Sample Assignment on Biology

Biology
Name
University

Biology 2
1.
A. A pathogen is defined as an organism capable of causing disease in the host. A
host provides a warm, moist and nutrient-rich environment for the parasite. The
human host besides maintaining a uniform temperature also renews itself and thus is
an appropriate habitat for pathogenic microorganisms where they can live, reproduce
and evolve (Alberts, et al., 2002).
B. Methicillin resistant Staphylococcus aureus (MRSA) is a resistant bacterium that is
a normal flora of the skin and nasal cavity but it can cause septicemia if it gains entry
into tissues and causes an infection which is rather difficult to treat because it is
resistant to most antibiotics. It usually causes sores or boils on the skin but it can also
infect the lungs and the urinary tract.
Norovirus or the Norwalk-like virus causes an infection that causes nausea, vomiting,
abdominal pain and watery diarrhoea. The virus is very contagious and can cause
infection through contaminated food and water and is common in crowded places like
schools, cruises, nursing homes and child care centres.
Athlete's foot or tinea pedis occurs due to a infection by a fungus. Trichophyton
mentagrophytes is the caustaive organism. It causes vesicular infections or often
appears as a toe web. The infection appears suddenly often due to prolonged warmth
and moisture but can be treated quickly.
Malaria is caused by the pathogen Plasmodium, a protozoan. Species of Plasmodium
that can infect human beings are P. vivax, P. ovale, P.malariae and P. falciparum. P.
falciparum is known to cause a rather severe form of malaria.

Biology 3
(CDC, 2018).
The female Anopheles culicifacies mosquito carries the pathogen and infects human
beings when it bites through the sphorozoites of the protozoan into the human blood
stream. The malaria parasite causes fever with chills and apathy in the patient.
Transmission of malaria occurs when a mosquito bites an infected person and
transfers the pathogen contained in the blood sucked from infected person and bites a
healthy individual where the pathogen gets lodged.
C. S. aureus is a gram positive bacterium and the cell wall comprises of a thick
peptidoglycan cell wall. It occurs as spherical colonies in clusters that are usually
arranged in two planes and this bacterium is devoid of flagella.
The norovirus is a non-enveloped virus that has an icosahedral geometry. The
diameter of the capsid can vary between 23 to 40 nm. The capsids are composed of
about 60 VP1 proteins and the surface of the capsid has an amorphous surface
structure and can be visualized under an electron microscope.
The structure of the fungus that causes Athlete's foot has septate hyphae and the
fruiting body is a branched conidiophore. Some strains may even have spiral-shaped
or coiled hyphae. Chlamydospores may also be found in some cases.
The Plasmodium lives in the red blood corpuscles of man as an intracellular parasite
and in an adult form it is called the trophozoite which is amoeboid, has a single
nucleus with a vacuolated and granular cytoplasm.

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D. Route of entry
Pathogens gain entry into a susceptible human body to cause infection. The mucus
membrane, the skin, the respiratory, the urogenital and the gastrointestinal tracts are
the routes of entry or portals of entry for disease causing micro-organisms. Contact
with clean disinfected, clean surfaces can reduce the chance of entry.
2.A. Resident flora are the microorganisms that reside on a particular site on the
human body. These are about 10 times more numerous than a person's own cells.
Some microorganisms are present on the body from a few hours to a few weeks and
are called transient flora.
2.B. Resident flora prevent infection by offering competition for space and nutrition
to the invading pathogenic organisms if any. So, the host remains protected due to the
presence of the resident flora.
There are several benefits of normal resident microflora. These organisms synthesize
and excrete vitamins and these are absorbed and utilized by host organisms. Enteric
bacteria that are normal residents of the human intestine secrete Vitamin K and
Vitamin B12. Lactic acid bacteria also produce some B-vitamins. The normal flora
offer competition in terms of attachment sites and nutrients to pathogenic bacteria in
the oral cavity, the skin, the vaginal epithelium and the intestine. Intestinal bacterial
flora produce bacteriocins that kill other bacteria. They may also produce peroxides
and nonspecific fatty acids that inhibit or even kill other bacteria. Normal flora induce
an immunological response which is an antibody-mediated immune response. This
helps in preventing infections because the low levels of antibodies may cross react
with certain pathogens and thus prevent infections.

