Chapter 2: Water- Hydrogen Bonding.

All living cells depend absolutely on water for their existence. In most living cell, water is the most abundant molecule, accounting for 60% to 90% of the mass of the cell. The macromolecule components of cells-proteins, polysaccharides, nucleic acids, and membranes- get their characteristics shapes in response to interactions with water and much of the metabolic processes of cells has to operate in an aqueous environment because water is an essential solvent as well as a substrate for many cellular reactions.

A water molecule (H2O) is V-shaped, with an angle of 104.5° between the two covalent O-H bonds.

A water molecule. Click on image for credit.

An oxygen atom has six electrons in the outer shell, but the outer shell can potentially accommodate four pairs of electrons in four sp3 orbitals. This means that oxygen can form covalent bonds involving two different hydrogen atoms, each sharing a single electron with the oxygen atom.

An oxygen nucleus (because it contains more protons or positive charge) attracts electrons more strongly towards it than the single proton in the hydrogen nucleus. This attraction of electrons defines oxygen atoms as being more electronegative than hydrogen atoms. As a result, an uneven distribution of charge occurs within each O-H bond of the water molecule, with oxygen bearing a partial negative charge and hydrogen bearing a partial positive charge (+). This uneven distribution of charge within a bond is known as a dipole, and the bond is said to be polar.

Dipolarity of water bonds.

The polarity of a molecule depends on both the polarity of its covalent bonds and its geometry. The angled arrangement of the polar O-H bonds of water creates a permanent dipole for the molecule as a whole.

A molecule of ammonia also contains a permanent diploe. Thus, even though water and gaseous ammonia are electrically neutral, both molecules are polar. The high solubility of the polar ammonia molecules in water is facilitated by strong interactions with polar water molecules.

Ammonia in the form of ammonium ions. Click on image for credit.

The reason why there’s an extra proton (H+) with ammonia is because due to the fact that it is highly polar, it will attract a hydrogen atom of a water molecule (which it has dissolved in; aqueous solution) and form a fourth hydrogen bond with it. In water, the attraction between a slightly positive hydrogen atom of one water molecule and the slightly negative oxygen atom of another produces what is referred to as a hydrogen bond.

Water is not the only molecule capable of forming hydrogen bonds; these interactions can occur between any electronegative atom and a hydrogen atom attached to another electronegative atom. In the case of ammonia, the N (Nitrogen atom) is the slightly electronegative atom and the hydrogen atom of a water molecule forms a hydrogen bond with it, converting it to ammonium ions (NH4+).

The distance between this hydrogen atom and the other oxygen atom, is about twice the length of the covalent bond and hydrogen bonds are much weaker than typical covalent bonds. A single water molecule can form hydrogen bonds with up to four other water molecules.

Hydrogen Bonds in water molecules. Click on image for credit.

Orientation is important in hydrogen bonding and the bonding is most stable when a hydrogen atom and the two electronegative atoms associated with it (the two oxygen atoms in the case of water) are aligned or nearly in line.

Linear H-Bonds. Click on image for credit.

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Introduction: Common Macromolecules- Nucleic Acids.

A nucleic acid is a polymer made up of many nucleotides. A nucleotide is generally made of;

Typical Nucleotide.

i. Nitrogen-containing base; a heterocyclic molecule, containing a closed ring of atoms of which at least one is not a carbon atom and replaced with a nitrogen atom.

ii. Pentose sugar; meaning contains five carbon atoms in the sugar molecule.

iii. Phosphate Group; usually a phosphorus atom surrounded by a double bonded oxygen atom, single bonded to two oxygen negative ions and an oxygen atom.

Since the least complicated molecule is the phosphate group, it can easily be distinguished. However, for now, the distinguishing features for the nitrogen containing base will be the nitrogen atom. If the phosphate group is absent, the sugar-base combination is called a nucleoside.

