CHEMISTRY GLOSSARY

octahedron    →   oktaedar

Octahedron is a three-dimensional geometric figure having eight triangular sides.

phase diagram    →   fazni dijagram

Phase diagram is a graphic representation of the equilibrium relationships between phases (such as vapour-liquid, liquid-solid) of a chemical compound, mixture of compounds, or solution.

The figure shows a typical phase diagram of an element or a simple compound. The stability of solid, liquid and gas phases depends on the temperature and the pressure. The three phases are in equilibrium at the triple point. The gas and liquid phases are separated by a phase transition only below the temperature of the critical point.

monosaccharide    →   monosaharid

Monosaccharides are carbohydrates, with the general formula C_n(H₂O)_n, that cannot be decomposed to a simpler carbohydrates by hydrolysis.

Depending on whether the molecule contains an aldehyde group (-CHO) or a ketone group (-CO-) monosaccharide can be a polyhydroxy aldehyde (aldose) or a polyhydroxy ketone (ketose). These aldehyde and ketone groups confer reduction properties on monosaccharides. They are also classified according to the number of carbon atoms they contain: trioses have three carbon atoms, tetroses four, pentoses five, hexoses six, heptoses seven, etc. These two systems of classification are often combined. For example, a six-carbon polyhydroxy aldehyde such as D-glucose is an aldohexose, whereas a six-carbon polyhydroxy ketone such as D-fructose is a ketohexose.

The notations D and L are used to describe the configurations of carbohydrates. In Fischer projections of monosaccharides, the carbonyl group is always placed on top (in the case of aldoses) or as close to the top as possible (in the case of ketoses). If the OH group attached to the bottom-most asymmetric carbon (the carbon that is second from the bottom) is on the right, then the compound is a D-sugar. If the OH group is on the left, then the compound is an L-sugar. Almost all sugars found in nature are D-sugars.

Monosaccharides can exist as either straight-chain or ring-shaped molecules. During the conversion from straight-chain form to cyclic form, the carbon atom containing the carbonyl oxygen, called the anomeric carbon, becomes a chiral center with two possible configurations (anomers), α and β. When the stereochemistry of the first carbon matches the stereochemistry of the last stereogenic center the sugar is the α-anomer when they are opposite the sugar is the β-anomer.

phenylalanine    →   fenilalanin

Phenylalanine is hydrophobic amino acids with aromatic side chain. It is quite hydrophobic and even the free amino acid is not very soluble in water. Phenylalanine is large aromatic residue that is normally found buried in the interior of a protein and is important for protein stability. It is an essential amino acid, which means that humans cannot synthesize it, so it must be ingested.

• Abbreviations: Phe, F
• IUPAC name: 2-amino-3-phenylpropanoic acid
• Molecular formula: C₉H₁₁NO₂
• Molecular weight: 165.19 g/mol

Newton’s gravitational law    →   Newtonov zakon gravitacije

Every object in the universe attracts every other object with a force (gravitational force F_G) directed along the line through centres of the two objects that is proportional to the product of their masses and inversely proportional to the square of the distance between them.

m₁ and m₂ are masses of the two objects and r is the distance between them. G is universal constant of gravitation, which equals 6.67•10^-26 N m² kg^-2. Strictly speaking, this law applies only to objects that can be considered pointlike object. Otherwise, the force has to be found by integrating the forces between various mass elements.

It is more properly to express Newton’s gravitational law by vector equation:

in which r₁ and r₂ are position vectors of masses m₁ and m₂.

Gravitational forces act on distance. Newton’s gravitational law is derived from Kepler’s law for planetary motion, using a physical assumption considering Sun as the centre and the source of gravitational force.

