acting on DNA.

Which of the following illness is caused by a retrovirus?

Atyphoid
Bmalaria
CAIDSAnswer
Dsleeping sickness

Why

AIDS is caused by HIV, which is a retrovirus (section 5.4): the virus reverse transcribes its RNA into DNA and inserts it into host DNA.

Typhoid, malaria and sleeping sickness are not viral diseases, so none of them can be caused by a retrovirus.

The HIV primarily infects

Aplasma cells
Bhelper T cellsAnswer
Call white blood cells
Dred blood cells

Why

HIV attaches to CD4 receptors, which are found on helper T cells, macrophages and certain brain cells (section 5.4.2). Helper T cells are its primary target.

C is wrong because HIV enters only certain types of white blood cells (section 5.2). D and A are wrong because red blood cells and plasma cells do not carry the CD4 receptor.

Poliomyelitis affects

Amotor neuronAnswer
Bsensory neuron
Cbrain
Dmuscles

Why

The poliovirus replicates in the motor neurones of the spinal cord. Death of these cells causes paralysis, and the damage is permanent (section 5.5.3).

D is the tempting option because the paralysis is seen in muscles, but the muscles are not the site of infection. C is wrong because the book places the damage in the spinal cord, not the brain.

HIV attaches to

ACD4 proteinAnswer
Bnucleoprotein
Clipoprotein
Dglycoprotein

Why

The gp 120 glycoprotein spikes of the virion bind to the CD4 receptor on the host T cell. This binding is the first step of the life cycle (section 5.4.2, step 1).

D is a trap: gp 120 is a glycoprotein, but it is on the virus. The host receptor it binds to is the CD4 protein. The lipid envelope is not the site of attachment.

Hepatitis D is caused by

Abacteria
Bvirus
Cprions
DviroidsAnswer

Why

The only human disease known to be caused by a viroid is hepatitis D (sections 5.5.1 and 5.8.2). The viroid needs a capsid containing a binding protein, obtained from the hepatitis B virus, to enter a liver cell.

B is the trap: hepatitis B virus is needed for the hepatitis D viroid to enter liver cells, but it is not the causative agent of hepatitis D. Prions cause kuru and mad cow disease, not hepatitis.

Short answer questionsp. 146–147

13 marks

What are the living and non-living characteristics of viruses?

Solution

Living characteristics	Non-living characteristics
They occur in different varieties or strains, and carry their own DNA or RNA, which can mutate.	They lack cellular structure, coenzymes and an enzyme system, so they have no metabolic activity of their own.
They reproduce using the metabolic machinery of the host cell they infect.	They can be crystallized and stored in bottles, and they do not respire.
They are intracellular obligate parasites that enter living cells and cause disease.	Outside the host they behave as inert, non-living particles.

Viruses show both sets of properties, which is why they are placed between living and non-living things (section 5.1.2).

23 marks

Give the classification of viruses based on their hosts.

Solution

Viruses are classified on the basis of the organisms they infect (section 5.1.4):

Bacteriophage viruses attack bacteria. They are DNA viruses with a polyhedral head and a tail.
Plant viruses cause more than 2,000 known plant diseases. Most have an RNA genome and many have a rod-shaped capsid, for example tobacco mosaic virus (TMV) and potato yellow dwarf virus.
Animal viruses occur as parasites of animals and cause diseases such as foot and mouth disease, cancer (Rous sarcoma virus), warts (papovirus), smallpox (poxvirus), polio and hepatitis A (picornavirus), and measles and mumps (paramyxovirus).

33 marks

What are the parasitic natures of virus?

Solution

Viruses are obligate intracellular parasites. The three main features are (section 5.2):

Host specificity. Protein spikes on the virus bind to specific receptors on the host cell. The bacteriophage infects only bacteria, TMV infects only tobacco plants and HIV enters only certain white blood cells.
Obligate parasitism. A virus cannot multiply outside a living cell. An isolated virus can do nothing except infect an appropriate host cell.
Host range. Some viruses have a narrow range, as the bacteriophage has, while others have a broad range: rabies virus can enter all mammalian cells, but poliovirus only the cells of humans and other primates.

43 marks

Justify why a virus must have a host cell to parasitize in order to complete its life cycle.

Solution

A virus needs a host cell because it cannot make the materials or energy for its own reproduction (section 5.2.1):

Viruses are obligate intracellular parasites. They cannot multiply outside a living cell, so an isolated virus cannot reproduce or do anything except infect a host.
They lack metabolic enzymes and ribosomes, so they cannot make their own proteins. The host's ribosomes and enzymes must be used.
After infection the viral DNA takes control of the host's metabolic machinery. Host DNA is broken down and the host makes the phage mRNAs and proteins.

53 marks

Explain how a virus survives inside a host cell, protected from immune system.

