the fun side of biochemistry

PROUD BIOCHEMIST

HI. I am SAVITA and proud to be studying Biochemistry at the University of the West Indies. I am a science enthusiast and this blog helps me share vital science information to the world. Philosophy is the science which considers truth. --Aristotle Scientists have become the bearers of the torch of discovery in our quest for knowledge.--Hawking

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Facts are the a…

Facts are the air of scientists. Without them you can never fly.– Linus Pauling

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ANOTHER REVIEW PAPER- ANTI FREEZE PROTEINS

Another review paper: Structure and function of antifreeze proteins. You can read the full article at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1692999/pdf/12171656.pdf.

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: http://www.rcsb.org/pdb/education_discussion/molecule_of_the_month/download/Antifreeze-Prot.pdf

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. 

Video

Video Review

Linus Pauling was introduced to the subject of vitamin C by biochemist Irwin Stone in 1966. Five years later, he would pen “Vitamin C and the Common Cold,” and then boldly go on to champion vitamin C as a fighter of more serious diseases such as cancer.
According to Pauling, the vitamin’s versatility in illness prevention arises from its role in the manufacture of collagen, the protein that gives shape to connective tissues and strength to skin and blood vessels.
Pauling discusses vitamin C’s connection with lipoprotein-a, a substance whose levels in the blood have been linked to cardiovascular disease. Lipoprotein-a is also a major component of the plaques found in the blood vessels of atherosclerosis patients.
He has published studies asserting that lipoprotein-a is a surrogate for vitamin C, serving to strengthen blood vessel walls in the absence of adequate amounts of the vitamin in the diet.
Pauling is convinced that doses of vitamin C can help prevent the onset of cardiovascular disease, inhibiting the formation of disease-promoting lesions on blood vessel walls and perhaps decreasing the production of lipoprotein-a in the blood. Vitamin C’s link to healthy blood vessels, Pauling said, is further supported by studies of scurvy, the disease caused by vitamin C deficiency. Fifty percent of patients who die of scurvy, he said, do so because of ruptured blood vessels.

You can also look at these videos:

http://www.youtube.com/watch?v=cYHHKJBRUxw

Video

ALPHA HELIX

Who know about this awesome man, Linus Pauling..
http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1954/pauling-bio.html

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CARBOHYDRATES WORDLE

CARBOHYDRATES WORDLE

Nucleotides and Nucleic Acids

Here are some brief points on Nucleotides and Nucleic Acids

NUCLEIC ACIDS

Functions of nucleic acids are:

  • Informational biomolecules – DNA, RNA

–       Function as polymers in the storage and transmission (expression) of the genetic information. (giant molecules)

  • Electron carriers – NAD+, FAD
  • Carriers of high energy intermediates

–       UMP, CMP, GTP

  • Energy currency of the cell – ATP
  • Signaling molecules – cAMP, AMP, etc

The monomeric units of a nucleotide polymer contain 3 components:

  1. 1.    A nitrogenous heterocyclic base, either:
  • Pyrimidine
  • Purine
  1. 2.    A pentose sugar which is either:
  • Ribose (furanose form)
  • 2-deoxy-ribose (furanose form)
  1. 3.    A phosphoric acid group in ester linkage at C-5 of the pentose
  • The phosphoester bond

Double Helical DNA:

  • 2 complementary anti-parallel strands – right-hand coil along a common axis
  • Held together by H-bonds – A-T & G-C
  • Bases on the interior – planes are perpendicular to helix axis
  • Sugar and P-groups on the outside, exposed to H2O
  • Sugar rings almost at right angles to the planes of the bases

Nitrogenous bases:

  • DNA – adenine, guanine, cytosine, thymine

–       A, G, C, T

  • RNA –  adenine, guanine, cytosine, uracil

–       A, G, C, U

  • A and G – purines

–       Purines are bicyclic fused rings of a pyrimidine & a 5-membered imidazole

  • U, T, C  – pyrimidines

–       6-membered ring

Chargaff’s Rules

  • Analysis of DNA from most species –

–       4 bases are not equal

–       Base composition varies between species

  • But, different tissues of the same species

–       Same base comp.

  • And always: A = T and G = C

–       sum of purines = sum of pyrimidines

  • Related species, similar base composition

 

NUCLEOTIDES

  •   nucleotides are the building blocks for DNA and RNA
  •   nucleotides are carriers for activated intermediates
  •   nucleotides are structural components of coenzyme A, FAD, NAD+, and NADP+
  •   defects in nucleotide metabolism are associated with several common and rare human disorders
  •   several drugs used to treat cancer and bacterial infections function at the level of nucleotide metabolism
  • Nucleotides are composed of a nitrogenous base, a pentose monosaccharide, and 1, 2, or 3 phosphate groups.
  • The nitrogenous bases are derived from 2 families called purines and pyrimidines.

There are 5 common bases found in DNA and RNA:

  •   Purines Adenine and Guanine common to both DNA and RNA
  •   Pyrimidines Thymine and Cytosine are found in DNA
  •   Pyrimidines Cytosine and Uracil are found in RNA

Nucleosides

  • Addition of a pentose sugar to the base produces a nucleoside. Base + ribose = nucleoside
  • Addition of a ribose sugar to the bases A, G, C, T, and U produces adenosine, guanosine, cytidine, thymidine, and uridine, respectively.
    •   If the pentose sugar is a deoxyribose, then a deoxyribonucleoside is produced.

Nucleotides

  • Addition of either 1, 2, or 3 phosphate groups to a nucleoside produces a nucleoside.  Monophosphate, nucleoside diphosphate, or a nucleoside triphosphate, respectively.  Base + sugar + phosphate = nucleotide.  
  • The phosphate groups are responsible for the negative charges associated with RNA and DNA.
Video

IRON DEFICIENCY ANEMIA

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.