DP Biology HL A2.3 Viruses

DP Biology HL A2.3 Viruses - Full notes

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DP Biology HL | A2.3 Viruses

DP BIOLOGY · THEME A: UNITY AND DIVERSITY

A2.3

Viruses

Full notes for HL · IB-style

Contents

1	What viruses are
2	Structural features common to viruses
3	Diversity of viruses
4	The lytic cycle
5	The lysogenic cycle
6	The origins of viruses
7	Rapid evolution in viruses
8	Structural features shared by all viruses
9	Diversity of viral structure
10	The lytic cycle
11	The lysogenic cycle
12	Replication of an enveloped RNA virus
13	The origins of viruses
14	Rapid evolution of viruses
15	Viruses and disease
16	Viruses as tools
17	Are viruses alive?
18	Mixed review: worked problems
19	Additional exam-style practice
20	Measuring viruses
21	Preventing viral spread
22	Bacteriophages in ecosystems
23	Comparing viral life cycles in different hosts
24	Common misconceptions and links
25	Exam-style question with markscheme
26	Check your understanding
27	Summary and topic map

These are full teaching notes. Read each section in order, try the Think about it question before you read on, and do every Quick check before moving to the next section.

Before you start

Rate yourself on each statement now, and again after you've worked through the notes. Shade R (not yet), A (getting there) or G (confident).

I can…	R	A	G
explain why viruses are not considered living organisms
describe the structural features common to all viruses
outline the diversity of viral structures and genomes
describe the lytic cycle of a virus
describe the lysogenic cycle of a bacteriophage
evaluate hypotheses for the origin of viruses
explain why viruses evolve rapidly and the consequences for treatment and vaccines

A2.3 is an Additional Higher Level (AHL) subtopic. It is studied by HL students only.

Guiding questions

How can viruses be so successful when they are not even cells? Why do some viruses, such as influenza and HIV, keep changing so quickly?

How this topic is examined

A2.3 is an HL-only subtopic. Questions ask you to describe the features of viruses, compare lytic and lysogenic cycles, and explain rapid viral evolution using data on influenza or HIV.

Use precise vocabulary: capsid, envelope, host cell, integration, prophage, lysis.

Command term	What the examiner wants
State / Identify	a brief answer with no explanation needed
Outline	a brief account or summary
Describe	a detailed account, including trends or features, without reasons
Explain	a detailed account including causes, reasons or mechanisms
Distinguish / Compare and contrast	give the differences (and similarities), point by point
Calculate	a numerical answer with working and units
Deduce / Suggest	reach a conclusion from data; propose a reasonable explanation
Evaluate / Discuss	weigh strengths and limitations and reach a judgement

How to use these notes

Each section teaches one part of the syllabus in full. You'll see these boxes throughout; each has one job:

Box	What it's for
Think about it	a question to get you thinking before a section; the answer comes in the section
Key point	the one idea you must not forget
Common mistake	an error examiners see every year, and how to avoid it
In the real world	where the biology shows up outside the classroom
Try this	something quick you can do yourself to test the idea
Worked example	full solutions with IB-style marks (M1 method, A1 answer, R1 reasoning)
Quick check	short questions to test yourself at the end of each section

1 What viruses are

Viruses are infectious particles that can only reproduce inside cells.

Think about it

A virus contains genetic material and can make copies of itself. Why do most biologists still say it is not alive?

A virus is a small infectious particle made of genetic material (DNA or RNA) enclosed in a protein coat. Viruses are typically 20 to 300 nm across, far smaller than most bacteria, and can be seen only with an electron microscope.

Viruses are obligate intracellular parasites: they can reproduce only inside a host cell, using the host's ribosomes, enzymes, ATP and raw materials. Outside a host they are inert particles called virions. Because they cannot carry out metabolism, respond, grow or reproduce on their own, viruses are not considered living organisms, and are described as acellular.

Every type of organism, from bacteria to humans, is infected by viruses. Viruses that infect bacteria are called bacteriophages (phages).

Quick check

1. Why are viruses described as obligate intracellular parasites?

2. What size range are viruses?

Answers: 1. they can reproduce only inside host cells 2. about 20 to 300 nm

2 Structural features common to viruses

Genes inside a protein coat; nothing more is essential.

All viruses share a small set of features. They are small and of fixed size. They have nucleic acid (DNA or RNA) as genetic material. They have a capsid, a coat made of protein subunits called capsomeres, which protects the genome and helps the virus attach to host cells. They have no cytoplasm and few or no enzymes: most carry only a few, such as reverse transcriptase in HIV.