Solution

Inside the host cell the virus is hidden and protected in three ways (section 5.2.2):

It hides from the immune system. Once inside the host cell the virus is out of reach, so the host immune system cannot find it.
It changes its genetic constitution rapidly. Because of this change, the vaccines or antibodies that the host has made become ineffective.
Its capsid protects the genome. The capsid shields the viral genome from the nucleases (DNAses and RNAses) of the host cell, which would otherwise break it down.

62025 Annual I, Set D, Q.2 (ix) OR3 marks

Determine the method a virus employs to survive or pass over unfavourable conditions when it does not have a host to complete the life cycle.

Solution

Outside a host a virus survives by going into a dormant state (section 5.2.3):

It is non-living outside the host. It needs no food and has no metabolic activity, so it remains dormant or inactive.
Its genome stays viable for a long time in inactive form. The only real threats are unfavourable pH and temperature, which denature its proteins.
Non-enveloped viruses survive for long periods (up to several days), while enveloped viruses survive for shorter periods, because their envelope is sensitive to sunlight and cleaning.

73 marks

Justify the name of virus i.e., “Human Immunodeficiency Virus” by establishing T-helper cells as the basis of immune system.

Solution

The name HIV follows from the role of helper T cells in immunity (section 5.4.2 and the HIV naming paragraph):

Helper T cells are the most important cells of the immune system. They activate B cells to secrete antibodies, and they activate cytotoxic T cells that kill virus-infected and cancerous cells.
Helper T cells also regulate immunity by enhancing the response of the other immune cells.
HIV destroys helper T cells. A decrease in their number causes a deficiency of the immune system, so the virus is named Human Immunodeficiency Virus.

83 marks

Reason out the specificity of HIV on its host cells.

Solution

HIV has host cell specificity because of the receptors it recognises (section 5.4.2):

The gp 120 spikes of the virus bind to CD4 receptors on the host cell surface, and this binding is the first step of infection.
CD4 receptors are present only on helper T cells, macrophages and certain brain cells. These are the CD4 cells that HIV infects.
Cells without CD4 receptors cannot be attached to or entered, so HIV does not infect them. This is why the virus attacks only a particular type of white blood cell.

93 marks

What are the symptoms of AIDS?

Solution

An HIV infection passes through three stages, each with its own symptoms (section 5.4.3):

Asymptomatic carrier: fever, chills, aches, swollen lymph glands and an itchy rash. These disappear, and there are no other symptoms for nine months or longer, but the person is highly infectious and the HIV antibody test is positive.
AIDS related complex (ARC): swollen lymph glands in the neck, armpit or groin that persist for months, with night sweats, persistent cough, flu, loss of memory and depression.
Full blown AIDS: severe weight loss and weakness, persistent diarrhoea and usually one or more opportunistic infections.

103 marks

Explain opportunistic diseases that may attack an AIDS victim.

Solution

Opportunistic diseases are diseases that attack a person whose defence system is weakened (section 5.4.4):

HIV destroys T cells, so the body cannot fight infections. A person with AIDS is then attacked by diseases that a healthy person would normally resist.
They include skin cancer (for example the lesions in Fig 5.6), fungal and viral infections, and gastrointestinal, respiratory, nervous system and eye diseases.
In full blown AIDS, one of these opportunistic infections is usually present, and it is the infection that makes the patient seriously ill (section 5.4.3).

113 marks

What are the common control measures against the transmission of HIV?

Solution

AIDS is controlled by preventing the transfer of body fluids (blood, serum, semen) from an infected person to an unaffected one (section 5.4.6):

Blood and needles: do not use used syringes or needles, and screen all blood for transfusion after proper testing for HIV.
Personal items and instruments: do not share toothbrushes, blades or towels, take care at barber and beauty salons, and sterilize surgical instruments properly.
Sexual behaviour and mothers: avoid immoral sexual activity and follow the teachings of Islam to lead a healthy, clean life. A mother with HIV should not feed her babies.

122025 Annual I, Set D, Q.2 (iii)3 marks

Describe the structure of prions and name any two diseases caused by them.

Solution

A prion is an infectious protein particle with no nucleic acid (section 5.8.1):

It contains no DNA and no RNA. It consists of a single protein, encoded by a single cellular gene.
It is smaller than a virus and much more resistant than a virus to inactivation by ultraviolet light and heat.
Two diseases caused by prions are kuru in humans and mad cow disease in cattle. These are fatal neurodegenerative diseases; there is no treatment or cure.

133 marks

Describe the structure of viroids and name the diseases caused by them.

Solution

A viroid is a pathogen made only of nucleic acid (section 5.8.2):

It is a short, circular, single-stranded RNA. It has no protein coat and no envelope.
Its RNA does not code for any protein. Some viroids are ribozymes, with catalytic properties that let them self-cleave.
Diseases caused by viroids are hepatitis D in humans, potato spindle tuber disease and cucumber pale fruit disease in plants.

143 marks

What do you mean by AIDS, HIV, ART, CLCuD and TMV?

