A2 BIOLOGY UNIT 4 NUTSHELL

IT IS NEVER TOO LATE!

DR. MOHAB MEGAHED

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Photosynthesis Revision Checklist
1. Describe the structures of chloroplast responsible for the Light Dependent reaction.
Chloroplast contains thylakoids that are grouped into grana and connected by intergranal thylakoids. Thylakoids are
the site of light dependent reaction as they contain chlorophyll pigment arranged as photosystems within the
membranes as well as ATP synthase enzyme and electron carriers on the membranes.

2. Explain how energy from sunlight is made available in ATP (Describe the role of light in LDR).
Light hits chlorophyll pigment in the thylakoids that are grouped in grana. This causes emission of electrons.
Electrons are accepted by an electron acceptor and pass through an ETC causing a series of redox reactions that
release energy. This energy is used for the active coupling of ADP and phosphate forming ATP in a process known
as Photophosphorylation which is catalyzed by the enzyme ATP synthase. The electrons lost from chlorophyll are
compensated by electrons released from photolysis.

3. Chloroplast drawing / phosphorylation diagram

Hydrolysis reaction

ATP ADP + Pi + Energy

Condensation reaction
“Phosphorylation”
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4. Describe how an oxygen molecule is formed in the process of photosynthesis.
When light hits water, it breaks the strong covalent bond in the water molecule releasing 2 H+ , 2 e-, and O (as a
waste product). This process is known as photolysis. For an oxygen molecule to be formed, two water molecules
must be broken.
5. Diagrammatic representation for the Calvin Cycle (mostly complete Q.).

6. Describe how GP is converted into Starch/Cellulose.

GP will be reduced by hydrogen ions from NADPH2 using energy from ATP forming GALP. Every sixth turn of the
Calvin Cycle a glucose molecule is formed. The formed glucose is α- glucose. α- glucose monomers are joined by α-
1,4 glycosidic bonds (condensation reactions between glucoses) forming Starch.

7. Describe how GP contributes to the formation of DNA.

RuBP fixes CO2 forming 2 GP. This process is catalyzed by RUBISCO enzyme. GP will be reduced by hydrogen ions
from NADPH2 using energy from ATP forming GALP. Every sixth turn of the Calvin Cycle a glucose molecule is
formed. This glucose is converted into deoxyribose or nitrates are added to glucose forming nitrogenous base or
glucose is broken down to release energy needed for DNA formation.
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8. Investigations showing the effect of the Light & Darkness on the Calvin Cycle. (see graph in
checklist)
Light: The Calvin Cycle is properly functioning and equilibrium is achieved between GP and RuBP.
Darkness: The Calvin Cycle stops due to lack of NADPH2 & ATP causing failure of GP reduction into GALP and
consequently failure of RuBP regeneration while carboxylation does not stop. This increases GP and reduces RuBP.
However, after a certain period of time they are either broken down or converted into other substances.
Light again: When light is resumed, regeneration of RuBP continues as the cycle is now functioning. This causes
initial increase of RuBP and initial decrease of GP until equilibrium is reached again.

9. Investigation showing the effect of sudden drop of CO2 concentration on the Calvin Cycle.
(see graph in checklist)
At 1.0% CO2 concentration:
Both RuBP and GP are constant. Equilibrium is present as the Calvin Cycle is uninterrupted.
At 0.003% CO2 concentration:
RuBP increases then decreases then stays constant. It increases as carbon fixation stops and it is regenerated from
GALP. It decreases because carboxylation is resumed. It is constant when a new equilibrium is reached at a lower
level.
GP decreases the stays constant. It decreases because carboxylation decreases due to less availability of CO2. It is
constant when a new equilibrium is reached again at a lower level as CO2 is still available but at lower levels.

10. Explain why the Calvin Cycle stops in the absence of sunlight.
The light dependent reaction produces NADPH2 and ATP which are needed in the Calvin Cycle. NADPH2 is a source
of hydrogen ions for the reduction of GP into GALP leading to formation of glucose. ATP is broken down into ADP
and phosphate releasing energy for glucose formation. Since the light dependent reaction stops in the darkness,
therefore no NADPH2 and ATP produced and Calvin cycle stops.
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Ecology Revision Checklist
1. Define Succession.
It is the progressive change in the composition of a certain community over a very long period of time until a
stable community is reached which is called Climax Community. It could be either primary or secondary.

2. Describe how succession takes place.

Pioneer species such as: algae, lichens and mosses are able to grow in abiotic land with no soil. They start to
colonize producing their spores which digest the surface of the bare rocks into smaller substances and organic
matter. Moreover, when pioneer species die they create rudimentary soil from their dead matter (Humus). This
is followed by the appearance of grass and shrubs that improve soil conditions such as: soil moisture, soil
texture, mineral availability and soil pH allowing for the growth of taller plants and more animals. This
continues over a very long duration (100+ years) until a stable climax community is reached.

3. Explain how a climax community is eventually reached after succession.

OR
4. Explain why a climax community is stable.
Increase in number of tall plants (tall plants outcompete shorter plants for sunlight as sunlight cannot reach
shorter ones) and increase in number of animal species until the original number of species is restored. Since
animals and plants are interdependent, this high biodiversity allows the ecosystem to function and self-
regulate. Also, the presence of dominant and codominant species maintains stability of the ecosystem. Finally,
the climax community remains stable unless a change in environmental factors or human influences occurs.

5. Explain why the population sizes of different species stay fairly constant once a climax
community is reached.
The population size is fairly constant because carrying capacity is reached, so the population sizes fluctuate
within a certain limit.
Carrying capacity is controlled by 3 main factors:
Ø Environmental Resistance that refers to environmental limiting factors such as: availability of food and
appearance of new diseases that reduce the growth of a certain population.
Ø Density dependent mortality that mainly affects the abundance of organisms and mostly caused by biotic
factors such as: predation and diseases.
Ø Density independent mortality that mainly affects the distribution of organisms and mostly caused by
abiotic factors such as: Temperature and rainfall.