Biology 5
If the mucosal surfaces are breached, infection of the host by normal flora are
possible. Dental caries, periodontal disease, abscess, release of foul smelling
discharge and even endocarditis can be caused by normal resident flora. At times
impairment of the host or the host immune system, such as, in patients of leukaemia,
immuno-suppression, irradiation therapy or chemotherapy can cause the normal
resident flora to cause disease or the normal flora may fail to suppress the growth of
transient pathogenic organisms and they could cause infections and the host may get
infected and suffer from disease.
3.C. Skin and the mucus membrane play an important part in the protection of the
body from pathogens. Often the first line of defence of the body is formed by the skin,
tears and mucous. Tears and mucous contain the enzyme lysozyme that kills bacteria.
The skin has its own resident microflora that offer competition to pathogenic strains
that may try to colonize the skin or the underlying tissues.
4. Blood clotting occurs when a blood vessel ruptures and several circulating
components of blood get converted into an insoluble gel that plugs the site of rupture
and prevent the loss of blood from tissues or organs.
It comprises of two systems, the first system involves platelets that help to form a
thrombus or a blood clot. The second system is mainly dependent on the clotting
factors that act to form a fibrin clot.
The clotting factors are formed in the liver, and utilize calcium ions from the blood
and the phospholipids which are platelet cell membrane components (Thrombocyte,
n.d.).

Biology 6
Injured tissue: exposure of endothelial cells
When a blood vessel gets injured it gets exposed to foreign substances, following this,
collagen adheres to the broken surface. The interrupted endothelium exhibits specific
cell membrane receptors where the platelet adhesion happens. Platelets play an
important role in blood clotting. The von Willebrand factor (vWF) that is released
from the platelets and the injured endothelial cells mediates the adhesion between the
platelets and the collagen fibrils that get exposed due to injured endothelial cell lining.
Narrowing of blood vessels

Biology 7
Blood vessel narrowing or vasoconstriction occurs when injury occurs in order to
reduce blood loss. The walls of vessels have smooth muscles that contract when
injury occurs and cause vasoconstriction. The reduced diameter of the vessel at the
site of injury helps in minimising the loss of blood. Blood vessels of intact vessels do
not allow clotting to occur because of a fibrinolytic heparin molecule and the
thrombomodulin. Together these two prevent platelet aggregation. But when injury
occurs and the endothelium is disrupted, the von Willebrand factor is secreted, the
vasoconstriction follows as a brief contraction to decrease blood flow to the area. This
is the first step in restoring haemostasis at the injury site.
Activity of platelets
The contents of the granules stored inside the platelets are also released and this
causes the aggregation of platelets. The platelet glycoprotein is linked to the collagen
and this activates the integrin protein of the platelets. As a result the platelets bind
tightly to the extracellular matrix. The release of granules into the blood plasma is
accompanied by ADP, vWF, serotonin and the platelet-activating factor. These
accelerate the activation of more and more platelets into the blood system. When
many platelets clump together at the site of the injury, it is known as platelet
aggregation.
The mechanism that leads to the activation of a protein receptor that increases the
concentration of calcium in cytosol of the platelets. The calcium plays a role in the
activation of protein kinase C. This culminates in the activation of a particular kind of
phospholipase. The phospholipase enzyme modifies the integrin of the glycoprotein
of the cell membrane. This cross linking between the platelets and fibrinogen

Biology 8
increases its ability to bind to fibrinogen. This increases the aggregation of platelets.
This is the first step towards establishing haemostasis.
Activity of clotting factors
Clotting factors are the part of the cascade that results in the formation of the clot.
There are 12 clotting factors that are given common names and assigned Roman
numerals. Vitamin K is an essential part of the cascade that culminates in the
formation of a clot. It helps in post translational carboxylation of clotting factors.
There are two pathways of coagulation, the intrinsic and the extrinsic pathway. The
extrinsic pathway leads to formation of the activation of the Factor X while the
intrinsic pathway amplifies the generation of the Factor Xa. The two pathways
converge at Factor Xa that plays a centrally important role in the coagulation
pathway.
The membranes of the TF (Tissue Factor) -bearing cells and platelets are the sites
where coagulation factors get activated through a process that involves initiation,
amplification and fibrin formation.
As soon as vascular injury occurs, initiation occurs when cells having the TF bind to
Factor VII, thus causing its activation. A small amount of thrombin then formed from
the prothrombin. The thrombin so produced, activates platelets. The formation of the
prothrombinase complex occurs, it is made up of Factor Xa and co-factors associated
with platelets. The complex once formed causes a burst of thrombin production. This
is called the amplification. This is followed by several protease reactions that convert
the soluble fibrinogen protein into the insoluble fibrin. This leads to the formation of
the thrombus. Thrombin plays a role in activation of Factor XII which helps in the
cross-linking of fibrin. The fibrin mesh so formed entangles cellular components like
the platelets and the red blood corpuscles.

