The DNA double helix-a story of 2 perfectly paired strands

Today was my niece's wedding day! They had a lovely Catholic church service followed by a delightful lunch reception. Weddings tend to leave a lingering sweet, warm feeling to all who witness the joyful union of 2 becoming 1.

Some couples have very similar characters and interests, yet others attract total opposites from themselves! As for DNA found in our cells...this is a story of the perfect complement. Each of the 2 strands comprising the DNA double helix were "made for each other"! Let me explain...

DNA - deoxyribonucleic acid, is made up of of 2 strands of polynucleotides. Each strand of polynucleotide is a polymer of monomer units called - nucleotides. Each nucleotide comprises 3 components - a phosphate group, a sugar group and a nitrogenous base.

Nucleotides join to make a single strand of polynucleotide via phosphodiester bonds between alternating phosphate and sugar groups. We call this the "sugar-phosphate backbone" of a single strand of polynucleotide.

Now, this is where the love story begins...How do 2 polynucleotide strands come together to become 1 DNA macromolecule? They do so through their complementary base pairing between their nitrogenous bases. There are 4 different nitrogenous bases - Adenine (A), Thymine (T), Cytosine (C) and Guanine (G). These display specific base pairing where "A" will always pair up with "T" and "C" will always pair up with "G". Hence, when there is an "A" on 1 polynucleotide strand, this will pair up with "T" on the opposite polynucleotide strand. Similarly, when there is a "C" on 1 polynucleotide strand, this will pair up with "G" on the opposite polynucleotide strand. It is via this complementary base pairing that 2 polynucleotide strands come together to make 1 DNA macromolecule. What wedded bliss!

Merry Christmas !!!

Here's a video of a group of Genetics Students singing Christmas carols with a DNA "twist"!
Have a funfilled, Merry Christmas :)

What the heck are macromolecules anyway?

My son's lego creation (as seen in this post) was built from individual Lego blocks. Similarly, our bodies are built from individual units called "cells". There is a big difference though - as Lego blocks are non-living objects whereas our cells are alive! Infact, a cell is the smallest unit of life!

What differentiates a living cell and a non-living Lego block? Well, all living things are capable of the following:
- acquire & utilize energy
- reproduce
- respond to the environment
- carry out controlled chemical reactions
- maintain homeostasis

What then can I say is the function of a Lego block? Perhaps, the following:
- It should be a non-toxic and safe toy
- It should be moulded into precise shapes for the precise connection to other blocks.
- It should be sturdy and durable

A Lego block's functional requirements are relatively simple. As such, its chemical composition that goes into making a Lego block should be relatively simple. My guess is that the Lego block would be made up of a durable, non-toxic type of plastic chemical.

In contrast, the living cell's functional requirements are very complex. Hence, the chemical composition that goes into making up a cell must be complex. Basically, our cells and its components therein are made up of 4 main classes of complex chemical structures. These chemical structures are what biochemists refer to as "macromolecules".

Macromolecules are called as such because they are relatively large, complex molecules made up from smaller chemical units. For details about the chemistry of macromolecules, please refer to the following link - http://oh.essortment.com/whataremacromo_rcpy.htm.

Just like the structure of a durable, non-toxic, plastic chemical would fulfill the function of a simple Lego block; the structures of macromolecules fulfill their respective functions in the cell to sustain life! So, let me briefly run through a few key structure-function relationships of the 4 main macromolecules in our cells.

1) Carbohydrates
From my earlier post about "why we have to eat", you would have read that our main energy source is from carbohydrates. Small carbohydrate units, like glucose, have polar chemical structures which render them soluble. This makes glucose easily accesible by our cells to be broken down by catabolism. As glucose is catabolised, energy is released. Our cells utilise this energy to drive essential biochemical reactions.

2) Lipids
Lipids are a secondary energy source. More importantly, phospholipids (a type of lipid), are a major component of cell membranes - the protective "envelope" that surrounds cells.

The structure of phospholipids comprise a hydrophilic (water-attracting) head and a hydrophobic (water-repelling) tail. As a result of these chemical properties, phospholipids tend to adopt a "bilayer" conformation where the hydrophilic heads are in contact with water, and hydrophobic tails are hidden away from water. This phospholipid "bilayer" is functionally important in cell membranes.
3) Proteins

Proteins form all the "working" structures of our cells. This class of macromolecules have many, diverse functions. These range from enzymes which drive chemical reactions; to ion channels in our cell membranes that control what goes in and out of cells; to structural components like the cytoskeleton which gives cells their shape. Hence, proteins must be able to adopt many different structures to suit their many, diverse functions.

Nature has enabled proteins to fulfill their roles by designing 22 different building blocks which can go into making up a protein molecule. These protein building blocks are called "amino acids". There exist about 22 amino acids, all with different biochemical properties which Nature can "pick and mix" together to make a particular protein. Thus, Nature can "customise" a specific protein structure to a correspondingly specific biological function!

