FAQ: Metals in Biological System

The questions are grouped into the following themes. Click the title to explore questions of the
corresponding theme.

Structures of Proteins

1. How do proteins form primary, secondary, tertiary, and quaternary structures?

Different types of structures of proteins are due to different types of interactions of the side-chain
from amino acids and different types of bonding, such as hydrogen bonding. In order to explain the
structures of proteins pictorially, please visit for link below for the detailed explanation with pictures.

Link: http://www.chemguide.co.uk/organicprops/aminoacids/proteinstruct.html (Links to an external

site.)

2. How do trace metals, other than Fe in haeme group, help in forming a quaternary structure protein?

With reference to Q1, the structure of protein depends on different types of interactions and bonding
but it does not depend on the presence of metal ions. In hemoglobin, iron ion does not participate in
proteins folding.

3. What holds different proteins together?

Van der Waals forces hold different proteins together.

4. Which bond is the strongest among ionic bond, covalent bond, disulfide bond, hydrogen bond and
Van Der Waals forces in proteins?

The bond strength values of ionic bond, covalent bond, disulfide bond, hydrogen bond, and Van Der
Waals forces are compiled as below and they are take from
http://bioweb.wku.edu/courses/biol22000/2Bonds/Lecture.html prepared by Dr. Claire Rinehart in
the department of Biology at Western Kentucky University.

Covalent bond: ~ 90 kcal/mol in water

Disulfide bond: ~ 90 kcal/mol in water (covalent bond in nature)

Hydrogen bond: ~ 4.5 kcal/mol in water

Ionic bond: ~ 80 kcal/mol in water

Van der Waals forces: ~ 0.1 kcal/mol in water

Peptide Bond

1. Can the peptide bond in proteins be man-made so as to make a strong polymer for daily use?

The class of organic compounds containing the peptide bond is called amide. There are polyamides
found in nature and synthesized artificially. Nylon is a very famous example of polyamides with high
strength.

Naturally occurred polyamides include wool and silk.

 2. How to break the peptide bond?

An amide molecule can undergo water hydrolysis to form carboxylic acid and amine.

Please visit the following link for the reaction mechanism for your interest.

Link: http://www.chem.ucalgary.ca/courses/350/Carey5th/Ch20/ch20-3-4-1.html (Links to an

external site.)

Nitrogenase

1. What is nitrogenase?

Nitrogenase is an enzyme (biological catalyst) that converts nitrogen gas (N2) to ammonia (NH3).

2. Where can we find nitrogenase?

Nitrogenase is found in some bacteria and plants. Some bacteria and some plants can make use of
nitrogen gas directly while animals cannot use nitrogen gas directly.

3. How does nitrogenase catalyse the conversion of nitrogen gas to ammonia?

The exact mechanism is not known yet but it is believed that the reduction of nitrogen gas works by
stepwise additions of a hydrogen ion followed by the addition of an electron. It may take 12 steps to
complete the catalytic cycle.

4. What is nitrogen fixation?

Nitrogen fixation is the process of conversion of nitrogen gas to ammonia.

5. What are the functions and significance of nitrogenase to plants together with the whole ecosystem?

Nitrogenase converts nitrogen gas to ammonia. Ammonia is a very important chemical because it is
the main ingredients of fertilizer for plants as a source of nitrogen to build different biomolecules,
such as RNA and DNA to maintain life. Some bacteria converts ammonia that is generated from
nitrogenase to glutamine (an amino acid) in which the process is essential to the metabolism of
nitrogen in bacteria.

6. What catalyst, or the conditions, can favour the nitrogenase to fix atmospheric nitrogen gas?

For plants, in the pea family, there is an enzyme (biological catalyst) called leghemogloin which
functions like hemoglobin in human to transport oxygen gas. Oxygen gas in root nodules can reduce
the activity of nitrogenase, so leghemoglobin is there to bind to oxygen gas and thereby oxygen gas
is transported away from the nitrogenase rich area.

Polymeric Nature of Materials

1. I have heard that organic plastic can conduct electricity in the future, how can it be done?

Please watch the video archives of the seminar, "Organic Conducting Polymers".

