Engineering Biology : Practice Questions and Answers

Because of secondary and tertiary structures, proteins adopt specific shapes. The spot at which two molecules with specific shapes fit together to interact is called the active site. This active site is the basis of the lock and key model. The active site is called active because interaction of the molecules in this way usually results in some chemical change or reaction.

Protein primary structure is the linear sequence of amino acids in peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequences.

Van der Waals forces are driven by induced electrical interactions between two or more atoms or molecules that are very close to each other. Van der Waals interaction is the weakest of all intermolecular attractions between molecules. However, with a lot of Van der Waals forces interacting between two objects, the interaction can be very strong.

The formation of protein complexes or aggregates in aqueous buffers is determined by a number of factors: physical properties of the protein itself, pH, temperature, type and concentration of the used co-solvent (salt). Salts interfere with intramolecular interactions mediated by non-covalent forces such as hydrogen bonds, van der Waals forces, and hydrophobic interactions, which, at high co-solvent concentrations, results in protein denaturation.

When an amino acid is incorporated into a polypeptide, the charges on the amino and carboxyl groups disappear. Among the 20 common amino acids, five have a side chain which can be charged. At pH=7, two are negative charged: aspartic acid and glutamic acid (acidic side chains), and three are positive charged: lysine, arginine and histidine.

Proteins consists of polar as well as non polar residues. The non-polar side chains are pushed to the interior of the protein allowing them to avoid water molecule and giving the protein a globular shape. There is, however, a substantial difference in how the polar side chains react to the water.

The side chains of amino acid which contain non polar nature are held in interactions called hydrophobic interactions. The tendency of non-polar molecules in a polar solvent (usually water) to interact with one another is called the hydrophobic effect. The interactions between the nonpolar molecules are called hydrophobic interactions.

About 12 kJ/mol of stabilization energy is contributed by each hydrogen bond. The core of most protein structures is composed of secondary structures such as (\alpha) helix and (\beta) sheet. This satisfies the hydrogen‐bonding potential between main chain carbonyl oxygen and amide nitrogen buried in the hydrophobic core of the protein.

Proteins are largely responsible for expressing the information present in DNA. The flow of genetic information, or gene expression, in normal cells is - This flow of information is dependent on the genetic code, which defines the relation between the sequence of bases in DNA (or its mRNA transcript) and the sequence of amino acids in a protein.

The proteins constitute about 50% of the dry weight of the cell with the essential proteins required for nourishment and transportation. Whereas the other 50% is constituted by the other cell constituents as well as the water content in the cell required for hydration of the cell.

The nucleus of an atom contains two things: Protons and neutrons. Because neutrons have no charge and protons have positive charge, the overall charge of the nucleus is positive. The DNA of the cell being negatively charged even does not affect the nucleus from being positively charged.

In RNA, uracil replaces thymine as the usual complement of adenine. Thus, thymine is usually seen only in DNA and uracil only in RNA. Methylation of uracil produces thymine, providing a mechanism for repair and protection of DNA and improvement of DNA replication. One of the common mutations of DNA involves two adjacent thymines.

A nitrogenous base is simply a nitrogen containing molecule that has the same chemical properties as a base. They are particularly important since they make up the building blocks of DNA and RNA: adenine, guanine, cytosine, thymine and uracil.

It is the characteristic of a nucleotide to contain phosphate group in their carbon chain at 3rd and 5th positions each. All nucleotides have a common structure: a phosphate group linked by a phosphor-ester bond to a pentose (a five-carbon sugar molecule) that in turn is linked to an organic base.

Nucleotides always have a nitrogenous base, a pentose sugar, and one or more phosphates. When nucleotides are polymerized, or joined together, they form a nucleic acid, such as DNA or RNA. Each nucleotide's phosphate is joined to another's sugar, forming a sugar-phosphate backbone with the nitrogenous bases hanging off the side.

Nucleotides are the subunit that is polymerized (connected into a long chain) to make nucleic acids (DNA and RNA). Nucleotides consist of three smaller components: a ribose sugar, a nitrogenous base, and phosphate group.

The genetic substance of all living creatures, from viruses to man is a complex chemical compound - the nucleic acid DNA. Chromosomes are made from DNA. Genes are short sections of DNA. DNA carries the genetic code that determines the characteristics of a living thing. A gene is a short section of DNA. Each gene codes for a specific protein by specifying the order in which amino acids must be joined together. The cell's nucleus contains chromosomes made from long DNA molecules.

DNA and RNA are both capable of encoding genetic information, because there are biochemical mechanisms which read the information coded within a DNA or RNA sequence and use it to generate a specified protein. Hence the monomeric units are defined such to form the large polymeric molecule.

The genetic information passed from parent to offspring is contained in genes carried by chromosomes in the nucleus. Sexual reproduction produces offspring that resemble their parents, but are not identical to them. Asexual reproduction produces offspring - clones - which are genetically identical to their parents.

The genetic information is found in the nucleus of the cell. The cell nucleus contains the majority of the cell's genetic material in the form of multiple linear DNA molecules organized into structures called chromosomes. Each human cell contains roughly two meters of DNA.