Monday, May 5, 2014

Practically Perfect Protein Primer

PhD’NtheSingleMom Presents: 
Practically Perfect Protein Primer 

In an amazing choose your own detail format. For beginners, just read the blue, for full blown Quals level read the blue + black (which is how I feel after all of this studying...)

Chapter 1 – Protein building blocks 

Proteins are large biochemical molecules that provide structure and support for cells. While we need nucleic acids to know what to build and carbs/lipids to get energy to build, it’s the proteins that do the work of building and catalyzing reactions. These large, varied structures are made possible by stringing together combinations of 20 different building blocks, called amino acids. 

Amino acids are pretty simple little molecules. They have a middle carbon, called alpha, with its four bonds attached to hydrogen, a carboxyl group, an amine group, or the distinctive R group. The 20 different amino acids differ simply by the composition of their R groups. R groups can be small, large, linear, cyclic, positive, negative, etc. and their combinations basically provide all the properties of proteins.
 Due to the tetrahedral shape of amino acids around the alpha carbon, each amino acid exists in two unique spatial states or stereoisomers, either D or L. It’s similar to looking at your hand, while both hands have four fingers and a thumb, they cannot be laid on top of each other without reversing one of them (so they are palm to palm). Most biological proteins use the L stereoisomer, which is the one in the above image.  

R groups are classified into 5 groups based on their chemical properties.
  1. Nonpolar, aliphatic R groups include alanine, valine, leucine, isoleucine, glycine, methionine and proline and are nonpolar and hydrophobic. Alanine, valine, leucine and isoleucine are often found clustered together inside proteins to stabilize the structure. Glycine is the simplest as its R group consists only of a single hydrogen atom while proline is the most complex consisting of a cyclic structure that loops back from the amine group to the alpha carbon.
  2.  Aromatic R groups include phenylalanine, tyrosine and tryptophan which all have hydrophobic ring side chains. Tyrosine is an important aromatic amino acid due to the ability of its hydroxyl group to form hydrogen bonds.
  3.  Polar, uncharged R groups include serine, threonine, asparagine, glutamine, and cysteine and all of the R groups are more soluble in water due to the ability to form hydrogen bond with water. Cysteine’s are important due to their ability to bond via the sulfide group to create a disulfide bond between the two resides.
  4.  Positively charged, basic R groups have a significant positive charge under normal cellular conditions and include lysine, arginine and histidine. Histidine has an ionizable side group that allows it to be either positive or neutral at pH 7.
  5. Negative charged, acidic R groups have a net negative charge at cellular conditions and include aspartate and glutamate.

Chapter 2: Protein structure 

Protein structure has four levels of increasing complexity. The primary structure is the sequence of amino acid linked together via peptide bonds into a polypeptide chain. The secondary structure consists of particularly stable arrangements that result in predictable structural patterns such as an alpha-helix or a beta sheet. The tertiary structure is the 3D folding that result in the functional shape of the protein. Quaternary structures only occur if several tertiary structures come together. 

Most of the proteins shape comes from non-covalent (“weak”) interactions between the R groups which make the shape more stable; the more non-covalent interactions the more stable the protein structure. Hydrophobicity, the desire for water-haters to hang out with other water-haters, is a primary driver of the shape. Hydrophobic amino acids are shoved down into the core of the large protein and hydrophilic amino acids surround the outside to allow interaction with the cytoplasm. 

By convention, primary structures are indicated by writing the amino acids bound together by peptide bonds in a line from amino terminal to carboxyl terminal. Peptide bonds occur between the carboxyl and amine group, so that the alpha carbon’s of the protein backbone are separated by 3 bonds (Calpha-C-N-Calpha).  Peptide conformation is determined by the rotation of the various R groups around the alpha carbons. These rotations can only occur between the alpha carbon and the amine nitrogen (phi) and/or the alpha carbon and the carboxyl carbon (psi). Theoretically, the angles can be any value between -180 and 180, but due to the steric (size) interference by the potential R groups it is unlikely that all angles can be occupied. 
HAHAHAHA Ok I was going to give you guys the whole Quals set up but it ended up being 4000 words and 8 pages of crazy so if you want to see it I put it on a Google doc for you to enjoy the other three chapters :) SEE GOOGLE DOC 

Chapter 3: Protein biosynthesis

The blueprints to build the proteins a cell is capable of creating are found in the cell’s DNA. This information is than transcribed into RNA (another story for another time) and translated into the functional protein. The RNA message is read such that 3 nucleotides = 1 amino acid/stop codon, this triplet of nucleotides is called a codon. The genetic code is described as degenerate due to the existence of multiple codons that encode a single amino acid (leucine for example has 6 codons). To me though, the negative connotation of degenerate does not fit with the actual positive mutation control attribute of this codon redundancy.  


Protein biosynthesis is known as translation and utilizes 3 types of RNA plus amino acid residues to create the primary protein structure. There are 5 main steps to translation.

  1. Activation: the 20 amino acid residues must be attached to the correct tRNAs so that the anticodon will match their codon. This takes place in the cytosol under the direction of aminoacyl-tRNA synthetases and uses ATP. 
  2. Initiation: the “factory” must be assembled. First the “blueprint” mRNA binds to the small subunit of the ribosome and to the starting tRNA+amino and then the large submit is added to complete the ribosome. All of this occurs under the direction of various initiation factor proteins and needs energy.
  3.  Elongation: the assembled ribosome then moves down the polypeptide chain, bringing in a different tRNA+amino’s that match the codons. Each amino acid is bound together inside the ribosome so that an empty tRNA is ejected as it moves down each codon. This requires elongation factors and energy.
  4. Termination: once a stop codon is hit, a special release factor comes in and causes everything to break down and release the newly formed polypeptide chain.
  5.  Folding/Processing: to become a fully active protein, the polypeptide chain must fold into its 3D conformation and occasionally will have other items added to it such as a lipid or carbohydrate.


Chapter 4: Protein Trafficking

A signal sequence is a short set of amino acids that direct the protein to its final cellular destination. In many cases, the signal sequence is removed during transport or immediately after its arrival to its destination. Signal sequences are usually located at the N-terminus are 13-36 amino acid long and always have 10-15 hydrophobic acids. These sequences are at the N-terminus as this is the first side of the newly synthesized polypeptide to emerge from the ribosome and can be recognized by proteins that will take it to the indicated cellular destination. Sometimes the ribosome is translocated with the polypeptide chain as it is being made. Signal sequences can target the protein to several cellular components/processes including lysosomes, nucleus, cell membrane, secretion from the cell and the protein degradation pathway. 


Chapter 5 Functions

Proteins provide many functions inside the cell they can provide structure, support, transport, and catalytic activity. Many proteins use reversible binding of other molecules to complete their tasks, such as moving oxygen around the bloodstream. These molecules are called ligands and they bind at binding sites that possess complementary features in size, shape, charge, hydrophobicity, etc. Interactions between proteins and their ligands are very specific. 

Enzymes can be inhibited in competitive and noncompetitive fashions. Competitive inhibitors occupy the active site of the enzyme preventing the substrate from binding. Noncompetitive inhibtors bind a site that is not the active site. Often the inhibitors are reversible being transiently bound based on concentration and this method provides biofeedback control for regulating enzymes. Some inhibitors are irreversible and bind covalently to an area important for enzyme function and destroy the function permanently.

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