2. Apart from proteins, what kinds of useful polymers are present in human bodies?

Glycogen: polyglucose, for energy storage in humans

Starch: polyglucose, for energy storage in plants. Some food contains starch.
 DNA: polymer of deoxyribonucleotide, for proper development and functioning of living organisms
except viruses
RNA: polymer of ribonucleotide, essential to all forms of life

3. How are proteins synthesized?

For proteins synthesis in biological systems, the process involves DNA and mRNA but it does not
start out by polymerising different amino acids. For your further information please visit the link
below.
Link: http://www.biotopics.co.uk/genes/trans.html (Links to an external site.)

Coordination Chemistry

1. What is the bonding between magnesium ion and porphyrin ring in chlorophyll?

Please see the response of Q2 in the Q&A section on biomolecules in Molecular Gastronomy.

2. How does oxygen gas bind to the heme group of hemoglobin?

In the heme group of hemoglobin, iron(II) ion is the central metal ion and it is coordinated to 4
nitrogens of the prophyrin ring. There is a histidine residue which is bonded to iron(II) ion as the
fifth ligand. Finally, oxygen gas is the sixth ligand that is bonded to iron(II) ion. To help you
understand visually more about how oxygen gas binds to the heme group in hemoglobin, please visit
the following website prepared by Washington University.
Link:
http://www.chemistry.wustl.edu/~edudev/LabTutorials/Hemoglobin/MetalComplexinBlood.html (Li
nks to an external site.)

3. Why does copper(II) ion bind to 6 water molecules but it only binds to 4 ammonia molecules?

The reaction actually proceeds as below when ammonia is added to the copper sulfate solution.

Dissolving copper(II) sulfate in water

CuSO4(s) + 6H2O(l) --> [Cu(H2O)6]2+ + SO42-

Adding small amount of ammonia in the blue copper solution to form a milky blue precipitate
in water

2NH3 +2H2O <--> 2NH4+ + 2OH-

[Cu(H2O)6]2+ + 2OH- --> [Cu(H2O)4(OH)2] + 2H2O

Adding excess ammonia in the milky blue precipitate in water to form a royal blue precipitate

[Cu(H2O)4(OH)2] + 4NH3 --> [Cu(NH3)4(H2O)2] + 2H2O + 2OH-

4. What is meant by coordination?

Please watch the pre-seminar material of "Metals in Biological Systems".

Photosynthesis

1. In photosynthesis, what roles do metalloproteins play throughout the process?

 As mentioned in the seminar, "Metals in Biological Systems", manganese ions are found in
Photosystem II in the process of photosynthesis. In addition to Photosystem II, two metalloproteins
called ferredoxin (iron-containing protein) and plastocyanin (copper-containing protein) are also
present in Photosystem I which participates the photosynthesis process. For the detailed information,
please visit the following site prepared by Dr. Lukas K. Buehler (Southwestern college).
Link: http://www.whatislife.com/reader2/Metabolism/pathway/photosyn.html (Links to an external
site.)

2. How does chlorophyll harness light energy?

When chlorophyll is exposed to sunlight, an electron is excited from ground state to the excited state.
Since the energy level of the excited electron is too high, it is ejected by the chlorophyll molecule
and chlorophyll is oxidized sat the same time. In order to compensate the loss of an electron in
chlorophyll, water is oxidized to hydrogen ions and oxygen gas by photosystem II. In case you are
interested in the mechanism of water oxidation, please visit the link below for details.

P.S. The explanation in here is over-simplified. There are actually a lot of organic compounds and
metalloproteins involved in the photosynthesis process. The above explanation only focuses on how
chlorophyll works and the production of oxygen gas in photosynthesis as a result of the photo-
oxidation of chlorophyll.

Link: http://employees.csbsju.edu/hjakubowski/classes/ch331/oxphos/olphotsynthesis.html (Links to

an external site.)

3. Do all plants have chlorophyll? If not, how do they survive?

Not all plants have chlorophyll in their tissues. If they do not have chlorophyll, they have to attach
themselves to other plants in order to survive.

4. Why is nitrogenase a suitable catalyst for chlorophyll to carry out photosynthesis?

Nitrogenase has nothing to do with photosynthesis. Nitrogenase is an enzyme which converts

nitrogen gas to ammonia. The cofactor that is responsible in photosynthesis is chlorophyll.