Additionally, every object moves in the direction of the force acting on it, with acceleration that is inversely proportional to the mass of object. For bodies on the surface of Earth, the distance r in gravitational law formula is practically equal to the Earth radius, R_E. If the mass of the body on Earth surface is m and the mass of earth is M_E, the gravitational force acting on that body can be expressed as:

where g is gravitational acceleration which is, although dependent on geographical latitude, usually considered as constant equal to 9.81 m s^-2.

pipette    →   pipeta

Pipettes are glass tubes which are tapers towards at both ends into narrow opened tubes. According to their design two types of pipettes can be distinguished:

Volumetric pipettes

Volumetric pipettes (transfer or belly pipette) are used in volumetric analysis, when there is a need for taking exact smaller volume of a sample solution or reagent. The upper tube of volumetric pipette has a ringlike marking (mark) which marks its calibrated volume. Pipettes calibrated to deliver (TD or Ex) the indicated volume. By sucking in (with mouth, propipette or a water pump) the liquid is pulled in a little bit above the mark and the opening of the pipet is closed with a forefingertip. Outer wall of pipet is wiped and, with a slight forefinger loosening, the liquid is released until it reaches the mark. Mark must figure as a tangent on a lower edge of the liquid meniscus. A pipette is emptied out by lifting the forefinger off and letting the liquid flow out of the pipette freely. After another 15 s and the tip of the pipette is pulled onto the inner wall of the vessel. It is absolutely forbidden to blow out the contents of the pipette

Graduated pipettes

Graduated pipettes (Mohr pipette) have a scale divided into units of one and of 1/10th of a millilitre. Because of their wide necks it is less accurate than the volumetric pipette. They are used when taking volume of solutions in which accuracy does not have to be very high. They are filled in the same way as volumetric ones and liquid can be gradually released.

proline    →   prolin

Proline has an aliphatic side chain with a distinctive cyclic structure. It is unusual because it is conformationally restricted. The secondary amino (imino) group of proline residues is held in a rigid conformation that reduces the structural flexibility of polypeptide regions containing proline. It is not an essential amino acid, which means that the human body can synthesize it.

• Abbreviations: Pro, P
• IUPAC name: pyrrolidine-2-carboxylic acid
• Molecular formula: C₅H₉NO₂
• Molecular weight: 115.13 g/mol

serine    →   serin

Serine is neutral amino acids with polar side chains. It is one of two hydroxyl amino acids. Both are commonly considered to by hydrophilic due to the hydrogen bonding capacity of the hydroxyl group. Serine often serves as a nucleophile in many enzyme active sites, and is best known for its role in the serine proteases. Serine is a site of phosphorylation and glycosylation which is important for enzyme regulation and cell signaling. It is not essential to the human diet, since it is synthesized in the body from other metabolites, including glycine.

• Abbreviations: Ser, S
• IUPAC name: 2-amino-3-hydroxypropanoic acid
• Molecular formula: C₃H₇NO₃
• Molecular weight: 105.09 g/mol

threonine    →   treonin

Threonine is neutral amino acids with polar side chains. It differs from serine by having a methyl substituent in place of one of the hydrogens on the β carbon. Threonine is a site of phosphorylation and glycosylation which is important for enzyme regulation and cell signaling. It is an essential amino acid, which means that humans cannot synthesize it, so it must be ingested.

• Abbreviations: Thr, T
• IUPAC name: 2-amino-3-hydroxybutanoic acid
• Molecular formula: C₄H₉NO₃
• Molecular weight: 119.12 g/mol

tryptophan    →   triptofan

Tryptophan is hydrophobic amino acids with aromatic side chain. Tryptophan is large aromatic residue that is normally found buried in the interior of a protein and is important for protein stability. Tryptophan has the largest side chain and is the least common amino acid in proteins. It has spectral properties that make it the best inherent probe for following protein folding and conformational changes associated with biochemical processes. It is an essential amino acid, which means that humans cannot synthesize it, so it must be ingested.

• Abbreviations: Trp, W
• IUPAC name: 2-amino-3-(1H-indol-3-yl)propanoic acid
• Molecular formula: C₁₁H₁₂N₂O₂
• Molecular weight: 204.23 g/mol