Biology 9
Factor Xa with Factor V as a co-factor causes the activation of prothrombin (Factor
II) to thrombin (Factor IIa). Each Factor Xa molecule can catalyse the formation of
1000 thrombin molecules.
Normal blood flow is restored when plasminogen breaks down the thrombin and
restoration of structural integrity of blood vessel is complete.
5. Macrophages play a role in preventing infection in multifarious ways. The
differentiation of macrophages occurs from the monocytes that migrate into tissues
and differentiate in a tissue specific way. When monocytes differentiate in the
presence of the cytokine interferon- γ, they form the microbial invaders and such
macrophages are called as the classically activated macrophages. When monocytes
differentiate in the presence of glucocorticoids and prostaglandins, the resulting
macrophages are known to play a role in immune regulation. While wound healing
macrophages differentiate in response to the cytokine interleukin-4. The macrophages
that play a role in immune regulation produce the cytokine interleukin-10 that
suppresses the immune system and limits inflammation in the later stages of the
immune response.
.

Biology 10
6. Mechanisms of acquisition of immunity
Naturally acquired
immunity
Artificially acquired
immunity
Passive Immunity Immunity acquired
through antibodies from
breast milk or through
the placenta. IgG
antibodies are the only
isotype that can cross the
placenta. The IgA
antibodies pass that are
transferred through the
breast milk also provide
passive immunity to the
new born baby and
protect from bacterial
infections in the gut until
the newborns can
synthesize antibodies by
themselves.
Immunity acquired
through antibodies taken
from another animal or
person. This type of
immunity protects from
pathogen or poison once
but there is no immune
memory associated with
this type of immunity. A
person is at risk if the
same pathogen is
encountered a second
time.
Active Immunity Immunity gained
after getting an infection
and recovery from the
infection. This type of
immunity confers
protection during
subsequent infections if
the pathogen is
encountered again due to
memory of the immune
response. Second
response is usually faster
and antibodies have
higher affinity for the
antigens.
Immunity acquired due to
vaccination. Vaccines
have been developed
against the measles virus,
chicken pox virus, polio
virus, diphtheria and
several infectious
diseases and provide life-
long protection against
pathogens.
7. Differences between antigens and antibodies-

Biology 11
 Antibodies are synthesized by the body to defend the body against antigens
while antigens are substances that stimulate the immune system to elicit a
response by forming antibodies.
 Antibodies are always proteins called immunoglobulins while antigens could
be proteins, lipopolysaccharides or lipoproteins.
 The structure of antibodies is Y-shaped, but antigens can vary in shape.
The structure of the antibody molecule is always Y-shaped. And antibodies are
polymeric protein molecules that are secreted by the plasma cells. The immune
system employs the antibodies to neutralize pathogens such as, bacteria and virus that
have infected the host. The recognition of the pathogen occurs through the antigen
and antibody that can bind together, if complementarity is established. The
mechanism involved in recognition is extremely precise. At times the antibody may
tag a microbe and block its function required for invasion and survival. At other times
the antibody may recruit other cells such as, natural killer cells or macrophages to
eliminate the pathogen. The antibodies are able to communicate with other
components of the humoral or cellular response through its Fc region which is located
at the base of the 'Y'.
Since antibodies are polymeric proteins, they are made up of two light chain
polypeptides and two heavy chain polypeptides. The heavy and light chains are held
together by disulfide bonds.

Biology 12
also called immunoglobulins, Y-shaped molecules are proteins manufactured by the
body that help fight against foreign substances called antigens. Antigens are any
substance that stimulates the immune system to produce antibodies. There are five
isotypes of antibodies- Immunoglobulin G, Immunoglobulin D, Immunoglobulin E
are monomeric, Immunoglobulin A is dimeric in nature and Immunoglobulin M is
pentameric. each polypeptide of the antibody molecule has a constant and a variable
region. The amino acid sequence of the variable region confers specificity on the
antibody and it can bind to the antigen complimentarily.
Heavy chains
Each isotype of antibody has a different type of heavy chain. Five types of mammalian
immunoglobulin heavy chain are named α in IgA, δ in IgD, ε in IgE, γ in IgG and μ in IgM
antibodies. The size and the composition of the heavy chains is different, α and γ heavy
chains are composed of 450 amino acids while the ε and μ heavy chains have 550 amino
acids. The constant part of the heavy chain is identical in all antibodies of one isotype. Heavy
chains for IgA, IgG and IgE have three immunoglobulin domains and a hinge region that
adds flexibility while the heavy chains of IgM and IgE have four immunoglobulin domains in