Solution

Abbreviation	Meaning
AIDS	Acquired immune-deficiency syndrome, the disease caused by HIV
HIV	Human immunodeficiency virus, the retrovirus that causes AIDS
ART	Antiretroviral therapy, a combination of medicines that controls HIV
CLCuD	Cotton leaf curl disease, a serious disease of cotton spread by whiteflies
TMV	Tobacco mosaic virus, a rod-shaped plant virus with an RNA genome

153 marks

Distinguish between:

Solution

(a) bacteriophage and HIV virus

Feature	Bacteriophage	HIV
Host	Bacteria	Helper T cells and other CD4 cells
Shape and capsid	Tadpole shape, icosahedral head, neck and tail (complex capsid)	Spherical, conical capsid of capsomeres
Genome	DNA, single stranded in the book (section 5.3.1)	Two single strands of RNA with reverse transcriptase
Envelope	Absent	Lipoprotein envelope with gp 120 and gp 41 spikes
Replication	Lytic or lysogenic cycle; about 200 phages made in the lytic cycle	Reverse transcription, integration as provirus, budding off from host
Effect on host	Lyses (breaks open) the bacterial cell	Destroys helper T cells and causes AIDS

(b) lytic and lysogenic cycle of bacteriophage

Feature	Lytic cycle	Lysogenic cycle
Type of phage	Lytic or virulent phage	Lysogenic or temperate phage
Host DNA	Disintegrated immediately by the viral DNAase	Phage DNA joins the host chromosome as a prophage
Phage DNA	Directs production of new phage components	Is copied with the host DNA at each binary fission
Result	Lysis of the cell and release of about 200 phages	Bacterium survives; phages are released only after induction

Feature	Prions	Viroids
Nature	Infectious protein particle	Short circular single-stranded RNA
Nucleic acid	None (neither DNA nor RNA)	RNA, which does not code for any protein
Protein	A single protein encoded by a single cellular gene	No protein coat
Resistance	Much more resistant to UV light and heat than viruses	Simpler and smaller than viruses
Diseases	Kuru (humans) and mad cow disease (cattle)	Hepatitis D (humans); potato spindle tuber and cucumber pale fruit disease (plants)

Extensive answer questionsp. 147

18 marks

Give the classification of viruses based upon capsid and genomes.

Solution

Classification based on the capsid

The capsid is the protein coat, made of identical capsomeres. Its arrangement gives the two forms of symmetry, and the book classifies viruses on this basis as follows (sections 5.1.3 and 5.1.4):

Type of capsid	Structure	Example
Helical	Capsomeres arranged in a hollow coil, so the virus is rod shaped	Tobacco mosaic virus (TMV)
Polyhedral (icosahedral)	Capsomeres arranged in 20 triangles, giving a spherical shape	Adenovirus
Enveloped	Capsid with an outer lipoprotein envelope from the host membrane, carrying glycoprotein spikes	Influenza virus
Complex	Icosahedral head, neck, tail sheath and tail fibres	Bacteriophage

Figure: the two forms of capsid symmetry. (a) Capsomeres in a hollow helix make a rod. (b) Capsomeres in triangular faces make a polyhedron.

Classification based on the genome

The genome is either DNA or RNA, and it may be single or double stranded. The book classifies viruses by genome type as follows (section 5.1.4 (ii)):

Genome type	Example
Double-stranded DNA (dsDNA)	Smallpox virus
Single-stranded DNA (ssDNA)	Mild rash virus
Double-stranded RNA (dsRNA)	Diarrhoea virus
Single-stranded RNA that serves as mRNA	Rubella virus
Single-stranded RNA that is a template for mRNA synthesis	Influenza virus
Single-stranded RNA that is a template for DNA synthesis	HIV

Note. The book lists enveloped viruses (influenza) among the capsid types in section 5.1.4 (i)(c). An envelope is an outer lipoprotein layer rather than a capsid shape, so it is shown here as its own type.

28 marks

Describe the general structure of a virus.

Solution

Virion

A complete viral particle is called a virion. Primarily, it has two parts, the core and the coat (section 5.1.3).

General structure of a virion, drawn from the description in section 5.1.3. The envelope is present only in some viruses.

Core

The core is the inner part. It consists of the viral genome, which is DNA or RNA, single or double stranded.
Core proteins include one or more enzymes that help the virus in its mode of action. For example, single-stranded RNA viruses have an enzyme that converts the single-stranded RNA genome into double-stranded RNA.
Retroviruses and hepatitis B virus contain reverse transcriptase, which converts the single-stranded RNA genome into double-stranded DNA.

Coat

Capsid: the protective protein coat surrounding the core, built from identical repeating subunits called capsomeres. The number of capsomeres is specific to a kind of virus: herpes virus has 162 and adenovirus 252.
Symmetry: the capsid is either icosahedral (polyhedral or spherical, with capsomeres in 20 triangles) or helical (capsomeres in a hollow coil that makes a rod).
Envelope: a few viruses have an extra lipoprotein envelope around the capsid, derived from the host cell surface membrane. It carries virally encoded glycoprotein spikes that help the virus recognise the host cell.

