Term 1 Reflection – Biomolecules

What interests me most about this topic is the sheer number of amino acids found in the body.

As such, I looked them up and put my findings here.


What I know from the syllabus

Amino Acids are the building blocks of proteins. There are 20 different types, which differ only by the R part of the structure.

Amino acids link together using peptide bonds through the process of condensation, creating many different varieties of proteins.

What else I found

When the body synthesizes protein, ammonia is formed in the liver as a waste product. Excessive protein in the diet can result in excess ammonia produced, stressing the liver and kidneys whose jobs are to flush it out of the body –> why eating too much meat is bad for your health

There are essential amino acids which cannot be manufactured by the body and must be taken in through the diet. These are generally found in soy, egg white, cheese, chicken and other protein-rich foods.

  1. histidine – (polar, basic) A precursor to histamine, which allows more WBCs to enter capillaries to engage pathogens during an immune response.
  2. isoleucine – (nonpolar) Hydrolyzes zein and edestin, proteins found in maize and hemp respectively.
  3. leucine – (nonpolar) Stimulates muscle protein synthesis and used in the formation of sterols.
  4. lysine – (polar, basic) Its derivative, allysine, is used in the production of collagen and elastin.
  5. methionine – (nonpolar) It is the only sulfur-containing amino acid besides cysteine. Reduces fat deposition in the liver, stimulates production of cartilage and strengthens hair and nails.
  6. phenylalanine – (nonpolar) The body changes it into tyrosine, which is needed to make brain chemicals such as dopamine and epinephrine (adrenaline).
  7. threonine – (polar) Helps in formation of collagen and elastin in skin. Also metabolizes fat.
  8. tryptophan – (slightly polar) Used to produce serotonin, a neurotransmitter important for normal nerve and brain functions.
  9. valine – (nonpolar) Needed for muscle metabolism, tissue growth and repair. [*In sickle-cell anemia, it takes the place of the hydrophilic glutamic acid in haemoglobin. As it is hydrophobic, it alters the shape of the RBC abnormally.]

The other 80% of amino acids can be manufactured by the body and thus classified as non-essential:

  1. alanine 
  2. arginine
  3. asparagine
  4. aspartic acid
  5. citrulline
  6. cysteine
  7. cystine
  8. gamma-aminobutyric acid
  9. glutamic acid
  10. glutamine
  11. glycine
  12. ornithine
  13. proline 
  14. serine
  15. taurine
  16. tyrosine

Because I don’t have a lot of time now, I will only be focusing on the essential amino acids for this post. Their polarity, acidity, natural sources and (very) summarized functions are as shown above.


Practical 2 – Effect of Environmental Conditions on Beetroot

Aim: To investigate the factors affecting the cellular homeostasis of Beetroot cells


  • Razor blade
  • Ruler
  • 5 test tubes and rack
  • Forceps
  • Distilled water
  • 25% and 50% alcohol solution
  • Beetroot (Beta vulgaris)
  • White tile (for cutting)
  • 3 droppers (water, 25%, 50% alcohol)
  • Thermometer
  • Stopwatch
  • 2 beakers
  • Tripod stand and wire gauze (for water bath)
  • Colorimeter


1. Set up a boiling water bath with the bigger beaker. When the water starts to boil, turn off the Bunsen burner.
2. Use a ruler and scalpel to cut the cylinder of beetroot into 25 discs of 2mm each.
3. Take 5 discs of beetroot and cut them further into smaller pieces.
4. Rinse the beetroot discs and pieces until the water is colourless.
5. Label and prepare 5 test tubes as follows:

Tube Content
A 4 ml of water
B 4 ml of 25% alcohol
C 4 ml of 50% alcohol
D 4 ml of hot water (900C – 1000C), in water bath
E 4 ml of water with chopped beetroot

6. Place 5 discs of beetroot in tube A – D and all the chopped beetroot in tube E using the forceps.
7. Leave the tubes to stand in your test tube rack for 15 minutes.
8. Shake the tubes gently after 15 minutes and hold it against the white tile to note the colour. Record your observations in a table. (You should be constructing a table during the wait time)
9. Use the colorimeter to record the percentage of transmission of light.
10. Decant a small amount of the liquid from each tube into a cuvette to measure the percentage of transmission. Hold the cuvette only at the ROUGH sides. Turn the cuvette so that the arrow is facing you when you insert it in to the colorimeter.
11. Dispose of the content of the tubes after the experiment. Please do NOT throw the beetroot into the sink.

