Field of study:

Health and pure Sciences

Class:

Integrative project

Methodology

Work written by:

Malek Dhane (1450170)

Work presented to:

François Lemoine

Winter 2016

1

Table of contentIntroduction................................................................................................................................3

Literature review.........................................................................................................................3

Background information………………………………………………………………………………..…………..….3 Instrumental advancements:PCR.……………………………………………………………………………..……4 Testing……………………………………………………………………………………………………………………………5 Nutrition…………………………………………………………………………………………………..……………………7 Research………………………………………………………………………………………………………………………..8

Conclusion – data gathering.......................................................................................................9

References..................................................................................................................................9

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Introduction 

For my integrative project, I have chosen to take on the position of an observant intern at the

Montreal University Health Center (CHUM) within the biochemistry department. The reason for

my choosing of this internship is twofold. Firstly, I have always wanted to work in a hospital-like

setting. Secondly, I have a profound admiration and curiosity towards to the field of

biochemistry. This internship would therefore allow me to determine whether or not I would

enjoy a career in such a field.

Biochemistry is the study of chemical applications within and related to living organisms. In the

last few decades of the 20th century, biochemistry has gotten so at explaining life processes that

it currently overlaps with multiple areas of life sciences, such as nutrition, genetics and

molecular biology. Multiple hospitals employ biochemists in order to aid in patient care. From

researching new ways of testing to evaluating severe nutritious problems, biochemists work on

multiple facets of patient care. The goal of my internship project is to examine the various

applications of biochemistry for patient care. Biochemistry can generally be separated into

various sub-aspects such as conducting tests, evaluating a patient’s nutrition and research.

Literature review

Background information

The now refuted scientific principle that living beings are fundamentally different from non-

living entities was a science named vitalism. Most chemists believed, in the 18 th century, that

organic compounds could not be synthesised using non-organic compounds (Bechtel and

Richardson, 1998). However, this was disproved in 1828 when Friedrich Wohler synthesised

urea using ammonium cyanate (Lajos Kossuth University, 1996). Following this discovery, many

chemists shifted towards studying organic compounds in a chemical setting. Gradually, scientists

began discovering various molecules which led to the discovery of DNA and genes. The

discovering of these molecular units of hereditary became the corner stone to multiple

advances in biochemistry.

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Instrumental advancements: PCR

In 1983, the biochemist Kary Mullis first replicated small chains of DNA. This was not the first

instrumental advancement in biochemistry, seeing as biochemists had been working on

spectroscopy and molecular dynamics for quite some time. However, the discovery of the

polymerase chain reaction (PCR) is often viewed as a critical shift in biochemical and biomedical

prioritization towards hereditary material. The

polymerase chain reaction relies on the cyclic

repetition of a chain reaction which happens in

three steps. This allows for an expanding of the

quantity of DNA molecules in an exponential

fashion. The cycle begins with the heating of the

sample at about 94-98oC for 30 seconds in order

to denature the sample as can be seen in Figure 1.

What this does is separate the strands of DNA by

disrupting the hydrogen bonds between

complementary bases. Then, the sample is cooled

to about 50-65oC for 40 seconds to allow the

annealing of the primers to the single stranded

DNA template. Finally, a DNA polymerase

resistant to heat will add the complementary

nucleobases to the template in the 5’ to 3’

direction. Taq polymerase, an enzyme commonly

used in PCR, is optimal for temperatures in the

75-80oC range. This cycle is repeated for a few

hours until the enzyme is exhausted and no more

product accumulates. In order to separate the

mixed DNA, agarose gel electrophoresis is

sometimes used. This process, which separates the nucleic acids depending on their size and

electrical charge, is done by placing the sample in a hole of the extremity of the agarose gel. The

Figure 1 : Polymerace Chain reaction (Campbell and Reece, 2007)

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agarose gel sits in a conducting liquid and a current passes through. The migration of the

molecules can then be viewed using UV light (Campbell and Reece, 2007).

It is important to note that the main goal of biochemical instrumental advancements is to

perfect testing. For example, the polymerase chain reaction is utilized in a number of tests such

as leukemia and lymphomas testing.