Moreover, population size is fairly constant due to competition which has 2 types:
Ø Intraspecific competition between organisms of the same species for space and food available.
Ø Interspecific competition between organisms of different species.
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6. Use a given graph to describe and explain dominance of certain species over others during
the various stages of succession. (see graph in checklist)
Ø Population A was not completely destroyed by the …. (Apply to Q.), as at year… there was still some of
population A.
Ø At year…. the population size of species A is decreasing while the population size of species B is
increasing. Species B is now dominant over species A.
Ø At year…. species C started to appear and increase in number until it became dominant over species B.
Ø By year…. Climax community was reached as population size of species C is fairly constant.
Ø Dominant species outcompete other species for limited resources such as: light intensity, water and
mineral availability in soil.

7. Define GPP & NPP.

GPP is the rate at which plant incorporate light energy into organic matter by photosynthesis. Its measuring
unit is energy/unit area/unit time.
NPP is the rate at which energy is leftover for plants to use in growth. It is directly proportional to biomass and
equivalent to (GPP – R).

8. Suggest why NPP is important to cattle growers / agriculture sector workers.

Cattles are primary consumers that feed on grass. Higher NPP means higher biomass and consequently more
energy is transferred from plants to animals through grazing. This increases grazing capacity leading to better
growth and higher meat & milk yield.

9. Explain why we measure NPP in terms of productivity not biomass.

Biomass shows many fluctuations over short periods so it might give a false indication. But this formula is
annual so it gives an indication about overall productivity in a year. Moreover, biomass might include
indigestible organic matter.
10. Mention 3 Biotic factors affecting NPP.
Ø Disease
Ø Grazing
Ø Trampling

11. Use given graphs to evaluate the correlation between certain abiotic factors and NPP.
(Remember if one factor is showing evidence of correlation while the second is just
fluctuating, maybe the first is limiting factor). (see graphs in checklist)
Q. 1)
Light & NPP graphs:
There is a strong positive correlation between light & NPP since both graphs show similar pattern of changes.
Moreover, the changes in light intensity precede the changes in NPP by 1 month.
This can be explained by: the increase in sunlight increases the rate of photosynthesis since more ATP is
available for the Calvin cycle and consequently more glucose is formed. Therefore, as light increases the mean
NPP increases.
Temperature & NPP graphs:
There is no correlation between temperature & NPP as fluctuation patterns never suggest a correlation.
This can be explained by: temperature should have been correlated to NPP but a very low light intensity was a
limiting factor.
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Q. 2)
As temperature increases NPP increases. This can be explained by: Increasing temperature increases kinetic
energy gained by enzymes, so more frequent successful collisions, so more enzyme-substrate complexes
formed, and consequently higher rate of photosynthesis.
As rainfall increases NPP increases. This can be explained by: more water available for light dependent reaction,
so more hydrogen ions produced by photolysis are available to reduce more NADP. So, more GP converted into
GALP and thus more glucose formed. This increases the rate of photosynthesis. Moreover, water dissolves soil
minerals and carries them up the plant in the xylem & photosynthesis produces carbohydrates which are
dissolved in water and carried from the leaf to the rest of the plant in the phloem.
In summary, NPP is dependent on the rate of photosynthesis, and photosynthesis is an enzyme-controlled
reaction. Therefore, as the rate of photosynthesis increases NPP also increases.

12. Describe what you can do further to support a correlation.

Place values on x-axis and y-axis, then plot a scatter graph. Then, observe pattern of change to look for a
correlation. Moreover, go for statistical analysis by dong appropriate statistical test such as: Pearson
correlation test. Repeat the whole process and take average of….. Finally, compare your results with results of
previous studies.

13. Explain why most of the sunlight energy in not converted by plants into GPP.
Ø Some wavelengths of light are reflected from the leaf surface.
Ø Some wavelengths of light are transmitted through the leaf but do not hit the chloroplasts.
Ø Some energy is used in transpiration.

14. Describe various causes of energy loss among trophic levels.

Ø Some energy is lost in respiration.
Ø Not all parts of the …… is eaten by the.…. Consumer. (Apply to Q.)
Ø Not all eaten parts are digested.
Ø Not all digested parts are absorbed as some are ejected and lost as feces.
Ø Some energy stays in.…. as locked up energy for decomposers.

15. Calculate the efficiency of energy transfer between trophic levels.

Efficiency of photosynthesis:
Ø (GPP / Total light energy falling on the plant) * 100

Efficiency of energy transfer between producers and primary consumers:

Ø (Energy available in primary consumers / Energy available in plants ‘NPP’) * 100

Efficiency of energy transfer in the rest of trophic levels:

Ø (Energy available in one trophic level / Energy available in the previous trophic level) * 100
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16. Describe the interdependence between animals & plants (Feeding niche/ habitat niche/
pollinator birds).
Plants are a source of food and shelter for animals while animal wastes fertilize the soil.
Pollinator birds transfer seeds and pollen grains of different species of plants. Decomposition of animals and
birds improve soil structure and conditions such as: increasing mineral availability in soil allowing for better
growth of plants. In such a high biodiversity, the ecosystem can function and self-regulate.

17. Explain how decomposers increase CO2 in the atmosphere.

Decomposers such as: bacteria digest the organic matter by releasing extra-cellular enzymes. For example,
protease enzymes break down proteins into amino acids by breaking peptide bonds. This external digestion
releases respiratory substrates such as: glucose. Decomposers absorb glucose by diffusion and break it down in
respiration releasing CO2 in the atmosphere. CO2 is now available to be used by plants in photosynthesis.
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Global Warming & Speciation Revision Checklist
1. Suggest why bacteria need special adaptations to survive in the guts of cattle.
There is no oxygen in the gut of the cattle. So, bacteria must be adapted to use anaerobic respiration.
Moreover, the gut has a very low pH due to presence of HCl. High acidity will denature the enzymes of the
bacteria. Therefore, bacteria must be adapted to withstand acidic conditions (e.g. enzymes working at an
optimum low pH). Also, protease enzyme in the gut might digest bacterial cell. Consequently, bacteria must be
resistant to digestive enzymes (e.g. formation of slime capsule).

