LEARNING OBJECTIVES CONCEPTS • Self and non self • Antigens and antibodies: structure and function • Components of the immune system • Pathogens • Antibiotics and antibiotic resistance • Innate and acquired immunity • Immune memory and vaccination • Zoonosis: how a disease can be spread between animals and humans • Viral infections and AIDS • Allergies and autoimmune diseases • Immunity and transplants
SCIENTIFIC SKILLS • Use diagrams • Carry out an experiment following instructions • Describe a graph • Interpret scientific data • Collect and organise information • Explain the mechanism of action of drugs • Apply a scientific approach to problems • Interpret the results of a diagnostic test
LANGUAGE SKILLS • Science learning action verbs • Vocabulary: unusual plurals • Listen and understand a podcast • Linking words • Prepositional phrases and compound nouns • Answer a job advertisement
UNIT
2
Immunity
Scan to access all the multimedia content of this unit
TUTOR
PLUS
28
UNIT 2
Immunity
LEAD IN
WORK IN PAIRS Discuss with a partner about last time you had influenza.
↑ Artwork
representing influenza virus.
1 How did you know you were ill? 2 Did you take any medication? If yes, what type of medication? 3 Did your physician visit you? 4 Do you think influenza is a severe disease? Why? 5 Do you think your body has fought against influenza? How do you
know? 6 How many days did it take for you to recover? 7 Do you think you have spread the disease? If so, how? 8 Did you ever get flu vaccine? Why or why not? PLUS VIDEO
TAKE NOTES How can structural biology help to fight flu? Watch the video and try to summarise the following aspects of influenza. 1 Symptoms 2 Why is influenza considered a «major infectious disease» 3 How influenza virus enters the body 4 Why the video introduces the metaphor of the copying machine 5 Is the flu virus always the same? 6 How influenza can become a pandemia 7 Results achieved by EMBL researchers through X ray
crystallography
LESSON 1 | Self/non self discrimination
LESSON
TUTOR
1 TASK 1
Self/non self discrimination
READING AND LISTENING
One of the key functions of the immune system is to distinguish between its own molecules and foreign molecules. In the same way football players use the colour of their strip to recognise team-mates, our immune system uses markers located on the membrane of every cell to differentiate self from non-self. In other words, foreign substances or foreign cells (non-self) must be differentiated from the background of the host (self).
TASK 2
29
VOCABULARY
marker: a thing that marks a place or shows the position of something surgery: the practice of treating diseases, injuries etc. by performing medical operations or procedures to mount: to increase in amount or intensity intruder: something going into a place where it is not wanted or welcome
LANGUAGE AND CONTENT INTEGRATION
Use grammar to match the sentences. 1 A fundamental ability of the immune system is 2 Your millions of cells and friendly microbes live
together
3 Your immune system does not usually attack 4 When the immune system recognises 5 The success of the immune system depends 6 When a person receives an organ from someone
else during transplant surgery, that person’s immune system 7 Immunological memory is the ability to remember previous contacts and mount
TASK 3
a in a state known as self-tolerance. b may recognise it as foreign. c an intruder, it naturally mounts an immune
response.
d to recognise itself – and to identify its non-self. e a faster and more effective immunological
response upon re-encounter.
f on a dynamic communication network of
millions of cells. g cells that identify themselves as part of your crew.
PRACTICE
Choose the correct phrase to complete each sentence. 1 Self tolerance is:
the identification of possible foreign substances. B the lack of immune response to self substances. C the communication between cells in order to eliminate possible threats. A
2 Immunological memory is based upon:
3 In order for a transplanted organ to be accepted
the possibility of mounting an effective immune response at the first contact with a non-self substance. B the presence in the body of cells that have already been in contact with the non-self substances. C the possibility of establishing an effective communication network between cells. A
by the recipient: A the recipient’s immune system has to mount an immune response. B the recipient’s immune system has to recognise the transplanted organ as an intruder. C substances present in the transplanted organ must be identical to the recipient’s self substances.
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UNIT 2
5
LESSON
TUTOR
TASK 1
Immunity
Pathogens: bacteria
READING AND LISTENING
Bacteria are prokaryotic (pro = before, karyon = nucleus, that means that they don’t have a nucleus) unicellular (uni = one, made by a single cell) organisms. The main components of a bacterial cell are: ▶ Plasma membrane that controls what can enter and exit the cell ▶ Cell wall, giving the bacterium shape and support ▶ Certain kinds of bacteria have another coat around the cell wall, called a capsule, made of polysaccharides. The capsule is considered a virulence factor because it enhances the ability of bacteria to cause disease ▶ The genetic material of bacteria is a circular piece of DNA floating in the cytoplasm. Despite their simple structure, bacteria present a great biochemical and metabolic diversity. There are several types of energy metabolism among prokaryotes that are not present in eukaryotic cells or organisms. The diversity of prokaryotes allows them to flourish in all habitats suitable for life on Earth.