Tubes A, B, C and E (from right to left)

2014-01-21 12.38.35

Tube D

2014-01-21 12.38.43


Tubes A, B, C and E (from right to left)
2014-01-21 12.48.12

Tube D
2014-01-21 12.48.16

Colour observations

Tube A
Very pale red

2014-01-21 12.48.48

Tube B

Pale red

2014-01-21 12.49.14
Tube C

Very red
2014-01-21 12.49.40

Tube D

Extremely deep red
2014-01-21 12.50.01

Tube E

2014-01-21 12.50.20

Colorimeter readings (results taken are 1-5)

2014-01-21 12.55.07

Discussion questions
Background knowledge
Beetroot contains a red betalain pigment in the vacuole.
1.    Why was it necessary to wash the beetroot slices thoroughly before using them in this exploration?

The beetroot cells contain a red pigment within the vacuole. After the beetroot slices have been cut, their vacuoles may have been damaged, causing the pigment to leak out. Therefore the leaked pigments have to be washed off so as to not contaminate the solution before the start of the experiment.

2.    Identify the independent and dependent variables in this experiment. Which was the control set-up for this experiment?

Independent variables: temperature of water, concentration of alcohol solution and exposed surface area of beetroot slices

Dependent variable: percentage of transmission of light of the colour of liquid in the test tubes

Control set-up: Tube A

3.    Construct a suitable table, with appropriate headings and units, to tabulate your data.
4.    Explain, with reference to the tabulated data, the effect of different solutions in tubes A-C on the readings obtained in the experiment.  You should make reference to the knowledge you acquired from the lessons on cell structure and cell membrane.

(The alcohol solution dissolves lipids in the cell membrane, thus making it more porous and allowing the red pigments in the vacuole to leak out of the cell and into the solution. Therefore, Tube B containing 25% alcohol allows only 84.57% of light to pass through the liquid compared to the control set-up Tube A containing only water, which allows 87.1% of light to pass through. With a greater concentration of alcohol in the solution, the cell membranes become even more porous. Thus Tube C containing 50% alcohol allows even less light, at 52.59%, to pass through.)
5.    Suggest an explanation for the observations of tube D & E.

(Only 26.83% of light could pass through the solution in Tube D, due to the high water temperature which denatured the proteins in the beetroot’s cell membranes, making it porous and allowing the red pigment to leak out and block light in the solution. In Tube E, only 38.17% of light could pass through as compared to Tube A with 87.1% of light passing through. This is because the greater surface area to volume ratio of the beetroot pieces greatly increased the rate of diffusion of the red pigments out of the cell.)

Reading: Claude Bernard

Article: Claude Bernard and the constancy of the internal environment


Claude Bernard is most famous for his idea that the maintenance of a stable internal environment is a prerequisite for the development of a complex nervous system.

Unlike some other prominent scientists, Bernard had received many awards for his contributions. Some of his discoveries include the function of the pancreas.

However, his most important contribution was ignored until around 50 years after his death. It gained attention after Leon Fredericq observed that the body fluids of crabs and lobsters were about as salty as sea water, while those of marine fish were much less salty. This connected Bernard’s idea to evolution and gave it new importance, with many prominent scientists referring to it and extending it even to the social environment.

Some reasons the author gave for it being largely ignored at first was that:

  1. Louis Pasteur’s new bacteriology was dominating the attention of scientists at that time.
  2. The constancy of the internal environment took on new, accessible meaning only after it helped to close the gap between evolution and physiology, bringing it to the attention of a much larger group of scientists.
  3. The tools for measuring the internal environment were not available at that time. For example, the work of Walter B. Cannon, the scientist who helped raise the importance of Bernard’s idea in neurophysiology and psychology, required the development of the cathode-ray tube oscilloscope. This hampered the ability of scientists to prove and expand Bernard’s idea in their fields of science.