38 marks

Describe the structure of bacteriophage with diagram.

Solution

Overall shape

A bacteriophage (phage) is a tadpole-shaped DNA virus with a complex capsid. It consists of a head, a neck and a tail (section 5.3.1).

Figure 5.1: Structure of bacteriophage. Only three of the six tail fibres are drawn.

Parts

Head: icosahedral in shape. Its inner core holds a single-stranded DNA genome, surrounded by the protein capsid.
Neck (collar): a narrow region below the head that separates the head from the tail.
Tail: a hollow tube of protein through which the nucleic acid passes into the bacterium during infection. It is surrounded by a contractile sheath, which contracts during infection.
Core tube and lysozyme: at the bottom of the core tube is the enzyme lysozyme, released when the sheath contracts. It digests part of the bacterial cell wall so the core tube can penetrate.
Base plate: at the end of the tail. It carries about six tail fibres and several tail pins or spikes at its lower surface, which bind the phage to the bacterial cell.

How the parts work

The tail fibres and tail pins attach the phage to receptors on the bacterial cell (adsorption). The binding makes the sheath contract and lysozyme opens the bacterial wall, so the hollow core tube is pushed through the envelope and the viral DNA is injected into the cytoplasm (penetration and genome injection).

48 marks

Describe the structure of human immunodeficiency virus with diagram.

Solution

Overall structure

HIV is a spherical retrovirus. It has an outer lipoprotein envelope, a matrix protein layer, a somewhat conical capsid and a core with two strands of RNA and enzymes (section 5.4.1).

Figure 5.4: Human immunodeficiency virus (HIV), cross section.

Parts

Envelope: a lipid bilayer borrowed from the host cell during budding. Glycoproteins are embedded in it: gp 120 (outer spike, needed to attach to the host cell) and gp 41 (transmembrane, critical for the fusion of the viral envelope with the cell membrane).
Matrix protein: a protein layer that lies between the envelope and the capsid.
Capsid: somewhat conical in shape and made of capsomeres.
Core: two single strands of HIV RNA and the enzymes needed for replication. Reverse transcriptase converts the viral RNA genome into viral DNA, integrase incorporates the viral DNA into host DNA, and protease breaks large structural proteins into smaller units.

The structural proteins are encoded by three of the nine virus genes.

58 marks

Describe the lytic and lysogenic life cycles of a virus.

Solution

Both cycles begin in the same way: adsorption of the phage to receptors on the bacterium by the tail fibres and pins, penetration by contraction of the sheath and release of lysozyme, and injection of the viral DNA into the bacterial cytoplasm. The cycles differ in what happens to the phage DNA afterwards (sections 5.3.2 to 5.3.5).

Figure 5.3: Lytic and lysogenic life cycles of bacteriophage.

Lytic (virulent) cycle

Host DNA is destroyed. The viral DNAase digests the host genomic DNA immediately. The phage DNA is not affected, because it has been chemically modified. The viral DNA now controls the host metabolic machinery.
Phage components are made. Phage mRNAs direct the host to make the structural proteins of the head and tail, and the lysis protein lysozyme.
Assembly (maturation). Nucleic acid is packed into the head, and then the tail is added, giving mature infective phages. About 200 phages are made within 20 to 25 minutes.
Lysis and release. Lysozyme accumulates, the bacterial cell breaks open (lyses), and the intracellular phages are released into the medium.

Lysogenic (temperate) cycle

Integration. The phage DNA inserts itself into the host chromosome and becomes a prophage. The bacterium carrying it is a lysogenic bacterium, and the process is called lysogeny.
Replication with the host. The prophage is copied with the bacterial chromosome at each binary fission, so every daughter cell carries the phage DNA. Genes carried by the prophage can change the properties of the bacterium (lysogenic conversion).
Induction. Adverse conditions such as UV or ionizing radiation, desiccation or mutagenic chemicals end the lysogenic state. The separated phage DNA then starts the lytic cycle, which causes lysis and the release of phages.

Comparison

Feature	Lytic cycle	Lysogenic cycle
Type of phage	Lytic or virulent phage	Lysogenic or temperate phage
Relationship with host	Master-slave relationship	Host-guest relationship
Host DNA	Disintegrated immediately by viral DNAase	Phage DNA joins the host chromosome and is copied with it
Result	Lysis and release of about 200 new phages	Bacterium survives and divides; phages are released only after induction

68 marks

Describe the usage of bacteriophage in genetic engineering.

Solution

Bacteriophages are used in genetic engineering in three ways (section 5.3.6).

a) Vectors and genomic libraries

Phage DNA, like bacterial plasmids, is used as a vector to carry foreign genes. A genomic library is a collection of bacteria or bacteriophage clones that contain multiple copies of all the genes of an individual's genome.