TASK 2
VOCABULARY
to float: to rest or move in a liquid to flourish: to be in a vigorous state
PRACTICE
In the diagram, indicate the following structures: plasma membrane, cell wall, capsule, genetic material
1
2 4
LABORATORY
3
Growing bacteria
Bacteria can reproduce very easily if they are given the nutrients they need. The culture medium can be liquid, very similar to a broth, or solid. In this case a gel-like substance (usually agar) is added to the nutrients and the gel is layered on a plate. These round plates with a lid are very easy to handle and are named after Julius Richard Petri, the assistant of Robert Koch, the German scientist considered as the founder of modern bacteriology. Individual bacteria are tiny organisms which can only be seen with a powerful microscope. As they reproduce they form colonies. Hundreds of thousands of bacteria make up a colony and can be seen with the naked eye.
VOCABULARY
agar: gel made from red algae colony: an aggregation of bacteria growing together as the descendants of a single cell
LESSON 5 | Pathogens: bacteria
VOCABULARY
SCIENTIFIC SKILLS Exercise with the following activities. 1 Put the steps of the lab procedure in the right order.
Sequence
Lab procedure a When everyone is finished, put a small piece of tape on opposite
sides of the plate to fasten the lid. b Gently swab your teeth with a swab. Then gently streak the plate. c Label the dish. d Observe the colour, size, and shape of the bacteria colonies at day 0, 3, and 6. e Incubate the plates at 37 °C. f Obtain a sterile Petri dish. g Record your observations on day zero in your table.
2 This is the typical aspect of a Petri dish after 0, 3 and 6 days of incubation.
Perform the experiment and describe your observations at day 0, 3 and 6.
day 0
TASK 3
day 3
day 6
PRACTICE
2 Can only reproduce in the host. 3 Can have a capsule. 4 Always contain DNA. 5 Reproduce only inside the host cell. 6 Exploit cell metabolic machinery. 7 Can damage host cells. 8 Reproduce by division. 9 Reproduce by assembling. 10 Can produce toxins. 11 Contain proteins. 12 Produce energy through metabolism. 13 Are invisible to the naked eye.
only bacteria
both
only viruses
Compare and contrast viruses and bacteria. Tick (✔) one box for each line.
Characteristics 1 Are cellular.
39
swab: a piece of cotton attached to the end of a stick to streak: to make long, narrow marks to incubate: to keep in a favourable condition to promote growth
40
LESSON
TUTOR
UNIT 2
6 TASK 1
Immunity
Antibiotics
READING AND LISTENING
↓ There are many
kinds of antibiotics.
The term antibiotic is formed by the prefix anti- meaning fighting, opposing, or killing, and bios, the Greek word for life. So antibiotic literally means life-killing, but the word is used to identify a category of substances which are toxic to bacteria. There are several classes of antibiotics, each of them interfering with some steps of bacterial metabolism. Since bacteria are very different from human cells, antibiotics do not act on them.
TASK 2
LANGUAGE AND CONTENT INTEGRATION
Watch the video and fill in the blanks. HOW DO ANTIBIOTICS WORK? Pathogenic bacteria in the body cause 1 , which can be treated by 2 . 3 antibiotics 4 the growth of bacteria by 5 with the processes the bacteria need to multiply. These processes include: 6 , 7 e.g. enzyme activity, 8 . 9 antibiotics 10 the bacteria, for example by 11 the bacteria from making a 12 . Antibiotics can be so-called 13 , affecting many different bacteria in your body including useful bacteria in your gut. Some antibiotics are more 14 , only affecting one or two types of bacteria. It is better to use 15 antibiotics where possible. Most antibiotics have no effect on your immune system. Antibiotics do not work on 16 because 17 have a different 18 to bacteria. Viruses incorporate themselves into a 19 cell in your body in order to multiply. Bacteriostatic antibiotics that affect bacterial DNA metabolism or protein production do not attack 20 and therefore do not slow the 21 of viruses. Viruses do not have a cell wall and therefore bactericidal antibiotics that act on cell walls cannot 22 viruses.
