Chapter 3 Post

Summary of Virtual Lectures:


Proteins


Proteins are defined as polymers found in all cells which play critical roles in nearly all life processes. They account for about 50% of the organic material in a typical animals body.


Proteins have multiple functions. One of these is structural support. They contribute to the stability of a cell. They are also catalytic in nature meaning some proteins act as enzymes. Enzymes are important because they speed up chemical reactions. In addition there is membrane transport. Membrane proteins regulate what comes in and out. Also, proteins contribute to cell motility, hormones, regulation, reception, defense and storage. The point is: they are VERY important to the cell.


There are four progressive levels of protein structure.

• Primary structure is the sequence of amino acids in a protein. The amino acids are connected through peptide bonds. Peptide bonds are formed through dehydration synthesis. Proteins differ in their primary structure. In order to make both the hydrophilic and hydrophobic amino acids happy, proteins are folded. Proteins must be folded based on the linear sequence of amino acids. By doing so, we're burying the ones that are hydrophobic, and exposing the ones that are hydrophilic.
• Secondary structure is when amino acids interact with their neighbors to bend and twist protein chains. The ultimite goal of this is to hide the hydrophobic amino acids. One type of secondary structure is the alpha-helix (α-helix). Hydrogen bonds are what stabilize the twists and turns the protein has. This is where electronegativity (and my favorite Pauling Scale!) comes back in. In the example, the hydrogen has a partial positive charge (a symbol that looks like this δ⁺) and the oxygen has a partial negative charge (δ^-). These opposite charges (remember, opposites attract!!!) in close proximity are what form hydrogen bonds. The other type of secondary structure is the beta-strand (β strand). The beta-strands are zig-zags in flat plane, looking almost like a linear chain. Beta-strands form beta-sheets. Beta-sheets run antiparallel so that hydrogen bonds can be formed by the δ⁺ and δ^- charges. The secondary structure makes the primary structure much more compact. 
• Tertiary structure is the overall conformation or three-dimensional shape of a protein. Proteins can ONLY function in their tertiary structure. In the tertiary structure, the protein ends up taking a globular (I love this word for some reason!) shape, or you can be boring and call it a spherical shape. At the core of our globular structure will be the hydrophobic non-polar amino acids, hiding behind the hydrophilic ones. R-groups, also known as side chains, form ionic bonds and stabilize tertiary structures. There are different interactions that occur, the strongest being disulfide linkages. Disulfide bridges help to stabilize a protein's compact structure. Also, there is denaturation, the loss of protein structure and function. Denaturation can be caused by high heat, a change in pH, or an increase in salt. This is why you can possibly die if you have a very high fever. However, not all hope is lost. It is possible to proteins to renature if the heat, pH, salt gets under control.
• Quaternary structure is two or more proteins joined together into a larger complex protein. Hemoglobin is an example. It contains 4 globin molecules and 4 heme groups.

Nucleic Acids

Nucleic acids are long polymers of nucleotide building blocks. The two classes of nucleic acids are DNA (which stands for deoxyribonucleic acid) and RNA (ribonucleic acid). DNA stores all the information for proper cell function. DNA information also determines the primary structure of proteins. Nucleotides are composed of a five-carbon sugar, nitrogenous base, and three phosphate groups. A difference between DNA and RNA is that DNA has H on its 2' C and RNA has OH on its 2' C.

Then, there are nucleosides. Nucleoside refers to the sugar and nitrogenous base. As you add phosphates, it becomes a nucleoside monophosphate (1 phosphate), a nucleoside diphosphate (2 phosphates), and a nucleoside triphosphate (3 phosphates).

Nucleotides vary in sugar (ribose or deoxyribose) and in nitrogenous base. There are 20 amino acids that are used to make a protein. But only 4 distinct amino acids are used in DNA and RNA. The 4 used in DNA are A, T, C and G. The 4 used in RNA are A, U, C, G. The categories of these are purine (double rings) including A, G and pyrimidine (single ring) including U, T, C.

The reason why DNA has its double helical structure is because of the hydrogen bonds that form between the δ^- oxygen and the δ⁺ hydrogen. DNA and RNA polynucleotide chains are formed by linking the phosphate group of one nucleotide to the sugar of the next one. These are linked together by phosphodiester bonds, covalent bonds specifically found in nucleic acids. DNA runs anti-parallel. One side runs 5' to 3' and the other runs 3' to 5'. Two strands of DNA are joined by hydrogen bonds between the nitrogenous bases following base-pairing rules: A-T and C-G. Adenine and thymine form 2 hydrogen bonds. Cytosine and guanine form 3 hydrogen bonds.

Note: I have not included useful materials in this post because I have done the Fold- It Assignment.