Some viruses also have an envelope: an outer lipid membrane taken from the host cell's plasma membrane as the virus leaves, studded with viral glycoproteins that bind to receptors on host cells. Influenza, HIV and SARS-CoV-2 are enveloped; bacteriophages are not.

Figure 1. A generalized virus: nucleic acid inside a protein capsid, with or without a lipid envelope.

Feature	All viruses	Some viruses
Genetic material	DNA or RNA	single- or double-stranded
Capsid	protein coat	helical, icosahedral or complex shapes
Envelope	absent in many	lipid membrane from host with glycoproteins
Enzymes	few or none	e.g. reverse transcriptase (HIV)
Cytoplasm, ribosomes	absent	never present

Quick check

1. What is a capsid?

2. Where does a viral envelope come from?

Answers: 1. the protein coat around the viral genome 2. the host cell's plasma membrane

3 Diversity of viruses

Viruses vary in genome, shape and host.

Despite sharing basic features, viruses are very diverse. Their genome may be DNA or RNA, single- or double-stranded, linear or circular. Retroviruses such as HIV have RNA and use the enzyme reverse transcriptase to make DNA copies of their genome, which are then inserted into the host's DNA. Capsids may be helical (tobacco mosaic virus), icosahedral (adenovirus) or complex (bacteriophage T4, with a head, tail and tail fibres).

This diversity suggests that viruses may have arisen several times, independently, rather than from a single ancestor (Section 6).

Virus	Genome	Envelope	Host
Bacteriophage lambda (λ)	double-stranded DNA	no	E. coli
Influenza	single-stranded RNA (segmented)	yes	birds, mammals
HIV	single-stranded RNA (retrovirus)	yes	human T cells
SARS-CoV-2	single-stranded RNA	yes	human airway cells
Tobacco mosaic virus	single-stranded RNA	no	plants

4 The lytic cycle

Infect, replicate, burst.

In the lytic cycle, a virus takes over the host cell to make new virus particles, then destroys (lyses) the cell to release them. Using bacteriophage lambda as an example:

1 Attachment. The phage attaches to specific receptor proteins on the surface of the bacterium.

2 Injection (entry). The phage injects its DNA into the cell, leaving the empty capsid outside. (Enveloped animal viruses enter by endocytosis or membrane fusion.)

3 Replication and synthesis. Viral genes are expressed using the host's ribosomes, enzymes and ATP. Host DNA is broken down. Copies of the viral genome and capsid proteins are made.

4 Assembly. New virus particles are assembled from genomes and proteins.

5 Release (lysis). A viral enzyme breaks down the cell wall; the cell bursts, releasing many new phages, which infect neighbouring cells.

Figure 2. The lytic cycle.

Quick check

1. List the stages of the lytic cycle.

2. Why can a virus infect only certain cells?

Answers: 1. attachment, injection, replication, assembly, lysis 2. it binds only to specific receptors on host cells

5 The lysogenic cycle

Some viruses hide in the host's DNA.

In the lysogenic cycle, the viral DNA does not take over the cell immediately. Instead, after injection, it integrates into the host chromosome, where it is called a prophage. Each time the bacterium divides, the prophage is copied along with the host DNA, so all daughter cells carry it. The virus is dormant, and the host survives.

Later, a trigger such as UV radiation or stress can cause the prophage to be cut out of the chromosome and enter the lytic cycle, producing new phages and killing the cell. Bacteriophage lambda can follow either cycle. Animal viruses show similar latency: herpes viruses lie dormant in nerve cells, and HIV integrates into the DNA of T cells.

	Lytic cycle	Lysogenic cycle
Viral DNA	stays separate; directs synthesis immediately	integrates into host chromosome (prophage)
Host cell	destroyed	survives and divides
New viruses	produced quickly	not produced until triggered
Spread	rapid	viral DNA passed to daughter cells

Common mistake

Saying that in the lysogenic cycle no harm is done. The prophage can later switch to the lytic cycle and kill the cell.

Quick check

1. What is a prophage?

2. What triggers the switch from lysogenic to lytic?

Answers: 1. viral DNA integrated into the host chromosome 2. e.g. UV radiation, stress

6 The origins of viruses

Three hypotheses, and possibly more than one is right.

Because viruses leave no fossils, their origin is uncertain. There are three main hypotheses.

The progressive (escape) hypothesis: viruses arose from pieces of cellular genetic material (such as plasmids or transposons) that 'escaped' from cells and gained the ability to move between them.

The regressive (reduction) hypothesis: viruses descend from free-living cells that became parasites and gradually lost the genes they no longer needed. Giant viruses such as mimivirus, with very large genomes, support this idea.