Catalysts and Proteins

1. What can alter proteins in our body?

1. Gene mutation
2. Proteins precipitation by ethanol or methanol
3. Free radicals oxidation of proteins

2. What are the applications of proteins in industry?

Please visit the site below for the list of applications of enzymes in industry.

Link: http://enzymes.me.uk/enzyme/enzymes-in-industry (Links to an external site.)

3. In what ways and how do catalysts speed up the metabolic reactions?

Please read the link below for detailed explanation.

Link: http://www.chemguide.co.uk/physical/basicrates/catalyst.html (Links to an external site.)

4. Is catalyst the substance that alters the chemical reaction?

 Catalysts do not alter the chemical reactions but they just speed up the reactions.

5. Catalysts can make more profit for industry but it also produces many environment issues, how can
we keep the balance between production and protecting the environment?

There are new catalysts which are designed with the principles of Green Chemistry.

Metal Ions

1. How do the metal ions in the protein contribute to the catalytic functions of them?

Metal ions in metalloproteins and metalloenzymes have a lot of differerent functions, such as
participating in redox reactions (some metal ions have different oxidation states), and signal
transduction, etc.

2. Why are metal ions necessary in proteins in order to perform different functions?

Metal ions can exist stably as different oxidation states so that they can participate in different
electrochemical reactions. Besides, the coordination numbers of metal ions are generally larger than
or equal to 4, this means that they can act as a cross-linking agent for proteins.

3. Apart from metal ions linked with some ligand molecules, what are the direct and contributory
actions carried by metal ions?

Free metal ions are found in electrolytes and they are essential to life. For your interest, please visit
the following site for detailed information.

Link: http://www.science.uwaterloo.ca/~cchieh/cact/applychem/waterbio.html (Links to an external

site.)

Oxygen Carriers

1. Can we all describe those compounds which can combine oxygen and release oxygen freely as
oxygen carrier?

No, we can't. Oxygen carrier is defined as a system which contains a metal complex that can provide
a delicate balance required to bind with oxygen gas (O2 (g)) without the metal ion or the ligands
being irreversibly oxidized. Generally, the overall reaction can be expressed by the following
equation.

nM(L) + O2 <--> [M(L)]n(O2)

where n = 1 or 2, M = metal ion, L = ligand

2. What can be examples of oxygen carriers? Are there any oxygen carriers other than the heme group?

Please take a look at the chart below.

3. What are the oxygen carriers in plants?

There is a type of metalloprotein called leghemoglobin found in the nitrogen-fixing root nodules of
leguminous plants (basically pea family). In the seminar ("Metals in Biological Systems"), Prof. Lau
 explained about nitrogenase. Oxygen gas can destroy nitrogenase, so leguminous plants have
leghemoglobin in the root nodules to transport oxygen gas away from root nodules in order to avoid
damaging nitrogenase. For your further understanding on leghemoglobins, please visit the links
below.

Link: Leghemoglobin Part 1 (Chinese) (Links to an external site.)

Link: Leghemoglobin Part 2 (Chinese) (Links to an external site.)

4. How does oxygen gas bind to heme?

Please visit the link below for detailed explanation of the oxygen-binding mechanism.

Link: http://www.chm.bris.ac.uk/motm/hemoglobin/hemoglobh.htm (Links to an external site.)

5. As an oxygen carrier, which factors can affect haeme groups in blood for the oxygen affinity?

The oxygen binding affinity to heme in hemoglobin depends on the local pH, CO2 concentration and
organic phosphates such as diphosphoglycerate.

6. How can the structure of hemoglobins fulfill its role as an oxygen carrier?

There are two parts in hemoglobin: heme and globin.

Structure of heme
-Heme is situated at a hindered environment which is necessary for reversible oxygen binding.
-The fifth ligand of iron in heme is an amino acid residue called histidine and it is of steric
importance and reaction important because oxygen gas binds to the iron a lot more effectively than
carbon monoxide with the presence of heme.

Structure of globin
-It prevents the auto-oxidation of iron in heme.
-It also prevents the formation of bridging oxygen ligand between two hemes (heme-O-heme).
-It provides steric hindrance of oxygen binding.