Nucleic Acids

Nucleic acids, DNA and RNA, are polymers of nucleotides that store genetic information and direct the making of proteins. These notes on nucleic acids cover their sugars, bases and phosphate, nucleosides and nucleotides, the phosphodiester backbone, Chargaff's rules, the Watson-Crick double helix, replication, transcription, translation and the genetic code, with every structure drawn. They end with vitamins and hormones, the other biomolecules in the syllabus. The topic is asked every year in NEET and JEE Main.

1. What Are Nucleic Acids?

Every generation of a species resembles its ancestors. The particles in the nucleus of a cell that carry heredity are the chromosomes, made of proteins and another kind of biomolecule: the nucleic acids. Nucleic acids are biologically important polymers present in all living cells. Their repeating unit is the nucleotide, so they are also called polynucleotides.

There are two types of nucleic acids:

• DNA (deoxyribonucleic acid), the store of genetic information.
• RNA (ribonucleic acid), which uses that information to make proteins.

2. Chemical Composition

Complete hydrolysis of DNA or RNA gives three kinds of product: a pentose sugar, phosphoric acid and nitrogen-containing heterocyclic bases.

2.1 Phosphate group

Phosphoric acid, ${\mathrm{H}}_3\mathrm{P}{\mathrm{O}}_4$, is present in the chain as a phosphate group, $-\mathrm{O}-\mathrm{P}{\mathrm{O}}_2^{-}-\mathrm{O}-$, bonded to hydroxyl groups of the sugars as a phosphate ester. At the pH of the cell its OH groups are ionised, which gives nucleic acids their acidic, negatively charged character.

2.2 Sugars

Two sugars are found, both as five-membered (furanose) rings (Figure 1):

• RNA contains $\beta$-D-ribose, ${\mathrm{C}}_5{\mathrm{H}}_{10}{\mathrm{O}}_5$.
• DNA contains $\beta$-D-2-deoxyribose, ${\mathrm{C}}_5{\mathrm{H}}_{10}{\mathrm{O}}_4$, which has H instead of OH at C-2. This one missing oxygen gives DNA its name.

2.3 Nitrogen bases

The bases are of two types (Figure 2):

• Purines (two fused rings): adenine (A) and guanine (G), found in both DNA and RNA.
• Pyrimidines (one ring): cytosine (C), in both; thymine (T), only in DNA; and uracil (U), only in RNA.

3. Nucleosides and Nucleotides

A nucleoside contains only two of the three components: a pentose sugar and a nitrogen base. N-1 of a pyrimidine or N-9 of a purine is joined to C-1′ of the sugar (ribose or deoxyribose) by a $\beta$-linkage, the N-glycosidic bond. Sugar carbons are numbered with primes (1′ to 5′) to tell them apart from the atoms of the base. Depending on the sugar, nucleosides are ribonucleosides or deoxyribonucleosides.

A nucleotide contains all three components. When the C-5′ OH of a nucleoside is esterified with phosphoric acid, the product is a nucleotide, so nucleotides are nucleoside monophosphates. They too are ribonucleotides or deoxyribonucleotides. Cytidine monophosphate (CMP), for example, is cytosine + ribose + phosphate (Figure 3).

Nucleotides also do other jobs in the cell. Adenosine triphosphate (ATP), with three phosphate groups on C-5′, is the cell's main carrier of chemical energy.

4. Polynucleotides: The Primary Structure

Nucleotides are joined into a chain through phosphate groups. The phosphate on C-5′ of one nucleotide forms an ester with the C-3′ OH of the sugar of the next, giving a 3′,5′-phosphodiester linkage and releasing water. Repeating this builds a sugar-phosphate backbone, with the bases hanging from C-1′ of each sugar (Figure 5).

• One end of the chain has a free C-5′ group (the 5′ end) and the other a free C-3′ OH (the 3′ end). Sequences are written from the 5′ end to the 3′ end.
• A chain of $n$ nucleotides contains $n-1$ phosphodiester links.
• The sequence in which the bases are attached to the sugar-phosphate backbone is the primary structure of the nucleic acid.