Some thoughts:

Scientists often stumble upon important discoveries that go unnoticed in their lifetimes. Many don’t know what impact their discoveries will have on the field of science, and some discoveries go through many scientists before their true value is found, such as in the case of the idea of homeostasis.

Don’t discount your findings. Science is a team effort.

Homeostasis – regulation of substances in our bodies during OBS

Regulation of water

When the body has too little water:

  • The blood will have a lower water potential than the RBCs, causing them to crenate. This reduces the amount of substances they can transport.
  • Information is sent to the hypothalamus, the “thirst centre” of the brain, from sensors in the blood vessels. It signals the organism to look for water to drink.
  • The hypothalamus increases the synthesis of an antidiuretic hormone (ADH) called vasopressin, which is secreted by the pituitary gland and travels to the kidneys. There, it increases the amount of water reabsorbed from the urine, thus reducing urine flow and conserving water in the body until more fluids are consumed.

= Visible effect: Less urine produced. Urine is more concentrated/yellow.

When the body has too much water:

  • The blood will have a higher water potential than the RBCs, causing them to cytolyses due to osmosis. Thus there will be fewer RBCs to transport substances around the body.
  • Information is sent to the hypothalamus, the “thirst centre” of the brain, from sensors in the blood vessels. It signals the organism to stop drinking.
  • The hypothalamus decreases the synthesis of vasopressin, thus decreasing the amount of water reabsorbed from the urine and increasing urine flow.

= Visible effect: More urine produced. Urine is less concentrated (lighter yellow/ clear).

Regulation of temperature

Our body temperature is affected by that of the surroundings. When the surrounding temperature increases, it increases as well.

When body temperature is too high:

  • Behavioural response: Finding shade to reduce temperature difference between core temperature and external environment, wearing thinner clothes to allow more heat from skin to be lost to the external environment
  • Receptors in the hypothalamus monitor the blood’s temperature as it passes through the brain (core temp). Receptors in the skin monitor the external temperature.
  • They send information to the brain, specifically the hypothalamus, which activates cooling mechanisms:

The body secretes sweat onto the skin from sweat glands. When the sweat evaporates, it draws latent heat away from the skin and thus reduces body temperature.

The arterioles expand to allow more blood to flow through the surface capillaries. More latent heat escapes from the blood to the skin and is lost through sweating, convection radiation.

= Visible effect: More sweat is produced. Face appears red/flushed.

When the body temperature is too low:

  • Behavioural response: Curling up to reduce surface area exposed to the external environment, putting on more clothes to reduce heat lost to the surroundings
  •  … The hypothalamus activates warming mechanisms:

Muscles around the vital organs involuntarily contract and relax repeatedly to convert more ATP to heat energy. This reduces the difference in temperature between the outside environment and the body.

The arterioles contract, causing less blood to flow through the surface capillaries. Less heat is carried to the skin.

(only effective for animals) Fluffing up hair
Erector pili muscles in skin contract, raising skin hairs to trap an insulating layer of still, warm air next to the skin. In humans, this is not very effective and only causes goosebumps.

= Visible effect: Extremities can turn blue or become damaged (frostbite).

Regulation of glucose concentration in blood

When there is too little glucose:
(e.g. after heavy exercise, lack of food for extended periods)

  • Behavioural response: Eating food
  • Receptor cells in the pancreas monitor glucose concentration in the blood.
  • The pancreas releases glucagon, a hormone which stimulates the breakdown of glycogen (stored glucose) to glucose in the liver (glycogenolysis). The glucose is released into the bloodstream, increasing blood sugar levels.

When there is too much glucose:
(e.g. after a meal)
– Behavioural response: Stop eating
– The blood would have a lower water potential than the RBCs, causing the RBCs to crenate. This reduces the amount of substances they can transport.
– The pancreas releases insulin, causing the liver to convert more glucose into glycogen (glycogenesis) and stimulates the uptake of glucose by cells for respiration. This reduces blood sugar levels.

*Both glucagon and insulin cannot be secreted at the same time.