Question

1. Discuss the composition and structure of enzymes and discuss the factors that modify enzyme structure and function

2. Describe the production and processing of a protein that will be exported from a eukaryotic cell. Begin with the separation of the mRNA from the DNA template and end with the release of the protein at the plasma membrane.

Answer 1

For a long time it was believed that only proteins have the capability of being an enzyme- the biocatalyst. But in 1989, discovery of catalytic properties of RNA, which were called ribozyme. detailed description about enzyme, like composition, str, factor affecting enzyme are mentioned below -

composition of enzyme:

In general, a functional enzyme has the following:
1. A sequence of amino acids i.e. peptide chain folded in higher structure such that the structure has a catalytic site and in some an allosteric regulatory site too. The active sites have certain critical amino acids that accounts for the electron donation and accepting relay during reaction.

2. Cofactors
A cofactor is a non-protein chemical compound that is required for the protein's biological activity.

Enzyme Structure:

Enzymes are a linear chain of amino acids that generate the three-dimensional structure. The sequence of amino acids enumerates the structure, which in turn identifies the catalytic activity of the enzyme. The structure of the enzyme denatures when heated, leading to loss of enzyme activity, which is typically connected to the temperature.

Enzymes are larger than their substrates, and their size varies, which range from sixty-two amino acid residues to an average of two thousand five hundred residues present within fatty acid synthase. Only a small section of the structure is involved in catalysis and are situated next to the binding sites. The catalytic site and binding site together constitute the enzyme’s active site. A small number of ribozymes exists which serves as an RNA-based biological catalyst. It reacts in complex with proteins.

factor affect enzymatic structure and function:

1. temperature - The shape of a protein is determined by its hydrogen bonds. Hydrogen bonds are easily disrupted by temperature changes.

2. pH - Most enzymes also have a pH optimum, usually between 6 and 8. For example, when the pH is too low, the H+ ions combine with the R-groups of the enzyme’s amino adds, reducing their ability to bind with substrate.

3. inhibitor - inhibitor binds to active or allosteric site of enzyme and allow confirmation change. that affect binding of substrate. this confirmation change may be reversible or irreversible.

4. effects of product - as reaction pathway proceed results in to product formation. this product may stop reaction by binding with enzyme known as feedback inhibition.

5. effects of activator - an activator responsible for spped up of chemical reaction. if an reaction have enzyme and activator, the rate of reaction will go at highest speed.

ans. 2. a gene on double-stranded DNA. What must first happen is the gathering of a pre-initiation complex at the TATA box (or other eukaryotic promoter). This complex contains two important enzymes: An RNA polymerase, and a helicase. Once the signal to go is received by the polymerase, it starts to travel down the DNA right behind the helicase. Helicase unwinds the DNA strands so that RNA polymerase can read the gene and construct a pre-mRNA (pre-messenger RNA). As the front end (the 5' end, pronounced five-prime) of the pre-mRNA emerges, it is capped with a modified nucleotide called 7-methylguanosine and three phosphate groups that protect the RNA from degradation (this is added before the RNA systhesis is complete). Once the whole pre-RNA has emerged and floats off, it is quickly polyadenylated. To do this, an extra region towards the back (the 3' end) of the pre-mRNA is chopped off, then an enzyme called poly-A-polymerase adds ~200 adenines to the 3' end. This is, again, to protect the mRNA from enzymes that would destroy it. At around the same time, the pre-mRNA is also spliced by large protein constructs called spliceosomes. This chops out non-coding regions of RNA called introns that are found between the important coding regions (which are called exons. Remember: EXONS are EXPRESSED). Our RNA now has a 5' cap, a 3' poly-a tail and no more introns. It is now ready for translation, and called mRNA.

The mRNA is now exported from the nucleus by means of large protein pores called nuclear pore complexes (NPCs). These are very specialized transport mechanisms in the nuclear membrane that, with the help of several transport proteins, allows import or export of chemicals into and out of the nucleus.

Once in the cytoplasm, the mRNA must be translated. The ribosome binds to the mRNA with the help of some other proteins and scans along the mRNA until it finds a start codon. I'm assuming this protein is destined to be exported from the cell entirely, since you said it is released at the plasma membrane. In this case, the ribosome also ends up bound to the membrane of the rough endoplasmic reticulum (find a diagram of this too, if you need to know it). Next, a tRNA (transport RNA) binds to the A-site inside the ribosome (I suggest you find a diagram of a ribosome. This will be easier to follow!). tRNAs are small ribozymes (enzymes made of RNA) that bind a specific amino acid, then bring that amino acid to the ribosome when needed. One by one, amino acids are added to the growing protein chain. As the protein emerges, it passes through a pore protein called a translocon and passes into the endoplasmic reticulum.

Here, it finds its way to the golgi apparatus, which packages the protein in a vesicle. This vesicle heads for the cell membrane and merges with it, forcing the protein out of the cell.