Testing

The Ames test, which was discovered by the biochemist Bruce Ames and determines if a given

chemical or substance is mutagenic, is also one that came forward following the discovery of

genes and DNA. Scientists began to realize that cancer was caused by the over-abundant

replication of cells due to a change in their DNA. Essentially, this test uses Salmonella bacteria in

order to determine whether certain substances would affect DNA. More precisely, this test

verifies if the chemical compound can mutate the already mutant strain of Salmonella bacteria

back to normal. The Salmonella typhimurium bacteria is one that cannot synthesis histidine, and

yet it needs this amino acid for growth. The goal of this test is basically to see if its contact with

a substance could alter this. Once the bacteria is placed in contact with the substance,

numerous genetic analysis are performed to see how it has reacted. The strain is first tested for

histidine dependence. What this

means is that the bacteria are

placed across a GM agar plate

which contains an excess of

biotin. If the bacteria remain

intact, and due to the fact that

they are histidine dependant, no

growth on the plate would

indicate that the substance was

not mutagenic. This can be seen

in Figure 2. This same application

is then repeated only with the

biotin being replaced with Figrue 2 : Ames test (Biomedical PPT Toolkits, 2016) 5

histidine. Once again, no growth should be observed except for the strain TA102. This is then

finally repeated with both biotin and histidine which would cause the growth in all strains. This

technique has been widely regarded as the easiest and most cost-effective way to determine if

certain substances can cause cancer.. Some scientists chose to perform other follow-up tests on

the bacteria strain, such as rfa marker, ampicillin resistance and spontaneous mutant frequency,

in order to get a better understanding of the mutation caused (Tejs, 2008).

Over the years, scientists have been utilizing genetic testing to try and determine a person’s

likelihood of eventually developing diseases, specifically types of cancers, as opposed to the

causes of the diseases. This is very often done with patients at risk for breast and ovarian cancer

and is incredibly common in hospitals (National Cancer Institute, 2015). BRCA screening is a test

performed by biochemists in order to test for

mutations on the BRCA1 and BRCA2 genes. These

mutations are often acquired hereditarily. BRCA

genes produce tumor suppressing proteins. A

predisposed malfunctioning of the gene would

mean the patient is predisposed to eventually

have a type of cancer. Often, doctors will ask for a

blood sample or a bit of saliva. Although there are

many types of genetic tests that can be used,

predictive genetic testing is most commonly used

for breast and ovarian cancer (Evans, 2007). After

multiplying the DNA sequences of the cells with a

variation of the PCR test, the sample is added to a

Biopulverizer H tube. The sample is then

homogenized and then transferred to a tube

using a syringe and a gauge-needle. The sample then goes on to be extracted and set on a 1%

agarose gel for analysis. The results of this test are often non-conclusive and can only give an

indication as to the patient’s eventual health. Its percent efficiency is somewhere between 30

and 70% (West et al., 2001).

(Martin, 2013)

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When a patient’s test demonstrates that he or she is suffering from a disease, he or she will

sometimes be advised to consult a nutritional biochemist. Whether it is diabetes, dental

diseases or even cancer, nutrition will sometimes have an integral part to play in patient care.

Nutrition

The link between biochemistry and nutrition is somewhat of a blurred line in the sense that they

often overlap. Often, once the appropriate tests are completed and show positive responses,

biochemists will either relay the information to medical professionals or, if the disease has a

nutritional aspect, will take the patient in hand themselves (World Health Organization, 2002).

The most common nutrition follow-up after a biochemical test is for diabetes. Once a patient

tests positive for plasma glucose levels that are superior to the norm, biochemists will work with

nutritionists and biochemical nutritionists in order to help in disease management. Depending

on the extent, changes to the patient’s lifestyle, medication and sometimes even surgery is

advised (National Cancer Institute, 2016). During cancer treatment, nutritional therapy is often

conducted by biochemists in order to aid the patient in keeping up their body weight, to assure

the maintaining of tissue and in infection fighting. Eating habits that are ideal for patients with a

certain type of cancer can often be incredibly different from usual healthy eating guidelines.

Furthermore, certain biochemists specialize in evaluating the way certain tumors make

chemicals that will affect the way the body uses certain nutrients. When a patient is fighting

stomach or intestine cancer, his or her body’s use of proteins, carbohydrates and fat will

sometimes be effected. In these cases, chemical analysis is needed (Mayo Clinic, 2014).