A bacteriophage DNA vector: a foreign gene is inserted into phage DNA, and the phage multiplies to give many copies of the gene.

b) Phage therapy

Phage therapy is the application of genetically engineered phages that kill pathogenic bacteria. It has advantages over conventional antibiotic therapy. Phages have a fairly narrow spectrum of activity, so pathogenic bacteria are killed while the normal, useful bacterial flora (our good bacteria) is not harmed.

c) Antibacterial nano medicines

Bacteriophages have been used for many years as tools for treating bacterial infections. A recent application, in antibacterial nano medicines, formulates bacteriophages as targeted drug-delivery vehicles.

72025 Annual I, Set B, Q.38 marks

Explain the life cycle of HIV.

Solution

HIV is specific to CD4 cells: its gp 120 spikes bind the CD4 receptors on helper T cells, macrophages and certain brain cells (section 5.4.2). Its life cycle has twelve numbered stages, shown in the figure in the order of the book.

Figure 5.5: Life cycle of HIV, numbered as in the book.

Steps

Attachment. The gp 120 envelope protein binds the CD4 receptor on the T cell.
Penetration and uncoating. The viral envelope fuses with the cell membrane, using gp 41, and the virion enters the cell by endocytosis. Uncoating releases the single-stranded viral RNA and the viral enzymes into the cytoplasm.
Reverse transcription. The enzyme reverse transcriptase synthesizes a single-stranded DNA complementary to the viral RNA, called cDNA.
RNA breakdown. Ribonuclease (RNAase) breaks down the viral genomic RNA after reverse transcription.
Replication of cDNA. The single-stranded cDNA is copied to form double-stranded cDNA.
Integration. Integrase, an enzyme encoded by the virus, inserts the double-stranded DNA into the host cell DNA.
Provirus. The integrated DNA is now called the provirus.
Transcription. Host RNA polymerase transcribes viral mRNA from the provirus. Viral genomic RNA is also produced, not only mRNA.
Translation. Host ribosomes translate the viral mRNA into several large proteins, which the virus-encoded protease cuts into the virion's structural proteins.
Assembly and maturation. The viral components are assembled and mature virions are produced.
Release. Mature virions bud off from the host cell, each enclosing a portion of host membrane. The host cell becomes smaller and non-functional.

Note. The book's figure labels stages 8 and 9 both as transcription, one for viral mRNA and one for viral genomic RNA.

88 marks

Describe the treatments available for AIDS.

Solution

HIV infection is treated with a combination of medicines, called antiretroviral therapy (ART), to fight the infection (section 5.4.5).

It controls the virus, but it is not a cure. ART keeps the virus under control so that the HIV positive person can live a longer, healthier life.
It is highly effective when started early. When it is accessible and started early in the course of infection, ART prevents the progression of the disease in the vast majority of recipients. The life span of HIV positive people is then close to that of comparable HIV negative people.
It reduces transmission. ART reduces the risk of transmitting HIV to others.
It has limitations. ART can have toxicities, is often costly, and requires strict daily pill taking, which can lessen the quality of life.

Because of these limitations, a cure for HIV infection remains a vital goal for research.

98 marks

Describe the causative agent, symptoms, transmission, treatment and prevention of the following diseases:

Solution

(a) Hepatitis

Hepatitis is inflammation of the liver, generally caused by a viral infection (section 5.5.1).

Type	Causative agent	Transmission	Treatment and prevention
A	Hepatitis A virus (HAV)	Faecal-oral route	No antiviral therapy; active immunization with a vaccine of inactivated HAV; observe proper hygiene
B	Hepatitis B virus (HBV)	Blood, sexual contact, and from mother to newborn	Alpha interferon is effective; vaccine highly effective; screen all blood transfusions
C	Hepatitis C virus	Only through blood	Alpha interferon with ribavirin for chronic cases; no vaccine; screen blood transfusions
D	Hepatitis D viroid	Needs a capsid with a binding protein from HBV to enter liver cells; spreads through blood or serum	Same as hepatitis B
E	Hepatitis E virus (HEV)	Faecal-oral route, like HAV	No antiviral treatment and no vaccine; observe proper hygiene

Symptoms: hepatitis A has fever, loss of appetite, nausea, vomiting and jaundice, with dark urine and pale faeces. Hepatitis B is similar; hepatitis C is like B; hepatitis D is as in B but more severe.

(b) Herpes

Herpes simplex is a superficial viral infection. One or more painful, fluid-filled sores or blisters appear on the skin or on the epithelium of the outer openings of the body. Tingling, itching or burning may be felt before they appear, and the sores last 7 to 10 days (section 5.5.2).