The virus-first hypothesis: viruses existed before cells, as self-replicating molecules in the RNA world (A2.1).

The great diversity of viral genomes and structures suggests that viruses probably arose more than once, by different routes. The similarities between viruses may be the result of convergent evolution: the obligate parasitic lifestyle favours a small genome inside a protein coat.

Quick check

1. Outline the regressive hypothesis.

2. Why might viruses have more than one origin?

Answers: 1. viruses descend from cells that lost genes as parasites 2. great diversity of genomes and structures; convergent evolution

7 Rapid evolution in viruses

Short generations, huge numbers and error-prone copying.

Viruses evolve very quickly. They have very short generation times and produce enormous numbers of offspring, so mutations accumulate rapidly. RNA viruses in particular have high mutation rates, because RNA polymerases and reverse transcriptase do not proofread. Influenza can also swap whole genome segments when two strains infect the same cell (reassortment).

Natural selection then acts on this variation. Variants that escape the host's immune response or resist antiviral drugs survive and spread.

Consequences: new influenza vaccines are needed every year because the virus's surface proteins (haemagglutinin and neuraminidase) keep changing (antigenic drift). HIV evolves so fast within a single patient that it escapes the immune system and develops drug resistance, which is why combination therapy with several drugs at once is used. SARS-CoV-2 produced a series of variants (Alpha, Delta, Omicron) with increased transmissibility or immune escape.

Figure 3. Estimated effectiveness of seasonal influenza vaccines varies from year to year as the virus evolves.

In the real world

The WHO meets twice a year to choose which influenza strains to include in the next season's vaccine, based on global surveillance of circulating variants.

Quick check

1. Give three reasons why viruses evolve rapidly.

2. Why is HIV treated with combinations of drugs?

Answers: 1. short generations; large numbers; error-prone replication / reassortment 2. rapid mutation makes resistance to a single drug likely

8 Structural features shared by all viruses

Small, acellular, obligate parasites.

All viruses are small (about 20–300 nm), have a nucleic acid genome (DNA or RNA), a protein coat (capsid), no cytoplasm, few or no enzymes, and cannot reproduce outside a host cell. They are not made of cells, so they are not considered living by many definitions.

WORKED EXAMPLE 1 Common features (standard)

List four features common to all viruses.

Solution

Genetic material (DNA or RNA)A1

Capsid of protein; small size; no metabolism of their ownA1

Quick check

1. Why are viruses described as obligate intracellular parasites?

Answers: 1. they can only replicate inside a host cell, using its machinery

9 Diversity of viral structure

Many forms.

Feature	Variation	Example
genome	DNA or RNA; single or double stranded	HIV (ssRNA), herpes (dsDNA)
envelope	present or absent	influenza (enveloped), bacteriophage T4 (non-enveloped)
capsid shape	helical, icosahedral, complex	TMV (helical), adenovirus (icosahedral)
host	bacteria, plants, animals	lambda phage (bacteria)

WORKED EXAMPLE 2 Envelope (standard)

Where does a viral envelope come from?

Solution

The host cell's plasma membrane, acquired as the virus buds outA1

10 The lytic cycle

Rapid replication and lysis.

In the lytic cycle (e.g. bacteriophage lambda): attachment to the host; injection of viral DNA; host machinery replicates viral DNA and makes capsid proteins; new viruses assemble; the host cell bursts (lysis), releasing many virions.

WORKED EXAMPLE 3 Sequence (exam level)

Outline the stages of the lytic cycle.

Solution

Attachment and injection of DNAR1

Replication of viral DNA and synthesis of proteins using host machineryR1

Assembly and lysis releasing new virusesR1

11 The lysogenic cycle

Hiding in the host genome.

In the lysogenic cycle, viral DNA integrates into the host chromosome as a prophage and is copied whenever the host divides. Stress (e.g. UV) can trigger the prophage to excise and enter the lytic cycle.

WORKED EXAMPLE 4 Comparison (exam level)

Compare the lytic and lysogenic cycles.

Solution

Lytic: immediate replication and lysisR1

Lysogenic: viral DNA integrated and replicated with host DNA; dormantR1

Both start with attachment and injectionR1

12 Replication of an enveloped RNA virus

The case of HIV.

HIV attaches to CD4 receptors on helper T cells; the envelope fuses with the membrane; reverse transcriptase makes DNA from viral RNA; integrase inserts it into the host genome; viral genes are transcribed and translated; new viruses bud out, acquiring an envelope.

WORKED EXAMPLE 5 Reverse transcriptase (standard)

Explain the role of reverse transcriptase in HIV.

Solution

Synthesizes DNA using viral RNA as a templateR1

Allows viral genes to be integrated into host DNAR1

13 The origins of viruses

Three hypotheses.

