Chapter 3: The Chemical Basis of Life (Macromolecules)

Valine

Alanine

Proteins

There are different types of proteins with various functions. These include (but are not limited to!): motility, receptor, membrane transport, enzyme, and catalyst proteins.
Amino acids are held together by peptide bonds caused by dehydration reactions. Amino acids can be polar, nonpolar, acidic, or basic. For example, glycine and proline are non polar, and glutamate is acidic. The structure of protein determines its function
There are four levels of proteins structure:
Primary Structure: This is the sequence of amino acids. Protein does not stay in a linear state due to the combination of hydrophobic and hydrophilic amino acids it contains, as the hydrophilic ones are "happy" by water while the hydrophobic ones are not. So, hydrophobic ones are protected while hydrophilic ones are exposed.
Secondary Structure: Amino acids interact with neighboring amino acids, forming hydrogen bonds, to bend and twist the protein chain. Some have distinctive shapes, causing them to be named (alpha helix or beta strand). The shape is stabilized by hydrogen bonds using "local folding" as specific parts of the chain can fold.

Alpha Helix

Beta Strand

Tertiary Structure: This is the overall three-dimensional shape of the protein. Non-polar (hydrophobic) parts are on the inside and polar (hydrophobic) on the outside. Ionic bonds (such as between acids and bases) as well as hydrogen bonds help to stabilize. R-groups are what determine stability.
All proteins exhibit primary, secondary, and tertiary structure. Folded proteins are functional but they can denature and become inactive or unfolded. Denaturation can occur due to an increase, in heat, pH, or salt levels.
Quaternary Structure: This is when two or more proteins chains join together in a complex protein. This level of strucutre may or may not be present in a protein.
Proteins often have non-protein components, such as the heme group in hemoglobin. This group is an iron-containing group to bind gases such as oxygen.


Nucleic Acids
Nucleic acids are polymers of building blocks called nucleotides. The two types of nucleic acids are DNA (deoxyribnucleic acid) and RNA (ribonucleic acid). DNA stores hereditary information, including all information for proper cell function. RNA helps in assembling proteins. Nucleotides are composed of a 5-carbon sugar, 3 phosphate groups, and a nitrogenous base. 4 carbons of the sugar are part of the ring while the 5th is branched from the ring. All nucleotides have a 3' hydroxyl group and the phosphates are linked at the 5' carbon. The nitrogenous base is linked at the 1' carbon. In a DNA nucleotide, the 2' carbon has simply a hydrogen while a RNA nucleotide has a hydroxyl group at the 2' carbon.
A nucleoside consists only of the sugar and nitrogenous base. A nucleoside with one phosphate group is called a nucleoside monophosphate. If it has two phosphate groups it is a nucleoside diphopshate, and if it has three phosphate groups it is a nucleoside triphosphate.
There are 4 nucleotides used to construct DNA and 4 to construct RNA. The nucleotides of DNA are adenine (A), thymine (T), cytosine (C), and guanine (G). The nucleotides of RNA are adenine (A), uracil (U), cytosine (C), and guanine (G). They differ in their nitrogenous bases. There are two basic groups of nitrogenous bases: purines and pyrmidines. Purines consist of two rings while pyrimidines have only one ring. 

The polar functional groups in the nitrogenous bases result in hydrogen bonds forming, which is what creates the double helix structure of DNA. The two strands are antiparallel, linked by phosphodiester bonds, which are covalent bonds specifically found in nucleic acids. This type of bond is analogous to a peptide bond in proteins. Nucleotides are linked to the next using a dehydration reaction. A and T bind while C and G bind in DNA. In RNA, A binds with U and C binds with G. A sugar-phosphate backbone is created that gives the skeleton for the molecule. DNA has opposite ends, called 5' and 3' ends, based off of which side of a sugar is facing what end.

Due to the double-stranded nature of DNA, the nucleotide sequence of one sequence is complementary to the other chain.
Differences between RNA and DNA:

• RNA has ribose sugars, DNA has deoxyribose sugars
• RNA exists as single strands, DNA has a double-helix structure
• Uracil replaces thymine in RNA
• RNA is synthesized from a DNA template
• At the 2' carbon, there is a hydroxyl group attached in RNA but only a hydrogen atom in DNA

DNA Double-Helix

Helpful Links

Click here for a link to a site that helps you remember the functional groups as well as learn to identify them. I especially liked the "U-Draw Functional Groups" animation. It basically gives you different molecules. You can draw on it and circle the functional groups. Then, you can hit "check" to see if you were able to find them all.

This video explains purines and pyrimidines. It made the structures clear and explain why and how they bind.


Article
http://www.ncbi.nlm.nih.gov/pubmed/21928440
This article pertains to this chapter because it is discussing a protein that may have anti-cancer, anti-HIV, and hemolytic properties. It is unknown whether this depends on the lipid-bilayer of cell membranes or the chiral receptors. A test was done using the enantiomer of the protein, which resulted in the exclusion of a chiral reception, indicating that the phospholipid bilayer is what has an impact on the effectiveness on this drug. This plays into macromolecules, as it includes both proteins as well as lipids (of the cell membranes).