2. Describe how greenhouse gases contribute to global warming.

Carbon dioxide, methane, CFC and nitrous oxide are greenhouse gases. They trap long wavelength radiations
reflected from the earth’s surface. Then, they re-emit those long wavelength radiations towards earth’s surface
again. This keeps the temperature of the earth’s surface within normal limits. This is known as the greenhouse
effect. However, human influences on the environment are causing marked increase in the greenhouse gases
e.g. burning of fossil fuels releasing CO2. This leads to enhanced greenhouse effect. This causes a rise in the
average temperature of the earth’s surface (Global Warming).

3. Describe how future predictions are made.

All future predictions are based on computer models. Computer models depend on extrapolation in which they
collect data from different sources and plot a line of best fit to predict the future change.

4. Explain how deforestation contributes to global warming.

Deforestation (removal of biotic carbon sinks) decreases photosynthesis and thus decreases carbon dioxide
removal from the atmosphere. Moreover, deforestation encourages burning of trees which release carbon
dioxide into the atmosphere. Also, deforestation stimulates decomposition of trees by decomposers which
respire adding carbon dioxide to the atmosphere. Finally, deforestation requires use of heavy machinery that
uses fossil fuels releasing carbon dioxide. In summary, deforestation results in net increase in carbon dioxide in
the atmosphere.

5. Suggest why biofuels may / may not be carbon neutral.

Carbon neutral means that carbon dioxide produced equals carbon dioxide used. Biofuels may be considered of
no net change to carbon dioxide levels since carbon dioxide released on their combustion is equivalent to that
up taken by the plants, from which biofuels are derived, recently in photosynthesis.
However, biofuels may be increasing carbon dioxide levels since their production involves clearing large areas
of land (deforestation). Deforestation (removal of biotic carbon sinks) decreases photosynthesis and thus
decreases carbon dioxide removal from the atmosphere. Moreover, deforestation encourages burning of trees
which release carbon dioxide into the atmosphere. Also, deforestation stimulates decomposition of trees by
decomposers which respire adding carbon dioxide to the atmosphere. Finally, deforestation requires use of
heavy machinery that uses fossil fuels releasing carbon dioxide. In summary, both deforestation and biofuel
production results in net increase in carbon dioxide in the atmosphere.
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6. Why are future predictions unreliable (scheme + tailored points).

Future predictions are based on extrapolation which is unreliable as extrapolation assumes continuity of the
trend unchanged. It also depends on limited data available while many other factors such as:…..(apply to Q.)
are not considered, and included data may not stay constant as well. Moreover, the validity of this method of
…...(apply to Q.) is questionable. Finally, not only data is collected from 1 site only but also fluctuation patterns
never suggest a correlation as there is no evidence of real trend.

7. Explain why future predictions include higher & lower estimates.

Ø Higher estimate assumes current conditions will not change.
Ø Lower estimate assumes better conditions.

8. Suggest why some scientists refuse linking Global Warming to increased CO2 levels.
The relationship between CO2 and global warming suggests only a correlation as there is no direct evidence to
establish a causal relationship because the increase in CO2 levels can be attributed to other abiotic factors such
as: volcanoes and solar flares. Moreover, there are other greenhouse gases such as: methane released form
bacteria in the guts of cattle or in rice fields. Furthermore, future predictions are based on extrapolation which
is unreliable as extrapolation assumes continuity of the trend unchanged. It also depends on limited data
available while many other factors such as:..…(apply to Q.) are not considered, and included data may not stay
constant as well. However, some scientists may be biased as they could be employed by companies with
specific interest.

9. Name 3 methods providing evidence for Global warming.

Ø Direct temperature records
Ø Dendrochronology
Ø Pollen from peat bogs
Ø
10. Explain how pollen from peat bogs could be used to provide evidence for Global warming.
Pollen grains in peat bogs are not decayed due to anoxic acidic conditions that inhibit proper enzyme activity of
decomposers. The outer coat of a pollen grain is used to identify its species since the outer coat is species
dependent. Then, we look for the climate at which this plant species normally grows. The depth of the pollen in
the bog is proportional to its age. Therefore, knowing the age and species, we can estimate the temperature at
this age.

11. Explain how the process of ice core analysis could be used to support Global warming.
The method depends on analysing trapped gases inside the ice core. The isotopes of oxygen give indication
about the temperature since temperature affects the ratio of 18O evaporation. Thus, measuring the 18O : 16O
ratio which is proportional to temperature may support Global warming.

12. Name two methods used to give evidence for rising CO2 levels in the atmosphere.
Ø Ice core analysis
Ø Air Sampling
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13. With reference to the core sample shown: suggest the age of the tree, describe how
dendrochronology is done & explain why the hole made should be sealed.
Age of the tree: 30 years
Mechanism: bore into a living tree stem using a drill and remove sample of wood. Count number of xylem rings.
1 ring is equivalent to 1 year.
Why hole is sealed: to prevent loss of water and also to prevent entry of microorganisms causing infection.

14. Explain how global warming affects Tree ring growth.

Increasing temperature increases kinetic energy of enzymes so enzyme activity increases and thus the rate of
photosynthesis increases. This leads to more nutrients laid down in the tree trunks increasing the thickness of
the rings. However, marked increase in temperature denatures enzymes.

15. Explain why some scientists prefer to classify certain organisms as subspecies rather than 2
different species.
Subspecies can interbreed producing fertile offspring while different species produce infertile hybrid offspring.
The offspring is infertile due to failure of pairing-up of homologous pairs of chromosomes in prophase I and due
to the odd number of chromosomes.

16. Suggest why 2 species don’t interbreed (causes of reproductive isolation).

If two species don’t interbreed, this is most probably due to reproductive isolation. Reproductive isolation
arises due to various causes:
Ø Habitat Isolation: individuals select different habitats in the same area.
Ø Temporal Isolation: individuals are reproductively active at different times of the year.
Ø Behavioral Isolation: the behavior of individuals changes so they fail to attract members of the other
gender. (e.g. change in bird songs)
Ø Mechanical Isolation: a mutation occurs changing the shape or size of sex organs so that they no
longer fit each other.
Ø Gamete Isolation: failure of female gamete to attract male gamete or failure of male gamete to
penetrate male gamete.
Temporal, behavioral, mechanical and gamete isolations are most probably caused by gene mutation while
habitat isolation is usually due to increased population size.

