Biological Connections

Studying biochemistry is a great way to realize what concepts you didn't necessarily understand while studying both biology, chemistry, and a little of organic chemistry. It seems to me that the information the other sciences left out (ie the chemical details of biological interactions) biochemistry picks up where they left off. I remember learning about amino acids in biology and how they form peptide chains in transcription/translation but I never understood how each individual amino acid interacted within the chain which would ultimately become a protein. To fully appreciate biochemistry, you must first understand biology. I remember after I had completely studied the process of protein synthesis, I was left with more questions than I had started with because there was much of the process I still hadn't learned yet. Now that I'm studying biochemistry, it's finally filling in some of the gaps for me.

Taking a closer look...

On PDB.org, I discovered a protein that is a integral part of our lives, Human Salivary Amylase (1SMD)

Function: Human Salivary Amylase, a type of alpha-amylase, is secreted in your salvia and is responsible for hydrolyzing alpha-bonds of large alpha linked polysaccharides such as starch. Eventually after chewing, the starch is broken down into polysaccharides composed of glucose and maltose.  It also plays a role in the colonization of bacteria that contribute to early dental plaque formation.

Salivary amylase works best in a neutral pH (5.6-6.9) at normal body temperature around 37° C. Surprisingly enough, Salivary amylase becomes inactive when is reaches the stomach by the acidic environment.

Biological Assembly Image for 1SMD 
HUMAN SALIVARY AMYLASE
http://www.rcsb.org/pdb/explore/explore.do?structureId=1smd 

Structure: Salivary alpha-amylase has 496 residues, one Ca+ ion, one Cl- ion, and 170 water molecules. This multidomain  protein has 3 domain (A,B, and C). Domain A contains 8 (beta/alpha) barrel structures whereas domain B has no definite secondary structures. Domain C has  Greek key-barrel structures made of beta-pleated sheets. The  placement of the calcium and chloride ions, as well as the residues, plays a role in the substrate-binding mechanism. Salivary amylase also has a suitable place for binding to tooth enamel surfaces where is can become a place of attachment for bacteria that live in the oral cavity.  For this reason, it is essential for people to brush their teeth regularly to prevent plaque buildup which can then leads to the formation of dental caries.

References/ Bibliography:

Ramasubbu N, Paloth V, Luo Y, Brayer GD, Levine MJ. (1996). Structure of human salivary alpha amylase at 1.6 A resolution: implications for its role in the oral cavity. Acta Crystallogr D Biol Crystallogr. 1996 May 1 ;52(Pt 3): 435-46. 

PubMed - http://www.ncbi.nlm.nih.gov/pubmed/15299664?dopt=Abstract

PDB.org - http://www.rcsb.org/pdb/explore/literature.do?structureId=1SMD

Science is Science, or is it?

If you are one of those people who are naturally curious, then you'll probably find yourself fascinated by science at one point in your life. Why wouldn't you be? The intricate mechanisms that make up our body resemble something of the imagination. For instance, every hour over 1 billion cells in the body regenerate - without us being conscious of it! Amazed yet? Below are some of the most important branches of science that have helped us come to understand how living organisms are able to function and survive.


Biology is an umbrella term for a lot of subjects, but in plain terms it is referred to the study of living organisms and the details that support their existence such as their (structure, function, growth, and reproduction etc.).  (http://en.wikipedia.org/wiki/Biology)

http://jamalifouru.com/education/biology.php

                             

There are many branches of biology including Molecular Biology. This subject mainly focuses on understanding the many communications that occur on a cellular level. This includes the interactions between DNA, RNA, and protein synthesis - how these processes are maintained, regulated and interrupted. (http://en.wikipedia.org/wiki/Molecular_biology)

http://yeon-park.blogspot.com/2010/04/who-discoverd-threacher-collins.html

Another branch made popular by the late Gregor Mendel in the mid-19th century, is the study of Genetics which describes the molecular makeup and function of genes and their role in cellular and organism development. Since every living organism has genes, we are able to study the patterns of inheritance from parent to offspring, the distribution and expression of gene(s), and how genetic material varies in populations over time. (http://en.wikipedia.org/wiki/Genetics)

 http://www.glennys.com/blog/parents-diet/                                                   

Living things are all made up of the same matter and molecules. The study of Biology would not be complete without knowing about chemistry and its integral role in the study of living organisms. Chemistry is the study of matter, more specifically, the composition, structure, and properties of chemicals and their reactions. These reactions involve atoms on the periodic table of elements and the different bonds that can be formed between atoms. (http://en.wikipedia.org/wiki/Chemistry)

http://www.lahc.edu/classes/chemistry/index.html

Finally, after talking about both biology and chemistry, we get to what this blog is truly about: Biochemistry!

Biochemistry is what governs all organisms and living processes. It describes the structures and functions of all basic cellular organic compounds (proteins, carbohydrates, lipids, and nucleic acids). Mainly it focuses on the metabolic and enzyme-catalyzed processes of these organic compounds and how they contribute to a living organisms physiology. (http://en.wikipedia.org/wiki/Biochemistry)