The progressive (escape) hypothesis: viruses arose from pieces of cellular genetic material that escaped cells. The regressive (reduction) hypothesis: viruses are descended from cellular parasites that lost most of their genes. The virus-first hypothesis: viruses predated cells. Viruses may have multiple origins (convergent evolution).

WORKED EXAMPLE 6 Evidence (exam level)

Suggest why giant viruses (e.g. mimivirus) support the regressive hypothesis.

Solution

They have large genomes with genes for translation-related proteinsR1

Suggesting descent from more complex cellular ancestorsR1

14 Rapid evolution of viruses

Mutation and selection.

Viruses evolve rapidly because they replicate quickly, produce huge numbers of offspring, and many (especially RNA viruses) have high mutation rates due to error-prone replication. Influenza changes its surface antigens by antigenic drift (small mutations) and antigenic shift (reassortment between strains).

WORKED EXAMPLE 7 Flu vaccines (standard)

Explain why a new influenza vaccine is needed each year.

Solution

Antigens change by mutation (antigenic drift)R1

Antibodies from previous vaccines no longer recognize the new antigensR1

In the real world

SARS-CoV-2 variants such as Delta and Omicron arose from mutations in the spike protein gene, with Omicron carrying more than 30 spike mutations.

Quick check

1. Why do RNA viruses mutate faster than DNA viruses?

Answers: 1. RNA polymerases (and reverse transcriptase) lack proofreading

15 Viruses and disease

Examples and impacts.

Viral diseases include influenza, HIV/AIDS, COVID-19, measles, polio and some cancers (HPV causes cervical cancer). Antibiotics do not work against viruses because viruses lack the structures antibiotics target; antiviral drugs and vaccines are used instead.

WORKED EXAMPLE 8 Antibiotics (standard)

Explain why antibiotics are ineffective against viruses.

Solution

Viruses have no cell wall, ribosomes or metabolism of their ownR1

Antibiotics target bacterial structures and processesR1

16 Viruses as tools

Biotechnology applications.

Viruses are used as vectors in gene therapy (modified viruses deliver functional genes), in vaccines (viral vector vaccines), and bacteriophages are being developed as phage therapy against antibiotic-resistant bacteria.

WORKED EXAMPLE 9 Phage therapy (standard)

Give one advantage of phage therapy over antibiotics.

Solution

Phages are specific to particular bacteria, sparing beneficial microbes; can kill antibiotic-resistant strainsR1

17 Are viruses alive?

Nature of science.

Viruses have genes, evolve and reproduce (in hosts), but they lack cells, metabolism and homeostasis, and cannot reproduce independently. Whether they are 'alive' depends on the definition of life used.

WORKED EXAMPLE 10 Arguments (standard)

Give one argument for and one against classifying viruses as living.

Solution

For: genetic material, evolve by natural selectionR1

Against: no cells or metabolism; cannot reproduce independentlyR1

18 Mixed review: worked problems

Bringing the ideas together.

WORKED EXAMPLE 11 Mixed problem (exam level)

Compare the structure of a virus with a bacterium.

Solution

Both have nucleic acid and proteinsR1

Bacteria: cells with membrane, cytoplasm, ribosomes, cell wall; reproduce independentlyR1

Viruses: capsid, no cytoplasm or ribosomes; reproduce only in hostsR1

19 Additional exam-style practice

Paper 1 and Paper 2.

WORKED EXAMPLE 12 Paper 1 question (standard)

Which feature do all viruses share? A. envelope B. RNA C. capsid D. ribosomes

Solution

CA1

WORKED EXAMPLE 13 Paper 2 question (exam level)

Explain why HIV infection eventually leads to AIDS.

Solution

HIV infects and destroys helper T cellsR1

Immune response weakens; opportunistic infections occurR1

20 Measuring viruses

Scale and microscopy.

Viruses are measured in nanometres and are only visible with electron microscopes. Influenza is about 100 nm; a bacteriophage T4 head about 90 nm; SARS-CoV-2 about 100 nm.

WORKED EXAMPLE 14 Scale (standard)

How many influenza viruses (100 nm) would fit across a red blood cell (8 μm)?

Solution

8000 nm/100 nmM1

= 80A1

21 Preventing viral spread

Public health measures.

Vaccination, hand hygiene, masks for respiratory viruses, safe sex and needle exchange for HIV, and vector control (mosquitoes for dengue and Zika) reduce transmission. Antiviral drugs reduce viral replication but resistance can evolve.