17. Explain how natural selection leads to speciation.

A mutation occurs in DNA introducing favorable alleles coding for desirable characteristic (apply to Q.).
Organisms with desirable characteristic are more adapted to the environment. So, they survive more and
reproduce more (explain). They pass the favorable alleles to their offspring. This increases allele frequency. The
process continues over years until a new species with the desirable characteristic evolves.
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18. Describe how two different species arise from a single ancestral species.
Two pockets of the same species became (geographically/non-geographically) isolated. For example, this ……
isolation is most probably caused by ……..(apply to Q.). Each pocket is subject to different biotic and abiotic
factors such as: different sources of food and different nature of habitat. So, they are facing different selection
pressures and consequently different behavioral adaptations. In addition, different mutations occur in each
pocket causing more variation. For example, (physical changes in population as an example of variation). So,
the adapted organisms survive more giving basis to natural selection. The above leads to reproductive isolation,
and thus restricted gene flow. This process continues over years until they become markedly different up to the
extent of being unable to reproduce giving fertile offspring. Now (sympatric/allopatric) speciation occurs.
19. Define: Gene pool/ Genetic diversity/ species richness/ Biodiversity.
Ø Gene pool: all genes with all alleles in a certain population.
Ø Genetic Diversity: variety of alleles within a certain gene pool.
Ø Species richness: number of different species in a certain area.
Ø Biodiversity: Species richness * Genetic Diversity
Ø Subspecies: varieties of same species. Despite being different, they can still reproduce giving fertile
offspring.

20. Records might show that change of appearance of different species (or 2 subspecies) is very
slow. Explain.
Both species share same habitat. So, they experience same biotic and abiotic factors and thus the same
selection pressures. Since both species are well-adapted to the environment, very few mutations occur that
change their phenotype. So, the gene pool is almost stable.
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Protein Synthesis & Forensics Revision Checklist
1. Describe the structure of a DNA molecule.
Two DNA strands run anti-parallel to each other with the 3’ end facing the 5’ end. The two strands are held together
by H-bonds between the nitrogenous bases according to complementary base pairing rules: A bonds with T & C
bonds with G. the two strands are coiled around each other forming a double helix.

2. Compare the structures of RNA & DNA.

Similarities:
Ø Both DNA and RNA are formed of repeated nucleotide monomers joined together by
phosphodiester bonds forming the sugar- phosphate backbone.
Differences:
Ø DNA contains deoxyribose sugar while RNA contains ribose sugar.
Ø The bases of DNA are Adenine, Thymine, Cytosine and Guanine while the bases of RNA are
Adenine, Uracil, Cytosine and Guanine.
Ø DNA is double stranded while RNA is single stranded.
Ø DNA is helical while RNA is straight.
Ø DNA is present in nucleus only while RNA is present in nucleus or cytoplasm.
Ø DNA can replicate itself while RNA cannot.

3. Compare the structures of mRNA & tRNA.

Similarities:
Ø Both mRNA and tRNA are forms of RNA that have single strands.
Ø Both mRNA and tRNA contain the sugar ribose and the bases adenine, guanine, cytosine and uracil.
Differences:
Ø tRNA is a clover-shaped molecule with 2 sides: amino acid binding site on one side & anticodon site on the
other side while mRNA is a simple straight strand with no sides.
Ø tRNA has anticodons while mRNA has codons.
Ø tRNA is involved in amino acid activation and translation while mRNA is involved in transcription and
translation.
Ø tRNA is found in cytoplasm only while mRNA is found in nucleus or cytoplasm.

4. Describe the process of DNA replication and explain what is meant by the term
semiconservative.
DNA replication: The length of DNA that will undergo replication unwinds. The two strands separate by breaking H-
bonds between base pairing (unzipping). This process is catalyzed by DNA helicase enzyme. Free active DNA
nucleotides join exposed bases according to complementary base pairing rules: A bonds with T and C bonds with G.
H-bonds are formed between complementary bases which are catalyzed by DNA polymerase enzyme. The
backbones of the newly formed strands are joined by DNA ligase enzyme. This is followed by winding of the two
newly forming DNA molecules forming a double helix.
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Semiconservative Replication: Each newly formed DNA molecules has one parent strand and one newly synthesized
complementary strand (half old & half new).

5. Define the term genetic code & state the properties of genetic codes.
Genetic code: Three successive nitrogenous base sequences on the DNA strand coding for a certain amino acid in the
polypeptide chain.
A genetic code is:
Ø Triplet: formed of 3 successive bases
Ø Degenerate: each amino acid may have more than one code
Ø Non-overlapping: no base from one triplet is part of another triplet
Ø Universal: amino acids have similar codes in almost all living organisms

6. Define the term mutation & explain how a mutation could lead to loss of function of named
enzyme.
Mutation: random change in the genetic codes of DNA leading to altered nitrogenous base sequence and thus
altered amino acid sequence in the polypeptide chain.
Mutation à different DNA sequence à different transcription à different mRNA à different translation à
different amino acid sequence à different primary structure à different arrangement of R groups à different
bonding between R groups such as: hydrogen bond, ionic bond, disulphide bond and hydrophobic interactions à
different bending and folding of polypeptide chain à different 3D shape à different tertiary structure à different
shape of active site à no enzyme-substrate complexes formed à denaturation of enzyme à non-functioning
enzyme.

7. State what is meant by the term: Template strand of DNA.

It is the antisense strand of DNA on which a complementary mRNA strand is formed according to complementary
base pairing rules in the process of transcription.

8. Describe the process of transcription / translation.

Transcription: unwinding and unzipping of a specific length of DNA (gene) which is catalyzed by DNA helicase
enzyme. One strand acts as a template for mRNA formation while the other strand remains inactive. The active
strand attracts free active RNA nucleotides according to complementary base pairing rules: A bonds with U and C
bonds with G. This process is catalyzed by RNA polymerase enzyme forming H-bonds between bases and also joins
phosphodiester bonds in the sugar phosphate backbone. This process produces pre-mRNA which is subject to post-
transcriptional changes. The newly formed mRNA detaches and leaves the nucleus through nuclear pores, into the
cytoplasm, to the ribosome. The active strand rejoins the inactive strand forming a double helix again.

