Proteins, Nucleic Acids, and Water in Cells

Proteins are polymers of amino acids that do most of the work in cells, nucleic acids (DNA and RNA) are polymers of nucleotides that store and use genetic information, and water is the solvent in which the chemistry of life takes place. In brief: there are 20 common amino acids, joined by peptide bonds into chains that fold into specific shapes. DNA uses the four bases A, T, C and G, and water’s special properties, such as being a good solvent and having a high specific heat capacity, come from hydrogen bonding between its polar molecules.

These molecules complete the main set of biological molecules. This guide explains the structure and functions of proteins, the structure of DNA and RNA, the properties of water, compares them in a table, tests for proteins and works through an example that calculates protein length from a gene and corrects common mistakes.

What are proteins?

Proteins are the most varied biological molecules. They contain carbon, hydrogen, oxygen, nitrogen and often sulfur. A human cell contains thousands of different proteins, and their functions include:

• Enzymes that speed up reactions, such as amylase.
• Structural proteins, such as collagen in skin and keratin in hair.
• Transport proteins, such as hemoglobin and membrane carriers.
• Hormones, such as insulin.
• Antibodies that defend against pathogens.
• Contractile proteins, actin and myosin, in muscle.

How is a protein built and folded?

The monomers of proteins are amino acids. Each has a central carbon atom bonded to an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen atom and a variable side chain called the R group. The 20 common amino acids differ only in their R groups, which can be nonpolar, polar, acidic or basic.

Two amino acids join by a condensation reaction between the carboxyl group of one and the amino group of the other, forming a peptide bond and releasing water. A chain of amino acids is a polypeptide, and a protein consists of one or more polypeptides folded into a specific shape.

• Primary structure: the sequence of amino acids, determined by the gene.
• Secondary structure: local folding into alpha helices and beta sheets, held by hydrogen bonds.
• Tertiary structure: the overall three-dimensional shape of one polypeptide, held by hydrogen bonds, ionic bonds, hydrophobic interactions and disulfide bridges between cysteine residues.
• Quaternary structure: the arrangement of several polypeptides, as in hemoglobin, which has four.

The shape of a protein determines its function. Heat, extreme pH or some chemicals can break the weak bonds and change the shape, called denaturation. A denatured protein usually loses its function, as when the white of an egg turns solid when it is cooked.

The biuret test detects proteins: add sodium hydroxide and dilute copper(II) sulfate. A color change from blue to purple or lilac shows that peptide bonds are present.

What are nucleic acids?

Nucleic acids store and transfer genetic information. The monomers are nucleotides. Each nucleotide has three parts: a five-carbon sugar, a phosphate group and a nitrogen-containing base. Nucleotides join by condensation reactions between the phosphate of one and the sugar of the next, forming a sugar-phosphate backbone.

DNA

DNA (deoxyribonucleic acid) contains the sugar deoxyribose and the bases adenine (A), thymine (T), cytosine (C) and guanine (G). It is a double helix of two strands that run in opposite directions. The bases pair by hydrogen bonds: A with T (two bonds) and C with G (three bonds). This complementary base pairing allows DNA to be copied accurately. The order of bases carries the genetic code.

RNA

RNA (ribonucleic acid) contains the sugar ribose, and the base uracil (U) replaces thymine. It is usually a single strand. The main types are messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA), which are all involved in making proteins. DNA is described in more detail in the article on molecular genetics.

Why is water important in living organisms?

Water makes up about 60 to 70 percent of the mass of most organisms, and over 90 percent in some cells. Its properties come from its molecular structure. The molecule is polar: the oxygen carries a slight negative charge and the hydrogens a slight positive charge. Neighboring molecules attract each other by hydrogen bonds.

• Solvent: ions and polar molecules dissolve, so water is the medium for reactions and transports substances in blood and sap.
• High specific heat capacity: a lot of energy is needed to heat water, so temperatures in cells and in bodies of water change slowly.
• High latent heat of vaporization: evaporation of water, as sweat, removes much heat and cools an organism.
• Cohesion and surface tension: water molecules stick together, which helps to pull water up plant stems and allows some insects to walk on water.
• Ice is less dense than liquid water: ice floats and insulates water below, so lakes do not freeze solid and aquatic life can survive the winter.
• Reactant: water takes part in hydrolysis and photosynthesis.

Biological molecules compared

Worked example: from DNA to protein length

A gene region that codes for a protein is 1 200 nucleotides long on the coding strand, not counting the stop signal. How many amino acids will the protein have, and how many peptide bonds?

1. Codons: each amino acid is coded by three bases (a codon). Number of amino acids = 1 200 ÷ 3 = 400.
2. Peptide bonds: a chain of n amino acids has n − 1 bonds, so 400 − 1 = 399.
3. Water released: one molecule of water is released per bond, so 399 molecules of water are formed in the condensation.
4. Approximate mass: the average mass of an amino acid in a chain is about 110 daltons, so the protein is about 400 × 110 = 44 000 daltons, or 44 kilodaltons.

The base pairing rule can also be applied: if one DNA strand reads 5′-ATGCCA-3′, the complementary strand reads 3′-TACGGT-5′, because A pairs with T and C pairs with G. If the first strand is the coding strand, the mRNA has the same sequence with T replaced by U, which gives 5′-AUGCCA-3′. The example assumes a gene with no introns, as in bacteria.

How were these molecules discovered?

Friedrich Miescher isolated “nuclein”, now known as DNA, from white blood cells in 1869. Frederick Sanger determined the first protein sequence, that of insulin, in the 1950s, and he received the Nobel Prize in Chemistry in 1958. In 1953 James Watson and Francis Crick proposed the double helix model of DNA, using X-ray data from Rosalind Franklin and Maurice Wilkins, and Watson, Crick and Wilkins shared the 1962 Nobel Prize in Physiology or Medicine.

Which mistakes are common?

Mistake 1: Mixing up the bases in DNA and RNA

DNA uses thymine, and RNA uses uracil. Adenine pairs with thymine in DNA and with uracil in RNA.

Mistake 2: Saying that denaturation breaks peptide bonds

It breaks weaker bonds that hold the folded shape. The primary structure stays intact.

Mistake 3: Thinking that water is a hydrocarbon or nonpolar

Water is polar. This is why it dissolves ions and polar molecules but not oils.

Mistake 4: Confusing the amino acid sequence with the overall shape

The sequence is the primary structure. The shape arises from folding of that sequence into higher-level structures.