Nutritional biochemistry was the heart of biochemistry before discoveries pushed the field

towards testing and being diseased based. Originally, biochemists would work with patients with

certain basic nutritious deficiencies (Bauman College, 2003). However, many biochemists still

work hand-in-hand with nutritionists on basic nutritional diseases such as protein-energy

malnutrition, scurvy and anemia. Scurvy is an example of a disease that certain patients of the

CHUM do actually have. It is mainly caused by a deficiency in ascorbate, more commonly known

under the name Vitamin C. Ascorbate plays a key role in multiple chemical pathways such as the

synthesis of collagen. An important function of ascorbate is protein hydroxylation. Without the

ability to add a hydroxyl group to collagen, the molecule is incredibly unstable which results in 7

the common symptoms of scurvy. The main symptoms of scurvy is fatigue and general

discomfort. If it goes untreated, the possibility of bone pain is also present. It can be treated by

making sure that the patient eats more foods rich in vitamin C.

Seeing as every patient is different, the nutritional aspect of biochemistry is often specialized

work. Depending on the patient’s disease and needs, the analysis of his or her management

requires a personalized analysis and, in rare cases, in-depth research.

Research

In biochemistry, research has an integral part in discovering and perfecting testing, all the while

being implemented to perfect patient care. Most research is funded by universities and is often

used to try and perfect medical procedures. Often working in relation with biomedical

engineers, biochemists are often at the forefront of the procedures that doctors use in order to

treat patients.

Currently, stem cell research is an aspect of biochemistry that is being heavily developed and

further researched. These cells have the remarkable ability to develop into various specializing

cells all the while being able to divide themselves. Most of the research done on these cells is to

try and understand the reason why they can stay unspecialized (Yanes et al., 2010). The current

tests being run on these cells are looking to understand the genes implicated in their

specialization and the corresponding proteins that work towards the cells specialization. Stem

cell therapy is a form of therapy in which these cells are being used in order to prevent certain

conditions such as diabetes and Alzheimer’s

disease. Currently, bone marrow transplant is

the only form of stem cell therapy widely used

and accepted. It utilizes healthy bone marrow in

order to replace destroyed bone marrow (US

National Library of Medicine, 2016). This is often

performed on patients with leukemia, a type of

cancer which begins in the bone marrow and

effects the patient’s blood cell count, in order to (Cancer treatment centers of America, 2015)8

replace degraded cells in the patient’s bone marrow (Cancer treatment centers of America,

2015).

Conclusion or data gathering or integrative project objectives

The data gathering of this project will mostly be observatory. By being present with biochemists,

I will get to see firsthand their roles. More precisely, I will work in the laboratory, with patients

and in research. Within the laboratory, I will have the chance to conduct certain tests and to

gather data on how the CHUM conducts various tests. With the patients, I will get to see the

kinds of conditions that are referred to biochemists as well as the way they go about solving

problems. This is mainly where the nutrition aspect of biochemistry is present. Finally, my time

with researchers will allow me to see how current biochemists are working on future

applications, including stem cell research. All three aspects together allow for a thorough

understanding of the role of biochemistry in patient care.

I will have the possibility to talk to multiple biochemist, specifically with those working in

research. Hence, I will have the opportunity to ask about their opinions of future applications of

biochemistry such as gene therapy and even cloning. All the data obtained will finally be

compiled and presented in a scientific poster.

References

Campbell, Neil, Reece, Jane. 2007. Biologie, 7 ed. Pearson education France. [accessed 2015].

Bauman College. 2003. Nutritional Biochemistry. [accessed 2016].http://sondrabarrett.com/wp-content/uploads/2010/09/barrett-biochem-chapter.pdf

Bechtel, William, Richardson, Robert. 1998. Vitalism. Routledge Encyclopedia of Philosophy. [accessed 2016].https://mechanism.ucsd.edu/teaching/philbio/vitalism.htm

Biomedical Powerpoint toolkits. 2016. Using the Ames test. [accessed 2016].http://www.motifolio.com/1021147.html

Cancer treatment centers of America. 2015. Stem cell transplantation for leukemia. [accessed 2016].http://www.cancercenter.com/leukemia/stem-cell-transplantation/

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Evans, James, Burke, Wylie, Skrzynia, Cecile. 2001. The complexities of predictive genetic testing. [accessed 2016].http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1120190/

