the fun side of biochemistry

Posts tagged “biochemistry


Another review paper: Structure and function of antifreeze proteins. You can read the full article at

Have you ever wondered why some insects, mammals and fishes do not freeze and die. 

Anti freeze proteins can be defined as proteins that have an affinity for ice. Ice is a big problem for organisms that live in cold climates. Once the temperature dips below freezing, ice crystals steadily grow and burst cells. Organisms, plants, animals, fungi and bacteria, have developed ways to combat the deadly growth of ice crystals. In some cases, they pack their cells with small antifreeze compounds like sugars or glycerol. But in cases where extra help is needed, cells make specialized antifreeze proteins to protect themselves as the temperature drops.

AFPs absorb to ice and restrict the growth of the ice front to the regions between the absorbed protein molecules. This region now grow with a curvature making it thermodynamically unfavourable for water molecules to add to the lattice.  In other words, antifreeze proteins bind to ice crystals, blocking the surface and preventing growth of the crystal.  For each of these structures, the ice-binding site of the AFP has been defined by site-directed mutagenesis, and ice etching has indicated that the ice surface is bound by the AFP.

In the crystal structure, the ice-binding surface of the protein is covered with strings of water molecules. The binding sites are also somewhat hydrophobic more so than that the portion of the protein is exposed to the solvent. Surface-surface complementarily appears to be the key to tight binding in which the contribution of hydrogen bonding seems to be secondary to van der Waals contacts. These water molecules are spaced similarly to the water molecules in ice crystals. Where AFPs are available, the ice crystals remain the same size for hours, even up to days at temperatures between the melting point and the lower non-equilibrium freezing point.


For extra reading on this rather “cool” topic:

Nice Ice- Antifreeze proteins don’t stop the growth of ice crystals. They actually limit the growth to manageable sizes. Antifreeze proteins counteract thre-crystallization effect and binds to the surface of the small ice crystals and slow or prevent the growth into larger dangerous crystals.

Supercooling- Antifreeze proteins lower the freezing point of water by a few degrees without changing the melting point. The most effective antifreeze proteins are made by insects, which lower the freezing point by about 6 degrees.

Icy Ice Cream- Antifreeze proteins have been useful in industry. For instance, natural antifreeze proteins have been used as a preservative in ice cream. They coat the fine ice crystals that give ice cream its smooth texture, and prevent it from recrystallizing during storage and delivery into chunky, icy ice cream.



So next time you are eating your delicious, heavenly, luscious, mellow, heart satisfying ice cream remember the anti freeze proteins. 



This video review is on Iron deficiency anaemia. Many people suffer from this, but are unaware of it. I was recently diagnosed with iron deficiency anaemia and this is the reason for me choosing this topic.

Iron-deficiency anaemia is a common type of anaemia. The term “anaemia” usually refers to a condition in which your blood has a lower than normal number of red blood cells. Anaemia also can occur if your red blood cells don’t contain enough haemoglobin. Haemoglobin is an iron-rich protein that carries oxygen from the lungs to the rest of the body.

• Haemoglobin count suppose to be within the range 14- 17 grams per decilitre in males and 12-15 grams per decilitre in females.

• Low iron levels usually are due to blood loss, poor diet, or an inability to absorb enough iron from the foods you eat.

• Iron-deficiency anaemia usually develops over time if your body doesn’t have enough iron to build healthy red blood cells. Without enough iron, your body starts using the iron it has stored. After the stored iron is gone, your body makes fewer red blood cells. The red blood cells it does make have less haemoglobin than normal. Haemoglobin is a protein that helps carry oxygen to your body.

• Infants and young children and women are the two groups at highest risk for iron-deficiency anaemia.

• The signs and symptoms of iron-deficiency anaemia depend on its severity. Mild to moderate iron-deficiency anaemia may have no signs or symptoms. Many of the signs and symptoms of iron-deficiency anaemia, such as fatigue (tiredness), apply to all types of anaemia.

• Treatment for iron-deficiency anaemia include dietary changes and supplements, medicines, and surgery.

• Eating a well-balanced diet that includes iron-rich foods may help prevent iron-deficiency anaemia. Taking iron supplements also may lower your risk for the condition if you’re not able to get enough iron from food. Large amounts of iron can be harmful.

• If you have iron-deficiency anaemia, see your doctor regularly, take iron supplements only as your doctor prescribes, and tell your doctor if you have any new symptoms or if your symptoms get worse.



My publish paper review is based on Systemic Lupus Erythematous. You can feel free to read this article at

Systemic Lupus Erythematous is a chronic auto immune inflammatory disease that has protean manifestations and follows a relapsing and remitting course.. This affects more woman than men and is considered one of the most dramatic, frightening and lonely terminal diseases. Lupus is neither infectious nor contagious but sadly there is no cure. It is characterized by an autoantibody response to nuclear and cytoplasmic antigens.  This disease causes pain and swelling. It can affect the skin, ,joints, ,kidneys, lungs, nervous system and other organs of the body. Lupus flares vary from mild to serious.