HISTORY OF SCIENCE
The discovery of penicillin
The discovery of the first antibiotic, penicillin, was a real breakthrough in medicine. Before the introduction of this «miracle drug» most infections such pneumonia could be deadly and doctors had no available treatment. The history of the discovery of penicillin and of the man who discovered it, Sir Alexander Fleming, is fascinating.
PLUS VIDEO
LESSON 6 | Antibiotics
SCIENTIFIC SKILLS Watch the video, answer the questions and complete the sentences. 1 How many people died in WW1? 2 Many of these deaths were caused
by .
3 What did Alexander Fleming notice while
studying Staphylococcus bacteria?
4 He observed that the bacteria surrounding the
mold Penicillum notatum . 5 What was Fleming’s hypothesis? 6 The name penicillin comes from .
ACADEMIC SKILLS
41
PLUS VIDEO
7 Did Fleming succeed in extracting
penicillin? 8 In 1935 scientists Howard Florey and Ernst Chain came across a record of Fleming’s incomplete work and decided to . 9 Were they able to extract and purify penicillin? 10 How did they test the activity of their extract? 11 Why penicillin (and antibiotics in general) were and still are, considered as «miracle drugs»?
Antibiotic resistance
After his discovery dated 1928, Alexander Fleming was awarded the Nobel prize in 1945 together with Florey and Chain. In his Nobel Prize lecture (1945) he showed his concern about antibiotic resistance, using the following sentences: ► It is not difficult to make microbes resistant to penicillin in the laboratory by exposing them to concentrations not sufficient to kill them, and the same thing has occasionally happened in the body. ► The time may come when penicillin can be bought by anyone in the shops. ► Then there is the danger that the ignorant man may easily underdose himself and by exposing his microbes to non-lethal quantities of the drug make them resistant. Many decades after Fleming’s discovery, antibiotic resistance has become a big threat to global health. ACADEMIC SKILL PRACTICE Watch the video showing how bacteria become
resistant, then answer the questions and complete the sentences. 1 The main cause of antibiotic resistance is . 2. They can cause changes in (tick ✔ all that applies)
Cell wall structure. Mechanism of diffusion. C Bacterial metabolism. A
Entry into the cell. DNA replication. F Protein production. 3 Selective advantage means . B
D E
4 Why is the gut important for antibiotic resistance? 5 Overuse and misuse of antibiotics . 6 What is the danger of antibiotic underdosage predicted
by Alexander Fleming?
PLUS VIDEO
46
LESSON
TUTOR
UNIT  2
8 TASK 1
Immunity
Innate immunity
READING AND LISTENING
The immune system has evolved two lines of defense to contrast pathogens. Innate immunity is a set of defenses that are active immediately upon infection and is the same whether or not the pathogen has been encountered previously. Innate defenses include external barriers like skin and mucous membranes. Microbes that breach a barrier, such as those that enter through a cut in your skin, are confronted by innate immune cells (natural killer cells, neutrophils and macrophages). Other components of innate immunity include proteins, such as interferon, that can either attack microbes directly or arrest their reproduction. The components of innate immunity can recognise certain common characteristics that are conserved across a variety of microbes without having to figure out exactly the kind of pathogen. These common features, called Pathogen Associated Molecular Patterns (PAMPs), are often lipids or sugars on the surface of pathogens.
VOCABULARY
to breach: to make a gap or hole cascade: a series of reactions that are activated sequentially to recruit: to involve, to activate increasing numbers
COMPLEMENT The complement system is a group of about 30 different proteins that circulate in an inactive form in the blood. These proteins, identified by the letter C and a number or a number followed by a letter, can act together (in complement) with other defense mechanisms. Substances on the surfaces of many microbes activate the complement system, resulting in a cascade of tasks that can lead to the lysis of invading cells. Some complement proteins attach to invaders to enhance phagocytosis, and others act as chemical signals to recruit more immune cells to the site of infection. Certain complement proteins also help trigger the inflammatory response.
� Macrophage engulfing bacteria.
