Chapter 3: Hunky-Dory Proteins and Nucleic Acids!

This blog will be based off of the virtual lectures on proteins and nucleic acids.

Proteins
Proteins are quintessential in our survival. They have so many functions in a cell, and thus in our lives. Proteins are used for support, as enzymes (speeding up biological reactions), membrane transport, and producing cellular movements. Amazingly, proteins functions don't stop there! Proteins are also regulators, receptors, hormones, antibodies, venom and toxins, and for storage. Proteins do so many things that allow us to live.

Proteins are able to do so many things because they are built differently. The structure of a protein determines its function. There are four levels of protein structure. These four structures are the primary structure, secondary structure, tertiary structure, and quaternary structure.

Primary Structure: The primary structure of a protein is the sequence of amino acids that characterizes a specific protein. The amino acids are joined together by dehydration synthesis. The bonds are commonly referred to as peptide bonds. There are about 20 amino acids. The sequence of these amino acids in a polypeptide is what determines its function. Of these amino acids some are acidic, some are basic, some are polar, and some are non polar.

Secondary Structure: The secondary structure occurs when amino acids interact with one another. They bend/twist and form hydrogen bonds with one another. Certain secondary structure have distinctive shapes and have been named alpha-helix and beta-strands. Secondary structures are stabilized by the presence of hydrogen bonds.
Tertiary Structure: The tertiary structure is the overall three-dimensional shape of a protein. As each secondary structure takes hold, the protein takes a globular shape. In an aqueous (polar) environment, the folding into a compact, globular structure would be to "hide" the hydrophobic amino acids by putting them in the interior, and exposing the hydrophilic heads to the exterior aqueous environment. In the tertiary structure, the R-groups are what stabilize the structure. Proteins can denature, or lose their structure and function. Proteins are function when folded, so when they are denatured, they become unfolded and inactive. Denaturation can be caused by an increase in heat, change in pH levels, and/or the addition of salt.
Quaternary Structure: Quaternary structures occurs when two or more proteins join together. This forms a larger, more complex protein.
Proteins exist all throughout our cells and bodies. Their many structures and functions keep us going and alive everyday.

Nucleic Acids

Nucleic acids are long polymers of nucleotide building blocks. The two types of nucleic acids are DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid). DNA stores our hereditary information, which includes all of the information for our cells to function properly. RNA is used in various forms to assemble proteins. Nucleotides are made up of a five-carbon sugar, a nitrogenous base, and three phosphate groups. In a DNA nucleotide, the 2' carbon only has Hydrogen (Hence the deoxy), while RNA has a hydroxyl (hydrogen and oxygen) at it's 2' carbon.
A nucleoside only consists of the sugar and nitrogen base. A nucleoside with one phosphate group is referred to as  nucleoside monophosphate. It is referred to as a nucleoside diphosphate and nucleoside triphosphate with 2 and 3  phosphates, respectively.

There are 4 nucleotides used to construct DNA  and 4 nucleotides used to construct RNA. DNA consists of the nucleotides adenine (A), thymine (T), cytosine (C), and guanine (G). RNA consists of the nucleotides adenine (A), uracil (U), cytosine (C), and guanine (G). What varies in nucleotides is the nitrogenous base. The two categories of nucleotides are pyrimidines and purines. Pyrimidines only have one ring and purines have two rings.

The double-helical structure in DNA is caused by the formation of hydrogen bonds. Phosphodiester bonds are covalent bonds found specifically in nucleic acids. The phosphodiester bonds are what link the two, antiparallel strands together. One nucleotide is linked to the next nucleotide by dehydration synthesis. In DNA, A links with T, and C links with G. In RNA, A links with U, and C links with G. DNA has opposite ends. One end is 5' and the other is 3', based off of which sugar is on what end. As previously stated, DNA is antiparallel.  This is because one strand runs in the 5' to 3' direction, while the other runs in the 3' to 5' direction. 
There are major differences between RNA and DNA. RNA is usually found in one strand rather than in a double-helix like DNA, and has a ribose sugar rather than a deoxyribose sugar. In RNA, uracil replaces thymine, which is found in DNA. Lastly, RNA is synthesized from a DNA template.


Helpful Hints!

Alright so this video is a song about DNA set to the tune of (You Drive Me) Crazy by Britney Spears. The only downside is you can't hear anyone singing, but the lyrics are there for you to follow. I guess it's like a karaoke thing... I wasn't going to include it as a helpful hint, but the lyrics actually fit into the song and make you memorize some DNA facts in fun, creative ways!

This video is extremely informative. The structure of DNA is explained in detail, yet is still understandable. The DNA is examined all the way down to atomic level, but it does not over-complicate the subject. If one had a few questions/uncertainties about DNA, or wanted a quick refresher, this would be a great video to watch!

Article

This article, talks about how there's increasing evidence showing that cancer cells. acquire "stem-like" epigenetic and signaling characteristics during the tumorigenic process. This includes global DNA hypo-methylation, gene-specific DNA hyper-methylation, and small RNA deregulation. In both stem cells and in differentiated cells, RNA has been shown to be an epigenentic regulator. Piwi-interacting RNAs (piRNAs), maintains genome integrity by epigenetically silencing transposons by DNA methylation. The human Piwi ortholog (a protein), Hiwi, has been found to be expressed in many human cancers. Unfortunately, there has not been much investigation about the role Piwi and piRNAs might play in contributing to the "stem-like" epigenetic state of a cancer.