Macromolecules and Enzymes - GRE

Uracil is one of the nucleotide bases that composes RNA. It is replaced by thymine in DNA.

Uracil, thymine, and cytosine are pyrimidine residues, capable of bonding and pairing with the purines adenine and guanine via hydrogen bonding. During DNA replication, thymine matches with adenine. During transcription, uracil matches with adenine.

Purines are defined by their two-ring structure. A six-member ring with two amine groups and a five-member ring with two amino groups join to form each purine molecule. Addition substituents on the rings (often ketones or other amines) determine purine identity.

Glycine, aspartate, and glutamine are necessary for purine synthesis, along with phosphoribosyl pyrophosphate (PRPP). Glycine is incorporated into the final purine product structure, while glutamine is converted to glutamate and aspartate is converted to fumarate. The final purine product is used to make useful molecules, such as adenine and guanine for nucleotide synthesis.

Template strand cytosine and adenine are methylated in DNA replication, which allows DNA mismatch repair enzymes to distinguish between old and new DNA strands.

In contrast, histone acetylation relaxes DNA coiling and allows for the DNA to be transcribed.

You can remember that methylation makes DNA mute, and acetylation makes DNA active.

Nucleotides (DNA monomers) and ribonucleotides (RNA monomers) are formed from a pentose sugar, phosphate group, and nitrogenous base. Each nitrogenous base has a complement that allows it to form hydrogen bonds to the template strand. This allows for the proper sequence of genetic code in DNA replication and RNA transcription.

Purine residues will always pair with pyrimidine residues. The purines are adenine and guanine. The pyrimidines are cytosine and thymine in DNA, and cytosine and uracil in RNA. Adenine will match with thymine or uracil, forming two hydrogen bonds, while cytosine will match with guanine to form three hydrogen bonds.

The difference between the binding of cAMP and phosphorylation is that the latter is a covalent modification. Covalent modifications are a different way to regulate proteins, and do not fall under the category of allosteric regulation. Allosteric regulation only occurs outside of the active site, often simply called an allosteric site. The non-covalent binding of cAMP to a region of an enzyme outside of the active site thus qualifies as allosteric regulation.

If the reaction rate has plateaued, this indicates that the enzyme has reached saturation. At this point, every active site on every molecule of enzyme is actively catalyzing the reaction as quickly as it can. The only way to change the reaction rate, at this point, would be to increase the concentration of the enzyme in the solution. Further increasing substrate concentration will have no effect.

We know that the enzyme has not become denatured because the reaction is still occurring. The rate of the reaction is constant during the plateau, and does not drop to zero.

A Lineweaver-Burk plot is a way to graphically represent enzyme kinetics. It is convenient because several portions of the graph readily display important information, such as rate constants. The y-intercept in particular is useful because it represents the reciprocal of the maximum velocity. The x-intercept describes the negative reciprocal of the Michaelis constant. The slope is the quotient of the Michaelis constant over the maximum velocity.

The two plots contain the same information. A Michaelis-Menten plot shows the relationship between initial reaction rate concentration of substrate ( versus ). A Lineweaver-Burk plot shows the relationship between the inverses of these same two variables, however, it is much easier to visualize important data on a Lineweaver-Burk plot. The x-intercept, the y-intercept, and the slope all contain points of interest. A downside of the Lineweaver-Burk plot, however, is that it is more susceptible to inaccuracy if there is some flaw in the accumulated data.

The only option that will alter the is to add a non-competitive inhibitor. The addition of this inhibitor will affect the amount of free enzyme available to catalyze the reaction, and thus lower the by reducing the effective enzyme concentration.

Addition of a competitive inhibitor will alter the , but not the . Increasing the substrate concentration will have no effect once saturation has been reached.

During a reaction, the reactants must pass through high-energy transition states before they evolve into the products. The catalyst reduces the free energy of this transition state, thus making it 'easier' for the reactant to undergo the chemical reaction since the activation energy has been lowered.

The genetic code refers to the sequence of DNA that codes for genes and proteins in the body. The genetic code is composed of three-nucleotide codons, each used to recruit an amino acid during translation and protein synthesis. Each codon codes for one and only one amino acid, making the code unambiguous; however, some amino acids have more than one codon that can be used to recruit them. This feature of the genetic code is known as degeneracy. Finally, the genetic code is universal. All living organisms use the same genetic material (DNA) in their cells and produce proteins through transcription and translation. Though the processes may change slightly between organisms, the general genetic code is universal to all cells.

The genetic code is not overlapping, meaning that the code is linear. Transcription of DNA has a fixed starting point and proceeds in a linear fashion, as does translation of mRNA. There is no overlapping or reverse reading of the genetic code.

These bonds are specifically referring to the invariable portions of the amino acid and, thus, do not involve the R group (functional group).

This is more of a definition-based answer. The phi angle refers to the bond between the amine nitrogen and the alpha carbon, while the psi angle refers to the bond between the alpha carbon and the carbonyl carbon of the carboxylic acid. These bonds play important roles in determining possible protein structures.

Amino acid sequences with a lot of alanine (A) residues are higly likely to form alpha-helices. Glycine (G) and proline (P) residues often cap alpha-helices, though glycine can sometimes be found inside alpha-helices as well.

Proline is never found inside an alpha-helix due to the conformational hindrance caused by the hydrogen bonding within the residue. Proline is usually found in bends in a protein structure.

Histidine has the following pKa values:

COOH - 1.82

R-group - 6.00

NH3 - 9.17

Any pH below the pKa will cause the molecule to be protonated, while any pH above the pKa will cause the molecule to deprotonate. At a pH of 7, the COOH group to deprotonate, but the NH3 and R-group will remain protonated.

Tertiary structure of a protein is determined by interactions between the R-groups of the amino acids that make up that protein. The secondary structure of a protein is mediated by the backbone atoms of the polypeptide chain which includes the carboxyl and amine groups. The alpha carbon are what the R-groups are attached to an do not directly contribute to any level of protein structure.

Hydrogen bonds between repeating units of the polypeptide backbone (namely the amino groups and carboxyl groups) mediate secondary structure in proteins.

Primary structure simply describes the order of amino acids in a polypeptide chain. Tertiary structures describe global folding of the entire chain, which may be made up of a multitude of secondary structures like alpha helices or beta sheets. Quaternary structure describes the position of numerous subunits in a protein complex comprised of two or more smaller protein. Huge multiunit proteins are ordered by supramolecular structure.

Since chymotrypsin uses a water molecule in order to cleave the polymer, it is considered a hydrolase enzyme.

Ligases are enzymes that catalyze the formation of new bonds between molecules. A classic example is DNA ligase, an enzyme that synthesizes phosphodiester bonds in the DNA backbone.

Transferases move small molecules from one molecule to another, sometimes altering the functional groups of a compound. Isomerases convert molecules from one isomer to another. Lyases are enzymes that break bonds through a means other than hydrolysis (typically by formation of a double bond).

Since the enzyme has changed the shape of the molecule without altering its chemical formula, the enzyme has simply made a new isomer of the molecule. This action is accomplished by isomerase enzymes.