4) Nucleic acids

This class of macromolecules include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). In contrast to proteins, nucleic acids have only 1 primary function. That is to store information. One may think of nucleic acids as the macromolecule that functions as an "instruction manual" for the cell.

All cells must be able to "read" this "instruction maual". Therefore, the structure of nucleic acids is very uniform in all cells. As most of you would know, DNA has the famous "double helix" structure. The instructions encoded in a DNA molecule comprise of just 4 letters - "A", "T", "C" and "G". In RNA, these are "A", "U", "C" and "G".

In my next post, I will talk more about DNA and how we "read" the "instructions" encoded in this macromolecule.

As for now...I hope you have come to understand what the heck are macromolecules and why the heck they are in our cells!

Let's start from the very beginning...

Going easy today. Hope you enjoy this "old school" movie video of one of the best loved songs ever! I remember going to see this movie when I was a kid and loving every moment of it. A true classic!

Why have I put this in my blog today? Well, my dearest girlfriend, who is science illiterate, has been so nice as to try to read through my last 2 posts. But, still she remains clueless!

For this dear friend and all who are still clueless about my writings, I shall "start from the very beginning because that's a very good place to start. When you read, you begin with A B C, when you sing, you begin with Do Re Mi" and when you learn biochemistry, you begin with carbohydrates,lipids,proteins and nucleic acids - the 4 major macromolecules of life.

I believe anyone and everyone can understand science. You just have to grasp the basic "notes" and then you'll be able to "sing a song". And it is for this reason that I have created this blog!

So! Look out for my next post where I will explain "What the heck are macromolecules anyway?". See ya!

Why we have to eat?

Some people live to eat but we ALL eat to live.

We may sit down to a simple meal or a lavish feast. We may find ourselves...in an office cubicle...eating a packed lunch all alone. Or dolling ourselves up for a fancy dinner gathering (as in the photo of myself in this post!). In Singapore, where everyone is leading such fast paced, "instant" lives, sitting down together, as a family, for a home-cooked meal is becoming a rarity! So sad but true.

In which ever way we may get our "daily bread", we all eat. We eat everyday. We do it so routinely that has anyone of you ever paused to think "Why do I actually have to eat?".

Now comes the science bit...
Food contain different nutrients that help our bodies in different ways.

Basically, there are 2 ways in which food is utilised by our bodies.
1) To provide energy to fuel our bodily processes.
2) To provide building blocks for growth, maintenance and repair of our bodily structures.

But before even getting to the above 2 points, food must first be digested. During digestion, food is broken down into its constituent parts. Then, by "absorption", these simpler digested food units are able to cross the intestinal wall into the blood stream, where they get distributed all around the body.

In order for the body to utilise these simple food units, various biochemical reactions occur to further breakdown these simple food units into essential molecules which the body can use. Collectively, these biochemical reactions that serve to breakdown food units are called "catabolism".

As I mentioned earlier, food contain different nutrients which help our bodies in different ways. Broadly speaking, these food nutrients can be divided into the 4 major macromolecules found in our bodies. These are lipids (which we covered yesterday), carbohydrates, proteins and to a lesser extent, nucleic acids. The latter 3 macromolecules, I will hope to touch on in the days to come (so keep checking back for new posts!).

Now, back to the 2 ways by which our body utilises the nutrients found in food.

1)To provide energy to fuel our bodily processes.

Carbohydrates are our bodies' main source of energy. Carbohydrates, like rice and potato, undergo catabolism to yield glucose molecules. These are the essential starting molecules (in biochemistry we call "substrates") for the energy generating reactions of cellular respiration (again another topic for a future post in this blog).

Lipids can also be used to generate energy. However, they are a secondary source of energy to that of carbohydrates.

Of last resort, would be to utilise proteins for energy. As you will read below, proteins are used for building structures in our body (like muscle, skin, hair and nails). So, when the body has to rely on using protein for energy, it will be under the circumstance of malnutrition!

2) To provide building blocks for the growth, maintenance and repair of our bodily structures.

As mentioned above, protein is the main source of nutrient from food for building our bodily structures. Protein is found in cheese, eggs, meat, poultry, fish and nuts.

As with carbohydrates, protein from our food must undergo catabolism. Protein molecules are catabolised into it's constituent "amino acid" molecules. These amino acids are like building blocks of the protein. So, basically, what the body does is to disassemble these amino acids from the protein from food, then reassemble these amino acids into other type of protein molecules required by the body. The biochemical reactions which are carried out to build up such new molecules are collectively termed "anabolism".

To sum up why we have to eat - we eat to sustain metabolism.

All of you must have heard of the term metabolism. Some people, like myself, thank our high metabolic rate for keeping our weight in check. Yet, others blame a low metabolic rate for their weight problems. What really is metabolism? It is how our body biochemically processes and uses energy and nutrients from food for daily functioning. From the above paragraphs, you should be able to make out that metabolism consists of catabolism (the breakdown of food to yield essential molecules and energy), as well as anabolism (the build up of new molecules for use in the body).