The immune system in the body’s defense system. When healthy, it protects the body by making antibodies that attack germs and cancers. With lupus, the immune system misfires. Instead of providing protective antibodies, an autoimmune disease begins and makes “autoantibodies,” which attack the patient’s own tissues. As the attack goes on, other immune cells join the fight. This then leads to inflammation and abnormal blood vessels. These antibodies then end up in cells in organs, where they damage those tissues. People with lupus may also have an impaired process for clearing old and damaged cells from the body, which causes an abnormal immune response.

The  specific cause of SLE is unknown but multiple factors are associated with the development of the disease, including genetic, epigenetic, ethnic, immunoregulatory, hormonal, and environmental factors.

T cells play a central role in SLE pathogenesis, and T cells from patients with lupus show defects in both signaling and effector function. These T cells secrete less interleukin (IL)-2, and one defect in signaling seems to be linked to an increase in calcium influx. The following seem to be adversely affected in T cells from patients with SLE: effector activity such as CD8 cytotoxicity; T-regulatory, B-cell help; migration; and adhesion. However, the method by which each of these deficits contributes to the exact clinical syndrome seen in an individual patient is still unknown.

Immune complexes form in the microvasculature, leading to complement activation and inflammation. furthermore, antibody-antigen complexes deposit on the basement membranes of skin and kidneys. In active SLE, this process has been confirmed by demonstration of complexes of nuclear antigens such as DNA, immunoglobulins, and complement proteins at these sites. Autoantibodies have been found to be biomarkers for future neuropsychiatric events in SLE. Serum antinuclear antibodies (ANAs) are found in nearly all individuals with active SLE. Antibodies to native double-stranded DNA are relatively specific for the diagnosis of SLE.

Lupus affects most people in their 20s and 30s. it occurs more often in women than men. This disease is more common in some ethnic groups, mainly blacks and Asians, and tends to be worst in these groups. There are certain countries in which the disease appears to be more prevalent, for instance the Caribbean, the far east, and China. Ultraviolet light stimulates keratinocytes, which leads not only to overexpression of nuclear ribonucleoproteins (snRNPs) on their cell surfaces but also to the secretion of cytokines that simulate increased autoantibody production. Photosensitivity is clearly a precipitant of skin disease. Silica dust and cigarette smoking may increase the risk of developing SLE. Administration of estrogen to postmenopausal women appears to increase the risk of developing SLE. Estrogen can raise the risk of blood clots. Breastfeeding is associated with a decreased risk of developing SLE.

Lupus has many symptoms. Some common ones are

  • Joint pain or swelling
  • Muscle pain
  • Fever with no known cause
  • Fatigue
  • Red rashes, often on the face (also called the “butterfly rash”)
  • Anaemia
  • Kidney involvement
  • Hair loss
  • Seizures
  • Abnormal blood clotting
  • Arthritis



Enzyme inhibitors are molecules which binds to the enzyme to decrease their activity. These can either be reversible or irreversible. The set we will look at today is the reversible inhibitors. reversible inhibitors binds to enzymes with non-covalent bonds such as hydrogen bonds, hydrophobic interactions and ionic bonds. Reversible inhibitors generally do not undergo chemical reactions when bound to the enzyme and can be easily removed by dilution or dialysis.


  Competitive inhibition Non-competitive inhibition Un-competitive inhibition Mixed inhibition
Does the inhibitor resemble the substrate? Yes- have similar shape to substrate No similarity in shape to substrate No No
Where does the inhibitor bind? • Inhibitor binds to Enzyme, not to ES• Substrate and inhibitor compete for the active site  • Inhibitor binds either to ES or to Enzyme and ES• Substrate and Inhibitor bind at different sites and the active site is unaffected by Inhibitor • I binds only to ES at a different site from the substrate active site • Binds at separate site from the substrate active site, to free enzyme or ES
What is the effect on Vmax  and Km? Vmax  unchanged and Kincreases. Vmax  reduced and Km unchanged Vmax  and Km are both reduced by same amount Vmax  reduced and Km may be increased or decreased
Line Weaver Burk plots  Image  Image  Image Image

Enzyme Nomenclature

There are six major classes in naming enzymes developed by the IUBMB.



  • Oxidation/reduction reactions
  • Transfer of electrons (H) is involved
  • Coenzymes are usually required
  • Also called dehydrogenases


  • Transfer of a functional group from a donor to acceptor molecule
  • Groups transferred – contain C, N, P
  • Examples – phosphotranferases, methyl-transferases
  • Kinases – transfer phosphate from ATP


  • Hydrolytic reactions
  • Cleavage of bonds by addition of H2O
  • Bonds – C-C; C-O; C-N; P-O
  • Acid anhydride bonds are also cleaved


  • Elimination reaction that splits one molecule into two without an additional acceptor.
  • Cleavage of C-C, C-S, and certain C-N bonds
  • Does not involve H2O (may be a product)
  • Addition of groups to double bonds


  • Conversion of one isomer to another
  • Geometric or structural changes within a molecule
  • Intramolecular rearrangement
  • Example- shift of a double bond- aldose to ketose


  • Joining of molecules
  • Bond formation- coupled to hydrolysis of a high-energy compound
  • ATP or other nucleoside tri-P involved
  • Bond formation –usually between C, O, S, N


Enzyme basics

Digestive enzymes