Quick check

1. Explain how herd immunity protects unvaccinated individuals.

Answers: 1. most people are immune, so the virus cannot spread easily to those who are not

22 Bacteriophages in ecosystems

Most abundant biological entities.

There are an estimated 1031 bacteriophages on Earth. In the oceans, phages kill a large proportion of bacteria each day, releasing nutrients and influencing carbon cycling (the 'viral shunt').

Quick check

1. How do marine phages affect nutrient cycling?

Answers: 1. lysis releases organic matter from bacteria back into the water

23 Comparing viral life cycles in different hosts

Plant, animal, bacterial.

Bacteriophages inject DNA through the cell wall; animal viruses enter by endocytosis or membrane fusion; plant viruses usually enter through wounds or insect vectors, and spread between cells through plasmodesmata.

Quick check

1. How do plant viruses spread from cell to cell?

Answers: 1. through plasmodesmata

24 Common misconceptions and links

Students often think…	Actually…
viruses are tiny bacteria	viruses are acellular, with no metabolism
all viruses have envelopes	many, such as phages, do not
antibiotics kill viruses	antibiotics act on bacteria; viruses need antivirals or vaccines
the lysogenic cycle is harmless	the prophage can switch to the lytic cycle

How A2.3 connects to the rest of the course

Topic	Connection
A2.2 Cell structure	prokaryotic and eukaryotic hosts
A1.2 Nucleic acids	DNA and RNA genomes
C3.2 Defence against disease	immune responses and vaccines
D4.1 Natural selection	selection of drug-resistant variants

25 Exam-style question with markscheme

Try this under exam conditions (about 15 minutes) before reading the markscheme.

Figure 4. One-step growth curve of a bacteriophage.

Text A. The graph shows the number of phage particles released per infected bacterium over time in a one-step growth experiment.

(a) State the number of phages released per cell. [1]

(b) Explain why no new phages appear for the first 40 minutes. [2]

(d) Explain why influenza vaccines must be updated each year. [3]

Markscheme

Part	Answer	Marks
(a)	about 150	A1
(b)	phages are replicating and assembling inside the cell	R1
	release only occurs at lysis	R1
(c)	attachment to receptors	A1
	injection of DNA	A1
	replication using host machinery; assembly	A1
	lysis releases new phages	A1
(d)	high mutation rate of RNA virus	R1
	surface antigens change (antigenic drift)	R1
	antibodies from old vaccine no longer bind	R1

Examiner's comments. In (b), the best answers recognised the 'latent period' as time for synthesis and assembly. In (d), mentioning that RNA polymerase lacks proofreading strengthened answers.

26 Check your understanding

Section A: multiple choice

1. Viruses are described as acellular because they

A. are not made of cells B. are very small C. contain RNA D. infect bacteria

2. The protein coat of a virus is the

A. envelope B. prophage C. capsid D. cell wall

3. In the lysogenic cycle the viral DNA

A. is destroyed B. integrates into the host chromosome C. forms a capsid D. leaves the cell

4. Reverse transcriptase makes

A. RNA from DNA B. protein from RNA C. lipid envelopes D. DNA from an RNA template

5. Viruses evolve rapidly partly because

A. they are large B. they have short generation times C. they proofread their genomes D. they lack hosts

6. Antibiotics are ineffective against viruses because viruses

A. lack the structures antibiotics target B. are too large C. have cell walls D. are alive

Section B: structured

7. Compare the lytic and lysogenic cycles. [4]

8. Explain why viruses are not considered living. [3]

9. Evaluate two hypotheses for the origin of viruses. [4]

Answers

1. A 2. C 3. B 4. D 5. B 6. A

7. Lytic: immediate replication and lysis; lysogenic: integration as prophage, host survives, later induction.

8. No metabolism; cannot reproduce independently; acellular; inert outside host.

9. Progressive (escape of genetic elements) vs regressive (reduced cells; giant viruses); diversity suggests several origins.

27 Summary and topic map

Idea	Remember
Virus	acellular, obligate intracellular parasite
Common features	nucleic acid, capsid, no cytoplasm, few enzymes
Envelope	lipid from host, in some viruses
Lytic cycle	attach, inject, replicate, assemble, lyse
Lysogenic cycle	integrate as prophage; induced later
Origins	progressive, regressive, virus-first
Rapid evolution	short generations, mutation, reassortment; vaccines, HIV

Before the exam, make sure you…

•state why viruses are not living
•sequence the lytic cycle correctly
•contrast lytic and lysogenic in a table
•link rapid evolution to vaccines and treatment

Viruses on one page

Cover this page with a sheet of paper and try to rebuild it from memory. Whatever you can't recall is what to revise next.

Figure 5. Topic map for Viruses.

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