Feature	Oral herpes	Genital herpes
Cause	Herpes simplex virus type 1	Herpes simplex virus type 2
Transmission	Oral secretions (saliva), contact with sores, or sharing toothbrushes and eating utensils	In general, through sexual contact with a person who has genital HSV-2 infection
Symptoms	Blisters mostly on the lips or around the mouth; sometimes on the face or tongue	Sores on the penis, vagina, buttocks or anus
Treatment	Antiviral drugs	Antiviral drugs
Prevention	Avoid contact with the affected area of the patient	Avoid contact with the affected area of the patient

Causative agent: poliovirus, which is also an enterovirus.
Transmission: by the faecal-oral route.
Symptoms: the virus replicates in the oropharynx and the intestinal tract, then spreads to the blood and central nervous system, where it replicates in the motor neurones of the spinal cord. Death of these cells paralyses the muscles they supply, and the motor nerve damage is permanent.
Treatment: there is no antiviral therapy. Physiotherapy for the affected muscles is important.
Prevention: a killed vaccine (Salk vaccine, or injectable polio vaccine, IPV) and a live, attenuated (weakened) vaccine (Sabin vaccine, or oral polio vaccine, OPV).

(d) Cotton leaf curl disease

Causative agent: begomoviruses, which cause cotton leaf curl disease (CLCuD), a serious disease of cotton.
Transmission: by the whitefly, an insect vector.
Symptoms: the youngest leaves first show a deep downward cupping. This is followed by the development of cup-shaped, leaf-like structures.
Treatment and prevention: control is mainly based on insecticide treatments against the insect vector (section 5.5.4).

Note. The book gives no separate symptoms for hepatitis E and no treatment for cotton leaf curl disease beyond insecticide control of the whitefly. Both are stated as the book gives them.

FBISE 2025 and 2026 questions

Questions from the FBISE HSSC-I 2026 (1st Annual) and FBISE HSSC-I 2025 (1st Annual) papers that belong to this unit, answered the way an examiner expects.

2026 Annual I, Set B, MCQ 51 mark

Viruses are classified structurally based on:

ASize only
BShape and nucleic acid typeAnswer
CColour
DHabitat

Why

The book classifies viruses by the structure and composition of the virion: the capsid (shape: helical, polyhedral, enveloped or complex) and the genome (DNA or RNA, single or double stranded). Size alone (A) and colour (C) are not used. Habitat (D) is close to the classification by host (bacteriophage, plant and animal viruses), which is a separate scheme, not a structural one.

2025 Annual I, Set B, MCQ 111 mark

Hepatitis-D is caused by:

ABacteria
BVirus
CPrions
DViroidsAnswer

Why

The book names the only human disease known to be caused by a viroid as hepatitis D: a short, circular, single stranded RNA with no protein coat. The tempting answer is the virus (B): hepatitis A, B and C are caused by viruses, and hepatitis D needs the hepatitis B virus to supply its capsid, but the cause of hepatitis D is the viroid. Prions (C) cause kuru and mad cow disease.

2026 Annual I, Set B, Q.2 (iv) OR3 marks

Enlist any six stages of HIV life cycle.

Solution

HIV has twelve numbered stages in the book. Any six, in order (half a mark each):

No.	Stage	What happens
1	Attachment (adsorption)	gp 120 binds the CD4 receptor of the T cell
2	Penetration and uncoating	Envelope fuses with the membrane using gp 41; the virion enters by endocytosis and sheds its coat
3	Reverse transcription	Reverse transcriptase makes cDNA from the viral RNA
4	Breakdown of viral RNA	Ribonuclease destroys the viral genomic RNA
5	Replication	Single stranded cDNA is copied into double stranded cDNA
6	Integration	Integrase inserts the DNA into the host DNA; it is then the provirus

2025 Annual I, Set B, Q.2 (v) OR3 marks

Write steps of lytic cycle in bacteriophage.

Solution

The lytic cycle of a bacteriophage (virulent phage) has these steps, in order:

Adsorption. The tail fibres and pins attach to receptors on the bacterial cell.
Penetration and genome injection. The sheath contracts, lysozyme digests the cell wall and the DNA is injected through the core tube.
Disintegration of host DNA. A viral DNAase breaks down the host DNA; the viral DNA takes control.
Synthesis of phage components. Phage mRNAs and proteins (head, tail and lysis protein) are made.
Assembly and maturation. DNA is packed into heads and tails are added; about 200 phages in 20 to 25 minutes.
Lysis and release. Lysozyme accumulates, the cell bursts and the phages are released.

2026 Annual I, Set B, Q.31+3+2 = 6 marks

Identify the cycle of Bacteriophage and explain its infection and replication in host cell.

Six drawings of a bacteriophage cycle joined by clockwise arrows.

Solution

Identification (1 mark)

The figure shows the lytic cycle of a bacteriophage. The infected bacterium is filled with new phages and ends as a burst cell with many free phages. The phage is a lytic (virulent) phage and has a master-slave relationship with its host.

The lytic cycle of a bacteriophage, the paper figure with its five stages numbered and named.