Translation: once in the cytoplasm, mRNA joins the cleft between the two subunits of the ribosome. The ribosome
reads the first codon and brings the first tRNA with the first specific amino acid. The anticodon and its
complementary codon bind together temporarily by hydrogen bonds. Then, the ribosome reads the second codon
bringing the second tRNA with the second amino acid in the polypeptide chain. Now, a peptide bond is formed
between the two adjacent amino acids. This process is catalyzed by peptidyl transferase enzyme. The first tRNA
detaches to collect another amino acid. The ribosome moves one place to read the third codon. This process
continues until a stop codon is reached which ends the amino acid sequencing and releases the polypeptide chain.
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9. Describe the role of RNA in protein synthesis (Note: This question could be split into roles of
mRNA & tRNA separately).
mRNA carries a copy of DNA genetic codes in form of RNA codons produced during the process of transcription that
occurs in the nucleus. Then, it is subject to post-transcriptional changes before exiting the nuclear pores on its way
to the ribosome.

tRNA binds to a specific amino acid on one side and has anticodons on the other side. It transfers the amino acid to
the ribosome where H-bonds are formed between the anticodons on tRNA and complementary codons on mRNA
ensuring proper positioning of the amino acid.

rRNA is the main component of the ribosome which is responsible for the process of translation in which amino acids
are sequenced and bonded by peptide bonds forming the primary structure of protein.

10. Explain how a mutation could lead to the formation of a defected protein (enzymes).Same as Q. 6
11. Describe how gel electrophoresis could be used to separate DNA bands/ proteins.
DNA bands: a blood sample is obtained, crushed with salt to open the cells then centrifuged to precipitate DNA. The
DNA is amplified by PCR forming large number of copies. The DNA sample is cut in fragments by restriction enzyme.
Electrophoresis: DNA fragments are loaded into agarose gel tank using a micropipette and electric current is applied.
DNA is negatively charged, so it moves towards the positive electrode. DNA fragments are separated into bands
according to their charge. Then, the DNA is labelled to be viewed using X- rays if radioactive or UV if fluorescent.

Proteins: proteins are cut into fragments by protease enzyme. Electrophoresis: a micropipette is used to load protein
parts into agarose gel tank and electric current is applied. Proteins will be separated into bands according to their
charge and weight. Negative charges move towards positive electrode and lighter parts move faster. Proteins will be
labelled using radioactive or fluorescent antibodies then they will be viewed by X-rays or UV light. Bands from
different proteins will be compared based to the following: 1. Size of bands 2. Location of bands 3. Number of bands
produced.

12. With reference to the theory of DNA fingerprinting, describe how it could be used in disrupted
paternity/ crime investigations/ ancestral relationships.
DNA fingerprinting assumes that all individuals have different DNA profile apart from identical twins. Despite the fact
that exons are incredibly similar, but introns are hyper variable. Introns have sequence of repeated nitrogenous
bases known as satellite or STR. Satellites are unique for a certain person as they produce many different
combinations at each locus.
Ø Disrupted paternity: bands in the child DNA not corresponding to the mother’s DNA is compared to the
alleged father.
Ø Crime investigations: DNA of the suspect is compared with DNA of blood sample found in crime scene. DNA
fingerprinting produces bands at each locus. Similar bands contain similar DNA fragments. If the bands
produced are similar, accusation is supported.
Ø Ancestral relationships: compare DNA from two different species. DNA fingerprinting produces bands at
each locus. Similar bands contain similar DNA fragments. So the more similar the bands, the more likely to
have a common ancestor. This helps in studying evolutionary relationships. Moreover, this helps in
classification of living organisms.
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13. Suggest why DNA profiling is never 100% conclusive.
Ø Long multiphasic process so artifacts might arise at any phase.
Ø Only a very small sample is examined, so it might be accidently similar to someone else.
Ø Might be similar in closely related individuals or the same if identical twins.

14. Describe how temperature/ rigor mortis/ decomposition/ forensic entomology could be used to
estimate the time of death.
Temperature: the drop in body temperature is linked to time after death (algor mortis).
The body cools with a rate of 1.5-2 °C per hour after the first hour of death due to heat loss. A cooling curve is used
to estimate the time of death. However, the drop in body temperature is affected by the environmental factors such
as: atmospheric temperature. So, atmospheric temperature must be taken into account while estimating the time of
death. Algor mortis is only useful for 24 hours following the time of death as the body finishes its cooling after 24
hours.
Rigor mortis: during the first 8 hours after death, anaerobic respiration takes place releasing energy needed for
muscles to relax. For 8 to 48 hours after death, the muscles become stiff (rigor mortis). This is due to accumulation
of lactic acid produced during anaerobic respiration inhibiting the respiratory enzymes. After 48 hours, muscle fibers
are broken down by hydrolytic enzymes released from lysosomes (autolysis). However, rigor mortis is affected by the
environmental factors such as: atmospheric temperature. So, atmospheric temperature must be taken into account
while estimating the time of death. After 48 hours, rigor mortis cannot be used to determine the time of death.
Decomposition: the body decomposes at different sequences with time. This sequence involves discoloration in
which new color spreads accompanied with its deepening, followed by bloating with gases and finally deflation.
However, the state of decomposition is affected by the environmental factors such as: atmospheric temperature. So,
atmospheric temperature must be taken into account while estimating the time of death. The state of
decomposition would be of no use if all body has decomposed.
Forensic entomology: it is the study of investigating the time of death using insects as a reference. The following
parameters are considered: 1. stage of life cycle 2. size of larvae 3. Stage of succession on corpse. However, those
parameters are affected by the environmental factors such as: atmospheric temperature. So, atmospheric
temperature must be taken into account while estimating the time of death.

15. Mention 3 factors affecting body temperature/ rigor mortis after death &describe their effect.
According to body temperature:
- Ambient temperature, air movements, clothing and found indoors are all factors that affect rate of loss of body
temperature after death.
- Any factor that increases the rate of cooling à prolonged initial phase à underestimate and vice versa.