Biology 13
the constant region. The variable region, as the name suggests, differs based on the B cell that
produced it. All antibodies produces by the same B cell have the same amino acid sequence.
The variable region of the heavy chain of the antibodies is made of 110 amino acids and has
one immunoglobulin domain.
The light chains of the immunoglobulins in mammals have just two types- the κ and λ chains.
Each light chain has two domains, one domain is constant while the other is variable. A light
chain can be 211-217 amino acids in length. Each antibody has two of these and both are
identical (Abcam, n.d.).
Humoral immunity is the immune response that involves B cells that are able to recognize
antigens of pathogens that have entered the blood or the lymph and are exogenous in origin.
The antigens bind to the B cells and interleukins or T helper cells cause the co-stimulation of
B cells. The B cells get activated and B cell proliferation also begins. Upon proliferation the
B cells form plasma cells. Antibodies specific to the antigens encountered are borne by the
plasma cells. The released antibodies circulate through the body and bind to antigens. These
could include cells that have been invaded by pathogens, tumour cells or even transplanted
cells.
The cell mediated response involves T cells and responds to cells that carry a display of
aberrant Major histo-compatibility complex markers or the MHC markers. The antigen
presenting cells or the APCs bind to T cells. The T cells then proliferate and produce
cytotoxic T cells. Cytotoxic T cells display the antigens. This occurs when MHC I are
displayed on cells. In case of MHC II and exogenous antigens displayed on the plasma
membrane, T cells proliferate to produce T helper cells which release interleukin and
stimulate B cells to produce antibodies. Once antibodies bind to antigens, non specific
Natural killer cells and macrophages are stimulated to destroy the antigens (Cliffnotes, n.d.).

Biology 14
8. According to the clonal selection theory, the immunological memory allows a rapid
response to occur when a second exposure to antigen happens (Klinman, 1996). Vaccinations
are used to artificially induce immunological memory, while infections and recovery allow
for naturally induced memory. B cells have specific antibody as a cell surface receptor. When
a soluble antigen is encountered it binds to the antibody displayed on the B cell surface that
has the correct specificity leading to the formation of clones that are the antibody-producing
plasma cells, also called the memory cells. B cells that are specific to the antigen can secrete
antibodies.
Low levels of soluble antibodies can be produced after one week of exposure to an antigen.
But a second exposure to an antigen elicits a much faster response. The levels of antibodies
are several orders higher in magnitude than the first response. The binding affinity of the
antibodies for antigens during the second response is about 1000 times higher. This happens
due to somatic mutations in the variable regions of heavy and light chains of memory cells. It
is a random process but the binding affinity to antigens can be higher and only those clones
that have a higher affinity proliferate while those with inactive antibodies die.

Biology 15
The inability of the immune system to distinguish between self and non-self forms the
basis of autoimmune response. The production of B- cell clones that produce
antibodies that destroy self-antigen displaying cells causes destruction of the body's
own tissue and causes diseases such as Type 1 diabetes, rheumatoid arthritis and
rheumatic carditis. Rheumatic carditis occurs when antibodies directed against the M
protein of Group A streptococcus begin to cross react with the cardiac myosin. This
leads to inflammation and acute damage. This can lead to impaired heart valve
function. Polyclonal activators might at times activate B cells. Due to a repetitive
structure, multiple B cell receptors can get activated and result in cross linking.
Autoantibodies can be produces by cross reactive antigens. Epitopes on an auto-
antigen may be recognised by B cells as also on a foreign antigen as a co-incidence.
When B cells present an auto-antigen there is no response from T helper cells that are
auto-reactive. But when there is a cross reactive antigen the T helper cells get tricked
into launching an auto immune response that leads to proliferation and production of
antibody producing clones.

Biology 16
References
Abcam, n.d. antibody-structure-and-isotypes. [Online]
Available at: http://www.abcam.com/protocols/antibody-structure-and-isotypes
[Accessed 12 May 2018].

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Alberts, B. et al., 2002. Molecular Biology of the Cell. 4th ed. s.l.:Garland Science.
CDC, 2018. parasites.html. [Online]
Available at: https://www.cdc.gov/malaria/about/biology/parasites.html
[Accessed 22 May 2018].
Cliffnotes, n.d. humoral-and-cell-mediated-immune-responses. [Online]
Available at: https://www.cliffsnotes.com/study-guides/anatomy-and-physiology/the-immune-
system-and-other-body-defenses/humoral-and-cell-mediated-immune-responses
[Accessed 12 May 2018].
Klinman, N., 1996. The “Clonal Selection Hypothesis” and the current concepts of B cell tolerance.
Immunity, Volume 5 , p. 189–195.
Thrombocyte, n.d. process-of-blood-coagulation/. [Online]
Available at: http://www.thrombocyte.com/process-of-blood-coagulation/
[Accessed 17 May 2018].