So, from asking a simple question of "why we have to eat?", I hope you have come to understand a fundamental biochemistry concept:

Concept #1

Metabolism = Catabolism + Anabolism

Understanding Cholesterol (Heart Basics #5)

FINALLY !!! Learnt how to embed a YouTube video onto my blog. So...THIS is the video I was trying to embed onto yesterday's post "R good fats, bad fats just a fad?". Hopefully, after reading yesterday's post you will be able to make total sense of this video :) Not only that...with the graphics in this video, I hope you'll be able to grasp what I had written about fats even better!

R good fats, bad fats just a fad?

Was sitting down to breakfast from a "certain fast food chain" when this idea about good fats and bad fats struck. Singaporeans love to eat and what better way to kick start this blog than with food!

Even my 6 year old son has become health conscious from the adverts he sees on TV. He tells me - we can still eat from this "certain fast food chain" because if you order the stuff with a "red pea" it is healthy. So why all this campaigning to consumers to convince us that fast food is healthy? Also, have you noticed that the latest buzz word with food operations is that their food contain "no trans fats"? So...are good fats and bad fats just a fad?

Two starting points to answer this question:
1) What are fats?
2) Why are fats bad for health?

1) What are fats?
Fats come under a group of biochemical macromolecules called "lipids". Where lipids are a large and diverse group of molecules characterised by their insolubility in water. Other lipid molecules include steroids, of which, cholesterol and sex hormones are well known compounds. So, fats and cholesterol are not the same compound but they are both lipids. Infact, the scientific name for fats is "triglycerides".

Our bodies utilise lipids for various functions such as energy, as components of our cells, to protect our nerves and many more. How are these lipids transported to the sites where it is needed by our bodies? It has to be transported via the blood stream. But remember...lipids are insoluble in water and our blood is aqueous in nature. So, how are lipids transported in the blood? The answer is using specialised lipid packing molecules called "lipoproteins". These are the LDL and HDL molecules that you so often hear about when one goes for a cholesterol test.

Low Density Lipoproteins (LDL) are considered "bad cholesterol". Actually, they aren't strictly speaking cholesterol molecules but cholesterol PACKING molecules. LDL is considered bad because these molecules circulate in the blood stream and having too much of these could result in lipids being deposited in one's arteries (more about this later).

High Density Lipoproteins (HDL) are considered "good cholesterol". Again, these aren't strictly speaking cholesterol molecules but cholesterol PACKING molecules. HDL differs from LDL in its function. HDL transports lipids away from the body to the liver for excretion. In other words, HDL removes any potentially damaging lipids from the body and, thus, is "good".

So why am I going on about LDL and HDL molecules? This is because these molecules hold the answer to my second question.

2) Why are fats bad for health?
Everyone has heard this - watch your diet if you do not want heart disease. What is the scientific basis for this saying?

As mentioned above, too much LDL circulating in the blood stream could result in lipids being deposited onto arteries (blood vessels). The consequence of this, is that the arteries become increasingly narrow and eventually totally blocked - a condition known as "artherosclerosis". When this occurs, no blood will be able to flow through the blocked artery which then leads to strokes and heart attacks.

For good health, a person needs to maintain high levels of HDL (to remove potentially damaging lipids) and low levels of LDL (to minimize the amount of circulating lipids in the body).

Fats become damaging when they alter this HDL/LDL profile in the body. Trans fats are especially damaging because they raise levels of bad LDL and lower levels of good HDL! It has been suggested that this negative effect may be so because trans fats are not naturally occurring and hence the body has not been designed to metabolise these type of fats. Trans fats are produced by heating liquid vegetable oils in the presence of hydrogen. This occurs during food processing as with potato chip snacks, french fries and onion rings, just to name a few. The findings of the effects of trans fats in the 1990s have been so pertinant to health that as of January 1, 2006, trans fats must be listed on food labels in the US.

For more about the effects of consuming different types of fats please refer to the following link:
http://www.hsph.harvard.edu/nutritionsource/fats.html

In closing, until some other scientific finding proves otherwise, it is not so much the amount of fat we eat but the type of fat we eat. To this end, good fats and bad fats are not just a fad but a fact (well, at least for now)!

Tried to embed this but couldn't. Do check out this YouTube video about "Understanding Cholesterol".
http://www.youtube.com/watch?v=hjv5OnbcjE8

Festive endings and new beginnings.

The festive year end is here and everyone is scurrying to get their Christmas shopping done. Have you tried driving into Orchard Road?! I haven't quite got round to doing my shopping yet but have put up our Christmas tree (as seen here in this post).
This is usually my favourite time of the year. Somehow though...amidst all the hustle and bustle...I'm sitting here with quiet anticipation...excited about new beginnings.
Next week, will be the start of a new school term and the start of a whole new series of lectures - Molecular and Cell Biology. But what I'm all excited about is this new blog! I hope all of you out there - students, friends, family and those "clueless about DNA" will enjoy my musings as I share my thoughts and views in the days, weeks, months and years (?!) ahead.