Lajos Kossuth University.1996. A demonstration of Wohler’s experiment: preparation of urea from ammonium chloride and potassium cyanate. [accessed 2016].http://pubs.acs.org/doi/abs/10.1021/ed073p539.2

Martin, Nina. 2013. The BRCA1 gene mutation. Public Health United. [accessed 2016].http://www.publichealthunited.org/category/cancer-2/

Mayo Clinic. 2014. Diabetes management: How lifestyle, daily routine affect blood sugar. [accessed 2016]http://www.mayoclinic.org/diseases-conditions/diabetes/in-depth/diabetes-management/art-20047963

National Cancer Institute. 2016. Nutrition in Cancer Care-Patient version: Overview of nutrition in Cancer Care. [accessed 2016]http://www.cancer.gov/about-cancer/treatment/side-effects/appetite-loss/nutrition-pdq

National Cancer Institute. 2015. BRCA1 and BRCA2: Cancer risk and genetic testing. [accessed 2016].http://www.cancer.gov/about-cancer/causes-prevention/genetics/brca-fact-sheet

Tejs, Sebastian. 2008. The Ames test: a methodological short review. Environmental biotechnology. [accessed 2016].http://environmentalbiotechnology.pl/eb_dzialy/eb_online/2008/vol4_1/ms035stejs.pdf

US national library of medicine. 2016. Bone marrow transplant. [accessed 2016]. https://www.nlm.nih.gov/medlineplus/ency/article/003009.ht

West, Mike, et al. 2001. Predicting the clinical status of human breast cancer by using gene expression profiles. [accessed 2016].http://www2.stat.duke.edu/~mw/.downloads/pnas01.pdf

World Health Organization (WHO). 2002. Diet, nutrition and the prevention of chronic diseases: report of the joint WHO/FAO expert consultation. [accessed 2016]http://www.who.int/dietphysicalactivity/publications/trs916/summary/en/

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Yanes, Oscar, et al. 2010. Metabolic oxidation regulates embryonic stem cell differentiation. [accessed 2015].http://www.natureasia.com/en/research/highlight/735

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Evaluation Grid for the Methodology of the Integrative Project (10%, due March 9th, 2016)360-200-SA, Integrative Project, Winter 2016

Name: . Total: /25

* NOTE: the “Material” box will not apply to all projects. Projects for which it doesn’t apply will have 6 marks on literature review.

Topic Very satisfying Satisfying Unsatisfying Very unsatisfying

Research Question or Goal

/3

The question or goal is clearly identified. It is realistic. It is clearly linked to the internship.

3

The question or goal is identified but could be more specific. It is clearly linked to the internship.

2

The question or goal is unclear OR it is unrealistic OR it is not linked to the internship.

1

The question or goal is absent, OR unclear AND and it is not linked to the internship.

0

Explanation

/5

There is a clear, 1 paragraph-long explanation of the question. It says what the main aspects of the question are.5

There is an explanation of the question but it is incomplete or there is extra, useless information.

3-4

There is a text following the question but it hardly explains anything about it.

2

There is no very little or no explanation.

1-0

Literature review There are 3 (or 5*) sources identified. They are all reliable and all relevant.

There are 3 (or 5*) sources identified; 1 of them is not completely reliable OR not completely relevant.

There are 3 (or 5*) sources, several of them are unreliable or irrelevant.

There are fewer than 3 (or 5*) sources.

/6 6 5-4 2-3 0

Variables to measure or information to gather

/5

All important variables (or information to gather) have been clearly identified.

5

Most important variables have been clearly identified.

3-4

Some important variables have been identified, but many missing.

2

None or next to none of the important variables have been identified.

1-0

How will the data or the information be gathered (protocol OR observation grids OR questionnaires)/5

All the main steps to be taken have been identified. The order in which they are presented is logical.

5

Most of the main steps to be taken have been identified. The order in which they are presented is logical. There might be some missing steps.

3-4

Some steps are given but: so many steps are missing that it will not be possible to gather data that way OR there is no logic in the order in which they are presented.

2

No steps are given, or steps given are unrelated to the data to be taken

1-0

Partitioning of time between internship and media production/1

Time partitioning is indicated and adds up to a minimum of 120 hrs.

1

Time partitioning is not indicated, or does not add up to a minimum of 120 hrs.

0