According to rigor mortis:

- Level of fitness, level of activity before death and age are all factors that affect amount of stored ATP.
Ø Increased stored ATP à prolonged initial relaxation à delayed rigor mortis à underestimate (and vice
versa)
- Rate of cooling of body affects rigor mortis.
Ø Rapid drop in body temperature à decreased enzyme activity à decreased production of lactic acid à
prolonged initial relaxation à delayed rigor mortis à underestimate (and vice versa)
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Immunity Revision Checklist
1. Describe the roles of (Gut flora/ keratin/ lysozymes/ interferon/ inflammation) in the NSR.
Gut flora: they normally outcompete pathogenic bacteria for space and nutrients. They also may create unfavorable
conditions for harmful bacteria e.g. lowering pH through lactic acid produced killing pathogenic bacteria. Thus, gut
flora prevents growth of pathogenic microorganisms.
Keratin: insoluble indigestible protein found in the epidermis layer of the skin. Keratin acts a physical barrier
preventing the entry of pathogens.
Lysozymes: hydrolytic enzymes that digest bacterial cell walls causing lysis of bacteria. It can be found in: 1. lysosomes
of phagocytes 2. secretions of sebaceous glands (sebum) 3. lacrimal glands 4. respiratory epithelium
Interferon: chemical secreted from infected cells that blocks viral receptors over the surface of the cells preventing
binding of viruses to more cells thus preventing viral replication.
Inflammation: rupture of mast cells secretes histamine. Histamine acts as a vasodilator that increases blood flow and
thus more WBCs delivered to the site of infection. However, this response is characterized by a triad of localized:
hotness, redness and oedema.

2. Suggest why antibiotics & alcohol based hand gels cannot destroy viruses.
Ø Antibiotics cannot destroy viruses as viruses are non-living.
Ø Alcohol is an organic solvent that dissolves the phospholipid bilayer proteins. Proteins in the protein coat of
the virus are hydrophilic so they are not affected by alcohol.

3. Describe how viruses infect cells/ Suggest why Influenza virus cannot infect host cells in the
digestive system.
Ø The virus binds to its specific complementary receptor over the cell surface membrane of the host cell. Then,
it injects its core inside the host cell leaving the protein coat outside.
Ø No complementary receptor over the cell surface membrane of the digestive cells so influenza virus cannot
bind to the digestive cells. There, the virus cannot inject its core inside the digestive cells and thus no viral
replication takes place.

4. Describe how viruses cause lysis of infected host cells/ How do viruses replicate inside host cells.
Lytic pathway
DNA virus: DNA of the virus is transcribed into mRNA. DNA is replicated forming new DNA strands. Both transcription
and replication use energy and enzymes of the host cell. mRNA uses the host cell ribosomes, enzymes, amino acids
and tRNA forming new protein coats. Assembly of new DNA inside the new protein coats forms new viral particles.
New viral particles cause lysis of the cell and infect nearby cells.
RNA virus: RNA uses the host cell enzymes to form new RNA strands. RNA uses the host cell ribosomes, enzymes,
amino acids and tRNA to form new protein coats. Assembly of new RNA inside the new protein coats forms new viral
particles. New viral particles cause lysis of the cell and infect nearby cells.

5. Why do viruses take few hours / few days until the development of symptoms takes place.
This is the time taken for the virus to causes lysis of a significant number of the host cells in order to develop
symptoms. This time is needed for formation of new genetic material, new protein coats and assembly of new viral
particles.
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6. Explain why an infected person might stay symptomless for years.
Lysogenic pathway ‘provirus’
DNA virus: The viral DNA is integrated into the host cell DNA using integrase enzyme. It only replicates with the
replication of the host cell.
RNA virus: reverse transcriptase enzyme catalyzes the conversion of RNA into viral DNA inside the host cell. The viral
DNA is integrated into the host cell DNA using integrase enzyme. It only replicates with the replication of the host cell.

7. Describe the role of T Helper cells in a specific immune response (role of cytokines).
T-helper cells secrete cytokines that activate and proliferate the selected clones of effector B-cells and T-killer cells. B-
cells differentiate into plasma cells that secrete antibodies specific to the foreign antigen. T-killer cells secrete perforin
that causes lysis of infected host cell (this allows for the occurrence of both humoral and cell-mediated immune
responses).

8. Describe how the immune system responds to a specific bacterium/ virus.

T-helper cell activation: macrophages engulf the pathogen and display its antigen over the MHC. The macrophage is
now called an APC to T-helper cells that divide by mitosis forming larger clone of effector and memory T-helper cells.
This is followed by humoral immune response or cell mediated immune response or both.
Humoral Immune Response: B-cells with complementary receptors bind to the foreign antigen and display the
bacterial antigen over its MHC. It is now called an APC (to self). T-helper cells with complementary CD-4 receptors
secrete cytokines which stimulate mitotic division of B-cells forming larger clone of effector and memory B-cells.
Effector B- cells differentiate into plasma cells that secrete antibodies.
Cell-mediated Immune Response: the infected host cell displays the viral antigen over its MHC. It is now called and
APC to T-killer cells. T-killer cells with complementary CD-8 receptors bind to the viral antigen. The active T-helper cells
secrete cytokines which stimulate proliferation of the selected T-killer cells forming larger clone of effector and
memory T-killer cells. The active T-killer cells secrete perforin which causes lysis of the infected host cell. The released
virus could be either engulfed by phagocyte or destroyed by antibodies.

9. Describe the structure of an antigen.

A specific glycoprotein located over the cell surface membrane of pathogens. It is recognized by the immune system
as non-self. So, it stimulates a specific immune response.

