MCB 100 Introductory Microbiology September 10 2018 Polar

MCB 100 Introductory Microbiology September 10, 2018

Polar Covalent Bonds vs. Non-polar Covalent Bonds A non-polar covalent bond forms when two atoms share a pair of electrons equally. Both atoms end up with no net charge. If two atoms share a pair of electrons unequally, one ends up with a slight negative charge while the other has a slight positive charge. This is a polar bond. The factor that determines if a pair of electrons will be shared equally or unequally is the electronegativity of the atoms that participate in the chemical bond. Electronegativity is a measure of the affinity of an atom for valence electrons.

Electronegativity of The Most Common Elements Found in Biological Molecules H 2. 1 C 2. 5 N 3. 0 Examples: Non-Polar Covalent Bonds H–H H / H–C–H H O 3. 5 P 2. 1 S 2. 5 Polar Covalent Bonds H–O H H / H–N H

A Bit About Water molecules are held together by polar covalent bonds, because oxygen atoms have a greater electronegativity than hydrogen atoms.

Redox Values of Elements in Covalent Compounds Of the 6 elements that are most common in biological macromolecules: C, H, O, N, P and S, Oxygen has the highest electronegativity (3. 5) & Hydrogen has low electronegativity (2. 1). Since oxygen atoms most often form 2 covalent bonds and have a relatively strong tendency to attract electrons, by convention we say that the redox level of an oxygen atom in a compound is -2 (more electrons than protons). Since hydrogen atoms form 1 covalent bond and have a relatively low affinity for electrons, we say that hydrogen atoms in a compound have a redox level of +1 (more proton than electron). The redox level of a carbon atom or a nitrogen atom in a compound varies, depending on how many oxygen atoms or hydrogen atoms it is associated with.

These weak non-covalent bonds are called hydrogen bonds. Because oxygen has a greater electronegativity than hydrogen, water is a polar solvent.

Significance of Polar and Non-Polar Compounds A solvent is a liquid that is used to dissolve something. Water is a polar solvent. Hydrocarbons and oils are non-polar solvents. Like dissolves like. Some compounds dissolve freely in water, but poorly in oils. Other compounds dissolve freely in oils but poorly in water. Since oils are non-polar, they dissolve molecules that include hydrophobic alkyl groups. Water is polar, it dissolves molecules with polar groups such as alcohols, aldehydes, carboxylates and amines.

There isn’t much difference in the electronegativity of hydrogen and carbon so the bonds in hydrocarbons have little polarity. Hydrocarbons don’t form hydrogen bonds with other compounds.

A Bit About Water molecules are polar enough that a small fraction of water molecules will always ionize. Water constant = 1 x 10 -14 M = [H+] x [-OH] A high concentration of H+ causes a low concentration of –OH, and vice -versa. p. H = -log [H+] p. OH = -log[-OH] p. H + p. OH = 14 if p. H = 1. 0, the [H+] = 1 x 10 -1 M or 0. 1 M if p. H = 4. 0, the [H+] = 1 x 10 -4 M or 0. 0001 M if p. H = 7. 0, the [H+] = 1 x 10 -7 M or 0. 0000001 M if p. H = 10. 0, the [H+] = 1 x 10 -10 M or 0. 000001 M A low p. H = a higher concentration of free protons (stronger acid). A high p. H = a higher concentration of free hydroxyl ions (stronger base)

Organic Acids and Bases Carboxylic Acid Carboxylate anion + proton Amine + Protonated Amine

Chemical Composition of an Escherichia coli Cell % Total Weight Organic Compounds Proteins Nucleic Acids RNA DNA Carbohydrates Lipids Miscellaneous % Dry Weight 15 50 6 1 3 2 2 20 3 10 8 6 Inorganic Compounds Water Ions and Minerals 70 1 3 Macromolecule = large molecule Polymer = a large molecule made of many smaller molecules stuck together in long chains

Proteins – polymers of amino acids held together by peptide bonds Lipids – amphipathic molecules that form the matrix of cell membranes – fatty acids and glycerol components are held together by ester bonds Polysaccharides (also known as complex carbohydrates) – polymers of sugars held together by glycosidic bonds Nucleic Acids – polymers of nucleotides held together by phosphodiester bonds

Proteins – polymers of amino acids held together by peptide bonds Lipids – amphipathic molecules that form the matrix of cell membranes – fatty acids and glycerol components are held together by ester bonds Polysaccharides (also known as complex carbohydrates) – polymers of sugars held together by glycosidic bonds Nucleic Acids – polymers of nucleotides held together by phosphodiester bonds

Amino Acids and Proteins are large globular molecules. There are many different types of proteins found in a typical cell and each type has a different function. Some proteins are found in the cytoplasm and others are embedded in the cell membrane. Some Functions of Proteins: - some act as part of the structure of the cell - many act as enzymes that catalyze biochemical reactions - others transport substances through the cell membrane - some regulate expression of genes or control other cell functions The function of a protein is determined by it’s solubility, shape and the three dimensional arrangement of organic functional groups on it’s surface.

2 -D Protein Gel Electrophoresis Gel electrophoresis is a way to separate large biological molecules like DNA fragments and proteins. In 2 -D protein gels each spot is a different type of protein molecule. Gels like this can be used to characterize the population of proteins present in a particular type of bacterial culture or in a particular type of plant or animal tissue.

Proteins are linear chains of amino acids • Typical proteins consist of 200 – 400 amino acids, but some are smaller than this and others are larger. The key factor that determines the structure and ultimately the function of an enzyme is the sequence of amino acids found in the protein.

AMINO ACIDS GROUPED BY TYPES OF SIDE CHAINS NON-POLAR (hydrophobic) Glycine Alanine Leucine Isoleucine Valine Proline AROMATIC (mostly hydrophobic) Phenylalanine Tyrosine Tryptophan POLAR (hydroxyl or amide groups) Serine Threonine Asparagine Glutamine SULFUR CONTAINING Methionine Cysteine ACIDIC Aspartic acid Glutamic acid BASIC Lysine Histidine Arginine