Infection process (3 marks)

Adsorption. The phage attaches to the bacterial cell. The tail fibres and tail pins (spikes) bind to specific receptors on the bacterial surface.
Penetration. Binding makes the sheath contract and releases lysozyme from the base of the tail. Lysozyme digests part of the bacterial cell wall and the hollow core tube is pushed through the envelope.
Genome injection. The phage DNA is injected through the core tube into the bacterial cytoplasm. Only the DNA enters; the protein coat stays outside.

Replication in the host cell (2 marks)

Host DNA breaks down and phage parts are made. A viral DNAase digests the host DNA (the phage DNA is chemically modified and is not affected). The viral DNA takes over the cell, and phage mRNAs direct the making of head and tail proteins and the lysis protein.
Assembly, maturation and lysis. DNA is packed into heads and tails are added; about 200 phages are made in 20 to 25 minutes. Lysozyme builds up, the cell lyses and the new phages are released.

2025 Annual I, Set B, Q.35+2 = 7 marks

Explain the steps of life cycle of Human Immunodeficiency Virus (HIV). Also draw its life cycle.

Solution

Steps of the life cycle (5 marks)

Attachment. The gp 120 envelope protein binds the CD4 receptor on the T cell.
Penetration and uncoating. The viral envelope fuses with the cell membrane, using gp 41, and the virion enters the cell by endocytosis. Uncoating releases the single-stranded viral RNA and the viral enzymes into the cytoplasm.
Reverse transcription. The enzyme reverse transcriptase synthesizes a single-stranded DNA complementary to the viral RNA, called cDNA.
RNA breakdown. Ribonuclease (RNAase) breaks down the viral genomic RNA after reverse transcription.
Replication of cDNA. The single-stranded cDNA is copied to form double-stranded cDNA.
Integration. Integrase, an enzyme encoded by the virus, inserts the double-stranded DNA into the host cell DNA.
Provirus. The integrated DNA is now called the provirus.
Transcription. Host RNA polymerase transcribes viral mRNA from the provirus. Viral genomic RNA is also produced, not only mRNA.
Translation. Host ribosomes translate the viral mRNA into several large proteins, which the virus-encoded protease cuts into the virion's structural proteins.
Assembly and maturation. The viral components are assembled and mature virions are produced.
Release. Mature virions bud off from the host cell, each enclosing a portion of host membrane. The host cell becomes smaller and non-functional.

Life cycle diagram (2 marks)

2026 Annual I, Set D, MCQ 51 mark

Viruses that infect bacteria are called:

APlant viruses
BAnimal viruses
CBacteriophagesAnswer
DRetroviruses

Why

A virus that infects bacteria is a bacteriophage (phage), the tadpole-shaped virus of the book. Plant viruses (A) infect plants (for example tobacco mosaic virus) and animal viruses (B) infect animals. Retroviruses (D), such as HIV, have an RNA genome and infect animal cells (HIV attacks CD4 cells).

2025 Annual I, Set D, MCQ 61 mark

Viroids cause:

AHepatitis A
BHepatitis B
CHepatitis C
DHepatitis DAnswer

Why

The book names the only human disease caused by a viroid as hepatitis D (a short, circular RNA with no coat). Hepatitis A is caused by the hepatitis A virus (A), hepatitis B by the hepatitis B virus (B) and hepatitis C by the hepatitis C virus (C). Hepatitis D needs the hepatitis B virus to enter a liver cell, which is why B can look right.

2025 Annual I, Set D, Q.2 (iii)2+1 = 3 marks

Write about the structure of prions. Enlist two diseases caused by them.

Solution

Structure of prions (2 marks)

A prion is an infectious protein particle with no nucleic acid: it contains neither DNA nor RNA.
It consists of a single protein encoded by a single cellular gene. It is smaller than a virus and much more resistant than a virus to inactivation by UV light and heat.

Two diseases (1 mark)

Kuru in humans and mad cow disease in cattle: fatal neurodegenerative diseases with clumping of proteins in the brain, memory loss and permanent damage. There is no treatment or cure.

2026 Annual I, Set D, Q.2 (iv) OR3 marks

Draw a labeled HIV life cycle.

Solution

Draw the twelve numbered stages of Figure 5.5 in order and label each with its stage name (the key enzymes are shown on the stages they act in). 1 mark for the diagram, 1 for correct order and 1 for labels.

Stages 1 to 2: gp 120 binds the CD4 receptor; fusion by gp 41; entry by endocytosis; uncoating.
Stages 3 to 7: reverse transcriptase (RNA to cDNA), RNA broken down by RNAase, double stranded DNA, integrase inserts it into the host DNA (provirus).
Stages 8 to 12: transcription by host RNA polymerase, translation on host ribosomes, protease cuts the large proteins, maturation, release by budding.