10. Describe the mechanism of antibody action.

The antibody binds to the foreign antigen forming Ag-Ab complex. This leads to:
Ø Bacterial cells clump together for easier phagocytosis (Agglutination)
Ø They mark bacterial cells for easier phagocytosis (Opsonization)
Ø They neutralize toxins secreted by bacterial cells (Neutralization)
11. Differentiate between the terms monoclonal & polyclonal response.
Polyclonal response: the pathogen has more than one specific glycoprotein over the cell surface membrane known as
antigens. Each of the antigens selects a specific clone of B-cells and T-cells. The selected clone of B-cells is activated by
cytokines to expand forming larger clones of effector and memory B-cells. Effector B-cells differentiate into plasma
cells secreting antibodies complementary to the antigen. This process occurs with each antigen so we end up with
several clones of antibodies.
Monoclonal response: same as polyclonal but ONLY ONE
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12. Explain why a monoclonal response is better in the detection of a foreign antigen. (diagnosis of
the disease)
Only one type of specific antibodies is secreted from the plasma cells. This specific antibody binds to only one type of a
specific complementary antigen forming Ag-Ab complex. Thus, we can detect the presence of only type of antigen.
This allows reaching a more definitive diagnosis so a specific treatment can be given avoiding the use of unnecessary
drugs.

13. Describe the role of antigen presentation in the specific immune response.
Ø Macrophages display antigens to the T-helper cells with complementary CD 4 receptors. T-helper cells
secrete cytokines that activate and proliferate B cells and T-killer cells.
Ø B cells present antigen to self as B cells differentiate into plasma cells that secrete antibodies.
Ø Infected host cell presents the antigen to the T-killer cells with complementary CD 8 receptors. Active T-killer
cells secrete perforin that causes lysis of the infected host cell.

14. List with definitions the types of natural & artificial immunity and Explain how vaccines work.
Active immunity: stimulates formation of antibodies and memory cells
Ø Natural: in which a person is exposed to the pathogen
Ø Artificial: vaccination
Passive immunity:
Ø Natural: antibodies are passed from the mother to the fetus through the placenta or breast milk
Ø Artificial: giving the person ready-made antibodies e.g. Tetanus antitoxins
Vaccination: a person is given a virus or bacterium that could be either killed or live attenuated. The introduction of
the pathogen with its specific antigen stimulates a specific immune response. A specific clone of T-helper cells is
activated and proliferated secreting cytokines. Cytokines activate and proliferate the selected clones of B cells and T-
killer cells forming effector and memory cells. In secondary exposure, antibodies will be produced faster and in larger
concentrations.

15. Differentiate between primary & secondary immune responses.

Primary exposure: no memory cells so antibodies are slowly produced and in smaller quantities.
Secondary exposure: a secondary immune response takes pace in which memory cells allow for production of
antibodies faster and in larger quantities.
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Antibiotics/ HAI/ TB & HIV Revision Checklist
1. Differentiate between the terms bacteriostatic & bactericidal antibiotics.
Antibiotic refers to a chemical substance produced by microorganisms such as: bacteria & fungi. Antibiotics are
used to control bacteria by killing it or inhibiting its growth.
Bactericidal antibiotic: chemical substances that kill bacteria.
Ø E.g. Penicillin that weakens bacterial cell wall so the cell cannot withstand osmotic pressure or burst during
cell division.
Ø E.g. Tetracycline that blocks respiratory enzymes causing death of bacterial cells.

Bacteriostatic antibiotic: chemical substance that stop bacterial replication.

Ø E.g. Nalidixic acid that block enzymes responsible for replication. So, no cell division occurs and thus
bacteria do not increase in number.

2. Design an investigation to test the efficacy of different antibiotics on a certain bacterium.

Spread bacteria evenly over a sterile nutrient agar plate using lawn distribution/ streaking method. Make 4 equal-
sized holes in agar. To each hole, add 0.1 cm3 of each antibiotic using sterile pipette. Add water in the fourth hole
(control for comparison). Vertically fix the lid to prevent anaerobic conditions and to prevent entry of pathogenic
bacteria. Incubate at 25 °C for 24 hours. This temperature is high enough for bacterial enzymes but not high up to
allowing growth of pathogenic organisms that grow at core body temperature. Observe without opening the lid.
Trace the outline using a graph paper to get the exact surface area of inhibition zone. To ensure reliability, repeat
the experiment several times and calculate the average inhibition zone around each hole. To ensure validity, make
sure to keep all other factors constant such as: concentration of antibiotics and species of bacteria.

3. Suggest how the overuse of antibiotics contributes to the increase in resistant bacterial strains.
The overuse of antibiotics selects for resistant strains and against sensitive strains (act as an artificial selection
pressure). The resistant strains survive more and reproduce more passing the favorable allele of antibiotic resistant
to their offspring. This increases allele frequency.

4. Suggest why bacteria are at advantage in the evolutionary race.

Ø Very rapid rate of reproduction (vertical evolution).
Ø Bacterial cells share the plasmids with resistance genes (horizontal evolution).
Ø Bacterial DNA is not perfect as human DNA so mutations are very common.

5. Explain how can hospitals limit the spread of HAI/ how could hospitals fight antibiotic
resistance.
Strict codes of practice should be applied which is:
Ø Careful monitoring of patients and isolating infected ones.
Ø Cleaning hospital premises: - proper sanitization of toilets and wards by disinfectants & - frequent changing
of bed sheets and use disposable pillow cases.
Ø Proper hygiene of hospital personnel: - handwashing with alcohol-based hand gels & - wearing disposable
clothes.
Ø Changing prescription policies: - do not prescribe antibiotic except if it is really needed & - use narrow
spectrum antibiotics & - use cocktail of antibiotics.
Ø Monitoring rates if HAIs, reporting to the local health and publishing in newspapers.
 20

6. What are the modes of transmission/ risk factors/ Symptoms & causes of death in TB.
Modes of transmission:
Ø Mycobacterium TB >> droplet infection
Ø Mycobacterium bovis >> ingestion of raw unpasteurized milk
Risk factors:
Ø Immune suppression >> TB is an opportunistic infection
Ø Low socioeconomic status >> over crowdedness and poor ventilation
Symptoms:
Ø Unexplained loss of appetite & loss of weight (general wasting of the body)
Ø Low grade fever
Ø Night sweating
Ø Coughing with blood tinged sputum
Causes of death:
Ø Severe erosion of lung tissues >> failure of oxygen uptake
Ø Erosion of nearby vessels to reach other organs causing organ failure
Ø Immune suppression which encourages other opportunistic infection and causing death

7. Describe how Multidrug regimens can be used in the treatment of TB.

Ø Cocktail of antibiotics is used: Rifampicin, Ethambutol and Isoniazid for 2 months
Ø For the next 7 months we continue only 2 antibiotics
Ø Most cases are disease free after 9 months. However, some require continuation up to 18 months.