LESSON 8 | Antibodies
TASK 2
47
USING DIAGRAMS
This is an oversimplified diagram of complement activation, but it gives a good idea of the cascade process. Use it to complete the text. certain bacterial polysaccharides + +
enzyme cleavage
C3
enzyme cleavage
C5
C3b
phagocytosis
C3a
+
+ chemotaxis inflammation C5b
C3a + assembly of membrane attack complex
+
cell lysis
Certain bacterial polysaccharides activate the enzyme which cleaves protein 1 into a larger fragment, 2 , and a smaller fragment, 3 Protein 4 activates the enzyme which cleaves protein 5 into proteins 6 and 7 Protein 8 activates a cascade of events leading to 9 that causes 10 . Protein 11 , called anaphylatoxin, is responsible of chemotaxis and 12 , while protein 13 increases 14 .
TASK 3
VOCABULARY
assembly: the process of putting together a number of parts lysis: the destruction or dissolution of cells to cleave: to cut off chemotaxis: movement in response to a chemical stimulus
LANGUAGE AND CONTENT INTEGRATION
Use the grammar to match the sentences. INFLAMMATION 1. Inflammation is 2 At the site of the injury, cells release molecular
signals that
3 The inflammatory process involves a complex
biological cascade of molecular and cellular signals ultimately 4 Swelling is due 5 Redness and heat 6 The first leukocytes to appear at the injured site 7 Then macrophages engulf and digest microorganisms and release TUTOR
a are granulocytes that phagocytose and kill
invading microorganisms. b to accumulation of fluid. c several different chemical mediators that perpetuate the inflammatory response. d an important component of innate immunity. e are due to the rise of blood flow in the inflamed area. f resulting in the familiar clinical symptoms of pain, swelling, heat, and redness. g cause a number of changes in the affected area.
Now listen to the audio for correct pronunciations.
VOCABULARY
swelling: enlargement in size or weight to engulf: to swallow up
62
LESSON
TUTOR
Immunity
UNIT 2
14 TASK 1
Immunity and transplants
READING AND LISTENING
HLA complex proteins are cell-surface proteins responsible for the regulation of the immune system in humans. HLA genes are highly polymorphic, which means that they have many different alleles (variants), allowing them to fine-tune the adaptive immune system. As a result, the proteins on the surface of each individual are different from the proteins of another individual. The success of transplantation greatly depends on matching the recipient’s HLA pattern to the donor’s. Because HLA genes are inherited, we can have similar HLAs as family members. In order to better understand HLA matching, watch the video “HLA matching is complex”.
TASK 2
PLUS VIDEO
PRACTICE
Now answer the following questions and complete the two sentences. 1 What type of cells are transplanted in a bone
7 What’s the chance for a brother or sisters to be a
marrow transplant? 2 HLA stands for …………………………. 3 HLA are …………………….. found on most of the cells of your body. 4 What’s the meaning of “engraftment”? 5 How many HLA markers have to match in order to have good probabilities of transplant success? 6 How many HLA markers have to match if the blood comes from the umbilical cord?
TASK 3
match? And for a parent or children?
8 What is the percentage of people who won’t have
a close match in the family? 9 What is the “Be the match” registry? 10 What is the likelihood of finding a match using the registry? 11 Why is ethnic background important?
SCIENTIFIC SKILLS
HLA MATCHING There are three general groups of HLA: HLA-A, HLA-B, HLA-DR. father
The following diagram refers to HLA markers in a family (parents and 5 children); use it to list the number of matches of each family member with the patient, then find out which family member would make the most suitable donor for the patient. patient A3 B6 DR3
A22 B34 DR5
A3 B6 DR3
sibling #1 A3 B6 DR3
A25 B41 DR2
mother
A1 B43 DR6
A22 B34 DR5
sibling #2 A1 B43 DR6
A22 B34 DR5
A25 B41 DR2
sibling #3 A1 B43 DR6
A25 B41 DR2
sibling #4 A3 B6 DR3
A22 B34 DR5
LESSON 14 | Is immune system always right?
ACADEMIC SKILLS
63
Job opportunity
This is the advertisement for the research of a scientist. Read it carefully and answer the questions.
JOB OPPORTUNITY PharmaCLIL Scientist (Cell biology) W hat
will you be doing ?
W hat
do we expect of you ?
1 What are therapeutic antibodies for? 2 How do they act against cancer cells? 3 What are the tasks of the scientist to be hired?
Permanent contract
VOCABULARY
hire: to employ a person
64
UNIT 2
Immunity
Now read the following cover letter and determine if the candidate is suitable, by filling in the table below.
4 The candidate (name)
yes
5 Has a PhD plus at least two years of successful international postdoc experience
and track record in immunology, immune-oncology, cell or other relevant discipline, preferably related to or involving therapeutic antibody discovery.