2025 Annual I, Set D, Q.2 (viii) OR3 marks

Following is the diagram of HIV: (a) Identify the parts A, B & C. (b) Write the functions of protein gp40, gp120 and enzyme integrase in HIV. [Figure]

HIV with the parts A, B and C marked.

Solution

(a) Identify A, B and C (1.5 marks)

HIV with the parts of the question named.

Part	Name	Note
A	Envelope	Lipoprotein bilayer borrowed from the host cell; carries the glycoprotein spikes
B	Matrix protein	Protein shell between the envelope and the capsid
C	Capsid	Conical, made of capsomeres; encloses the two RNA strands and the enzymes

(b) Functions (1.5 marks)

Protein or enzyme	Function
gp 120 (outer glycoprotein)	Attaches the virus to the CD4 receptor of the host cell
gp 41 (transmembrane; printed gp40 in the paper)	Critical for cell fusion: the envelope fuses with the host membrane
Integrase (enzyme)	Incorporates the viral DNA into the host cell DNA to form the provirus

Note. A, B and C mark the envelope (A), matrix protein (B) and capsid (C), the three layers in order from outside. The paper prints gp40; it should be gp 41.

2025 Annual I, Set D, Q.2 (ix) OR3 marks

How can a virus survive under unfavorable conditions outside the host?

Solution

Outside a host a virus survives by going into a dormant state (3 points, 1 mark each):

It is non-living outside the host. It needs no food and has no metabolism, so it remains dormant or inactive.
Its genome stays viable for a long time in inactive form. The only threats are unfavourable pH and temperature, which denature its proteins.
Non-enveloped viruses survive for long periods (up to several days), while enveloped viruses survive for shorter periods, because their envelope is degraded by sunlight and cleaning.

2026 Annual I, Set D, Q.31+3+2 = 6 marks

Identify the cycle of bacteriophage and explain its infection and replication in host cell.

Six numbered stages of a bacteriophage infection.

Solution

Identification (1 mark)

The figure shows the lysogenic cycle of a bacteriophage. The phage DNA enters the bacterium, but the cell is not lysed: it divides (stage 5) into two daughter cells that still carry the phage DNA. The phage is a lysogenic (temperate) phage and has a host-guest relationship with its host.

The lysogenic cycle of a bacteriophage, the numbers of the paper figure with the stages named.

Infection process (3 marks)

Adsorption. The phage attaches to the bacterial cell. The tail fibres and tail pins (spikes) bind to specific receptors on the bacterial surface.
Penetration. Binding makes the sheath contract and releases lysozyme from the base of the tail. Lysozyme digests part of the bacterial cell wall and the hollow core tube is pushed through the envelope.
Genome injection. The phage DNA is injected through the core tube into the bacterial cytoplasm. Only the DNA enters; the protein coat stays outside.

Replication in the host cell (2 marks)

Integration. The phage DNA inserts itself into the bacterial chromosome and becomes a prophage. It is copied with the chromosome before binary fission.
Division of the host. Binary fission gives two daughter cells, each with the prophage. They survive and the prophage can change their properties (lysogenic conversion). Adverse conditions such as UV radiation cause induction: the phage DNA leaves the chromosome and starts the lytic cycle.

Exam focus

Explain the steps of the life cycle of HIV and draw it (twelve stages in order with the key enzymes). (long)
A 7-mark Section C question in 2025 (Set B Q.3); also 2026 Set B Q.2 (iv) OR (six stages) and Set D Q.2 (iv) OR (labelled diagram).
Go to answer
Identify and explain the lytic and lysogenic cycles of a bacteriophage: infection, replication and the diagram. (long)
Both 2026 sets asked it as the 6-mark Q.3 (Set B lytic, Set D lysogenic); 2025 Set B Q.2 (v) OR asked the lytic steps.
Go to answer
Identify the parts of HIV from a diagram and state the functions of gp 120, gp 41 and integrase. (short)
Asked in 2025 (Set D Q.2 (viii) OR); book long question 4.
Go to answer
Describe the structure of prions and viroids and the diseases they cause (kuru, mad cow disease, hepatitis D). (short)
Prions asked in 2025 (Set D Q.2 (iii)); viroid and hepatitis D MCQs in 2025 (Set B MCQ 11, Set D MCQ 6).
Go to answer
How a virus survives outside the host in unfavourable conditions, and inside the host cell. (short)
Asked in 2025 (Set D Q.2 (ix) OR); book short questions 5 and 6.
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Classify viruses on the basis of capsid, genome and host. (long)
2026 Set B MCQ 5 (structure) and 2026 Set D MCQ 5 (bacteriophage); book long question 1.
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Describe the structure of a bacteriophage (head, sheath, tail, base plate, fibres) with a labelled diagram. (long)
No paper question in 2025 or 2026, but the parts must be known to label the Q.3 phage cycle; book long question 3.
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Compare the lytic and lysogenic cycles in a table (host relationship, fate of host DNA, release of phages). (short)
Supports Q.3 of both 2026 sets; book long question 5.
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