The most common two forms of nucleotides are Ribonucleotides which form the nucleic acid Ribonucleic acid (RNA) and Deoxyribonucleotides which form the polynucleotide or nucleic acid Deoxyribonucleic acid (DNA), the molecules responsible for coding the proteins in the cell. In ribonucleotides, the sugar is ribose. In deoxyribonucleotides, the sugar is deoxyribose.

DNA V/S RNA.

The difference between the two is that the pentose sugar in DNA has one oxygen atom less in the hydroxyl group of Carbon atom 2. Also, since these two are the prime nucleic acids we shall be focusing on, their polymer structure is generally helical.

Another popular nucleotide is Adenosine Triphosphate (ATP) which is used as an energy currency in the cell. This will be clearer in later chapters.

ATP

Thus, nucleic acids are biopolymers composed of monomers called nucleotides. The term polynucleotide is a more accurate description of a single molecule of nucleic acid.

The nitrogenous bases of nucleotides belong to two families known as purines and pyrimidines.

In nucleotides, the base is joined to C-1 of the sugar and the phosphate group is attached to one of the other sugar carbons, usually C-5.

There are three phosphoryl groups; alpha(α), beta(β), and gama(γ) esterified to the C-5 hydroxyl group of the ribose. The linkage between ribose and the α-phosphoryl group is a phosphoester linkage because it includes a carbon and a phosphorus atom, whereas, the β- and γ-phosphoryl groups in ATP are connected by phosphoanhydride linkages that don’t involve carbon atoms. All Phosphoanhydride have considerable chemical potential energy, and ATP is no exception. This potential energy can be used directly in biochemical reactions.

The Phosphate Business

In polynucleotides, the phosphate group of one nucleotide is covalently linked to the C-5 oxygen atom of the sugar of another nucleotide creating a second phosphoester linkage. The entire linkage between carbons of adjacent nucleotides is called a phosphodiester linkage, because it contains two phosphoester linkages.

Nucleic acids contain many nucleotide residues and are characterized by a backbone consisting of alternating sugars and phosphates. In DNA, the bases of two different polynucleotide strands interact to form a helical structure.

DNA Back bone.

RNA contains ribose rather than deoxyribose, and is usually a single stranded polynucleotide. There are four kinds of RNA molecules: Messenger RNA (mRNA), transfer RNA (tRNA), Ribosomal RNA (rRNA), and a heterogeneous class of small RNAs that carry out a variety of different functions.

Introduction- Organic Compounds, Functional Groups and Linkages.

Much of biochemistry deals with biopolymers that are macromolecules created by joining many smaller organic molecules (monomers) via condensation (removal of element of water). Each monomer that makes a macromolecular chain is called a residue.

In some cases like carbohydrates (more on it later), a single monomer or residue is repeated many times, in other cases like proteins and nucleic acids, a variety of residues are connected in a specific order.

The residues are added and converted into a polymer by repeating the same enzyme catalyzed reaction. Thus all of the residues in a biopolymer are aligned in the same direction.

Biopolymers have properties that are very different from those of their constituent monomers. Example: Starch is not soluble in water and does not taste sweet although it is a polymer of the sugar Glucose, which has both those properties.  So we can conclude that each new level of organization results in properties that cannot be predicted just from those of the previous level.

The levels of complexity in increasing order are atoms, then molecules, then biopolymers, then organelles then cells, tissue, organ, and all organisms and systems.

 

The types of organic compounds, functional groups and linkages commonly seen in biochemistry are;

Organic Compounds, Functional Groups and Linkages.

PS: Under most biological conditions, carboxylic acids exist as carboxylate anions: COO and amines exist as ammonium ions: NH3+ .

Please make sure you memorize the names and structures of the functional groups.

Biochemical reactions involve specific chemical bonds or parts of molecules called functional groups which we will deal with several times.

  • Ester and Ether are common linkages found in fatty acids and lipids.
  • Amide linkages are found in proteins.
  • Phosphate ester and Phosphoanhydride linkages occur in nucleotides.