6 Has experience in the pharmaceutical or biotech industry. 7 Has knowledge of cutting-edge developments in the fields of tumor
microenvironment and interacting immune cells.
8 Has strong abilities in conceiving and performing in vitro functional experiments. 9 Has solid expertise in cellular immunology and especially in laboratory cell
culture techniques, isolation and characterisation of cells from blood or organs, and in vitro immunological assays.
10 Has knowledge in transcriptomic analysis and/or next generation sequencing. 11 Is well-organised and rigorous, flexible and agile, able to rapidly acquire
scientific and technical notions relative to new projects.
12 Has outstanding verbal and written communication and interpersonal skills. 13 Understands common office and laboratory software. 14 Knows English (writing and speaking).
no
Not declared needs further investigation
UNIT
2
Immunity
SUMMING UP Final review and practice 1 True or false. Tick (✔) the true statements and correct the false ones.
Inflammation mobilises the adaptive immune response. adaptive immune response counters specific invaders. C The lymphatic system becomes a crucial battleground during infection. D Antibodies bind to specific regions on an antigen. E Clonal inhibition mobilises defensive forces against specific antigens. F The primary and humoral responses differ in speed, strength and duration. G Helper T cells stimulate the humoral and cell mediated immune response. H HIV destroys helper T cells, compromising the body’s defenses. I Immune system disorders result from self-directed responses. J An antibody has one antigen binding site. K Vaccination stimulates the production of memory cells. A
B The
2. The story of Brian will help you to use the vocabulary you have learnt to sum up the
events involved in the fight against a viral infection. Complete the text choosing the words from the word box (some words can be used more than once). antibodies • antigens • antigen-binding sites • bone marrow • clone • days • decades determinants • effector • immune • innate • lymph • lymphocytes • longer • memory • plasma • primary • protein • quicker • secondary • selection • slow • stronger • T-lymphocytes
Brian had never had pertussis and has never been vaccinated. Once he had been exposed and his 1 defenses had been breached, it was too late to do anything. Now it was up to the adaptive 2 response to fight the invading viruses. White blood cells called 3 carry out the adaptive immune response. These cells originate from stem cells in 4 One type of lymphocyte, called B lymphocyte, continues to develop there; another type, called 5 , matures in the thymus in the upper part of the chest. Both B and T cells were involved in defending Brian’s body against the pertussis virus but we will concentrate on the B cells. The viruses’ outer coats contained 6 molecules foreign to Brian’s body; these 7 are what triggered his immune response. Throughout his body were many different types of B cells, each capable of responding to a different antigen. On each of these B cells were 8 that acted as receptors for various potential foreign antigens. Only a specific B cell type possessed antibodies whose 9 were complementary to the shape of antigenic 10 on the pertussis virus antigens. Eventually, the pertussis viruses encountered some of these B cells in a 11 node only these cells were “chosen” to be activated to fight the invading viruses. This process is called clonal 12 The stimulated B cells began to multiply, forming a 13 , a population of genetically identical 14 cells. When B cells do this, the activated cells
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66
UNIT 2
Immunity
are called 15 cells. These cells secrete 16 capable of locking on to the viral antigens and inactivating the pertussis viruses. The initial phase of immunity described so far is called the 17 immune response. Unfortunately, Brian. had to suffer and cough a lot because this response is too 18 . To wipe out the invaders before they cause harm. It usually takes several 19 for lymphocytes to become activated and form effector cell clones, and by that time Brian was already sick. After he recovered, however, Brian was 20 to pertussis. When his college roommate came down with pertussis just before final exams, Brian was safe. A second exposure to the same antigen triggers the 21 immune response, which is much 22 and 23 than the primary response and also lasts 24 .The explanation for this is that the first exposure actually triggers the formation of two cell clones, the effector cells that fought the original infection and also a clone of 25 cells, which are held in reserve. Whereas effector cells may live only a few days, these other cells may last for 26 : they are capable of mounting a quick and powerful secondary response. 3 Complete the flowchart using the terms given from the word box.
antigen presenting cells • plasma cells • helper T cell • memory helper T cells • active cytotoxic T cells • memory cytotoxic T cells • B cell • cytotoxic T cell • memory B cells • secreted antibodies humoral immune response
cell-mediated immune response key
1st exposure to antigen engulfed by
+
+
stimulates give rise to
+
1
+ +
2
+
3
4
5
+
+ 2nd exposure to antigen
6
7
+
8
9
10 defend against extracellular pathogens
defend against intracellular pathogens and cancer