8. Describe different methods used to fight the spread of TB.

Ø BCG vaccine: live attenuated vaccine prepared from mycobacterium bovis. BCG is given to: -infants below
age of 40 days -travelers to areas with high rates of TB -chest ward workers.
Ø Improving life conditions by avoiding over crowdedness & ensuring proper ventilation
Ø Proper pasteurization of milk

9. Using a given example, Compare the structures of HIV & another virus (Adenovirus)/ Compare
the genetic material of HIV & TB.
HIV & Adenovirus:
Ø HIV has RNA while adenovirus has DNA
Ø HIV has single-stranded RNA while adenovirus has double-stranded DNA
Ø HIV has an envelope while adenovirus has no envelope
Ø Only HIV has reverse transcriptase and integrase enzymes
Ø Only HIV has GP 120
HIV & TB:
Ø HIV has RNA while TB has DNA
Ø RNA is linear in HIV while DNA is circular in TB
Ø TB may have plasmids while HIV has no plasmids
 21
10. Use your own knowledge to give 3 modes of transmission of HIV.
Ø In secretions of the penis/ vagina
Ø Blood-borne infections: - contaminated blood transfusion - contaminated surgical and dental equipment -
contaminated razors - sharing needles - contaminated dialysis machine
Ø From mother to fetus in early stages of pregnancy, during birth or breast feeding

11. Name 2 cells that HIV enters in the immune system & describe how it enters each of them.
HIV enters both T-helper cells and phagocytes.
T-helper cells: GP 120 antigen on HIV binds to its complementary CD4 receptor on the cell surface membrane of T-
helper cell. Then, HIV injects its core into the T-helper cell.
Macrophage: phagocytosis takes place in which opsonized HIV is engulfed by forming pseudopodia. Then, HIV is
trapped in a vacuole and lysozymes are secreted into the vacuole. This breaks down the virus and products of
digestion are absorbed back into the cytoplasm.

12. Describe how HIV infects/ enters T helper cells.

GP-120 are complementary to CD-4 receptors of T-helper cells. So, GP 120 binds to CD4. Then, it injects its core
(RNA, reverse transcriptase and integrase). Reverse transcriptase uses viral RNA as a template to form viral DNA.
Integrase incorporates viral DNA into the host cell DNA.

13. Suggest the effect of HIV on different cells in the immune system few days after infection.
HIV destroys T-helper cells decreasing their count. However, T-killer cells and B-cells proliferate (increase in
number) to combat HIV. T-killer cells secrete perforin which destroys HIV and B-cells secrete antibodies which bind
to HIV destroying it. This stops viral replication but does not eliminate all viral particles of the body.

14. Explain why an infected person would stay symptomless for years.
GP 120 are complementary to CD4 receptors of T-helper cells. So, GP 120 binds to CD4. Then, it injects its core
(RNA, reverse transcriptase and integrase). Reverse transcriptase uses viral RNA as a template to form viral DNA.
Integrase incorporates viral DNA into the host cell DNA. The viral DNA only replicates with replication of the host
cell (the virus remains dormant for years ‘provirus’).

15. Explain why HIV reduces T helper cell count/ causes death.
GP 120 are complementary to CD4 receptors of T-helper cells. So, GP 120 binds to CD4. Then, it injects its core
(RNA, reverse transcriptase and integrase). Reverse transcriptase uses viral RNA as a template to form viral DNA.
Integrase incorporates viral DNA into the host cell DNA. The viral DNA gives orders to synthesize new viral particles
that bud off the host cell membrane acquiring their envelopes from the membrane causing the lysis if the T-helper
cells reducing their count. This leads to immune suppression as destroying T-helper cells reduces production of
cytokines and thus reduces the ability to activate & proliferate both B-cells and T-killer cells. This causes paralysis to
the immune system so death might occur due to opportunistic infections. Moreover, Kaposi Sarcoma is very
common with cases of HIV which is a main cause of death.
16. Explain how we screen for carriers.
Screen for carriers by doing HIV antibody test in high risk groups:
Ø Partners of cases or known carriers
Ø IV drug addicts
Ø Handlers of blood
Ø Patients on dialysis
 22

17. Use your own knowledge to describe different ways for prevention & control of HIV.
Ø Promoting safe sex by advising people to avoid having multiple sexual partners and to use condoms
Ø Careful sterilization of dental & surgical equipments
Ø Careful screening of donated blood
Ø Raising awareness about risk of sharing needles
Ø Screening for carriers
18. Scientists classify HIV as a ‘difficult to treat virus’. Explain.
• It is a virus so cannot be treated by antibiotics
• It is a continuously mutating virus so it is difficult to produce a vaccine
• It doesn’t commonly infect animals, so trials of safety and efficiency are not easily done for new drugs

19. Treatment of HIV requires continuous development of a mixture of drugs. Explain. Then suggest
how drugs might work against HIV.
HIV has a rapid rate of replication and a rapid rate of mutation. This means that HIV has variety of strains so it
might develop different resistance to different drugs. Resistant strains would survive if only one drug is used. A
mixture of drugs reduces chances of surviving such strains.
Anti-viral drugs might bind to GP120 antigen on HIV or block CD4 receptors on the cell surface membrane of the T-
helper cells. Thus, no binding between GP120 and CD4 takes place and HIV cannot inject its core into the host cell.

20. Explain why the number of HIV cases recorded in most studies lower than the actual number.
Ø Most infected individuals are carriers with no symptoms so they don’t know
Ø Even those who have symptoms, symptoms are not characteristic
Ø The might know but hide the fact due to social stigmatization or fear to lose their jobs
Ø Many individuals refuse doing HIV antibody test and screening is never obligatory

GOOD LUCK J