5. Structure of DNA and RNA

5.1 Chargaff's rules

Erwin Chargaff analysed the base composition of DNA from many organisms and found that:

• the amount of adenine equals the amount of thymine (A = T), and the amount of guanine equals the amount of cytosine (G = C);
• so the total purines equal the total pyrimidines: A + G = C + T;
• the ratio (A + T)/(G + C) differs from one species to another, but is the same in all cells of one species.

5.2 The Watson-Crick double helix

In 1953 James Watson and Francis Crick proposed that DNA is a duplex: two polynucleotide strands coiled round each other in a double helix. The sugar-phosphate backbones are on the outside and the bases are stacked inside. Each base on one strand is paired with a base on the other by hydrogen bonds:

• Adenine pairs with thymine through two hydrogen bonds (A=T), and guanine pairs with cytosine through three (G≡C). A purine always faces a pyrimidine, which keeps the width of the helix constant (Figure 6). This pairing explains Chargaff's rules.
• The two strands are complementary, not identical: the sequence of one fixes the sequence of the other.
• The strands run in opposite directions (antiparallel): one 5′ to 3′, the other 3′ to 5′.
• The helix is right-handed, about 2 nm wide, with one complete turn every 3.4 nm and 10 base pairs per turn (Figure 6).

5.3 Structure of RNA

RNA is similar to DNA in its backbone but is usually a single strand, which may fold back on itself where short stretches of complementary bases pair (with U pairing with A). RNA molecules are of three types, with different functions:

• Messenger RNA (mRNA) carries the genetic message from DNA to the ribosomes.
• Ribosomal RNA (rRNA) forms the ribosomes, with proteins, where proteins are made.
• Transfer RNA (tRNA) brings the right amino acid to the ribosome and reads the codon.

6. DNA and RNA Compared

7. Biological Functions of Nucleic Acids

DNA is the chemical basis of heredity and is responsible for keeping the identity of each species over millions of years. It can replicate (copy itself) during cell division, passing identical DNA to the daughter cells, and it holds the message for making proteins. The proteins are actually made by the RNA molecules of the cell, under DNA's direction.

7.1 Replication

Replication is the process by which one DNA molecule produces two identical copies of itself. It is enzyme-catalysed. The two strands of the helix unwind, and each strand acts as a template (pattern) for a new strand: nucleotides line up by base pairing (A with T, G with C) and are joined by DNA polymerase. Each new strand is the exact complement of its template, so both daughter molecules are copies of the original, each keeping one old strand (semi-conservative replication, Figure 8). In this way hereditary characteristics are passed from one cell to the next.

Meselson and Stahl proved the semi-conservative model in 1958 by growing bacteria on heavy nitrogen and then on light nitrogen, and separating the DNA by density:

7.2 Protein synthesis: transcription and translation

Transcription is the synthesis of RNA (mRNA) on a DNA template. It resembles replication, with two differences: ribonucleotides (not deoxyribonucleotides) assemble along the unwound template, and uracil (U) takes the place of thymine (T). Nucleic acid chains are always built in the 5′ $\to$ 3′ direction, here by the enzyme RNA polymerase. In this way DNA passes its genetic code to mRNA. The mRNA then separates from the DNA and moves from the nucleus to the cytoplasm, where it acts as the template for protein synthesis, and the DNA returns to its double helix.

Translation is the synthesis of protein, directed by mRNA in the cytoplasm with the help of tRNA and ribosomes (RNA-protein particles). The mRNA attaches to a ribosome and dictates the amino acid sequence. Its bases are read in threes: each triplet, called a codon, codes for one amino acid. Each tRNA carries an amino acid and an anticodon that pairs with the codon, so the amino acids are placed in the right order and joined by peptide bonds. When the chain is complete it is released from the ribosome. Protein synthesis is fast: about 20 amino acids are added every second.

Translation always runs one way (mRNA to protein), but transcription can sometimes be reversed: in retroviruses such as HIV, RNA is copied into DNA by the enzyme reverse transcriptase (reverse transcription).

7.3 The genetic code

A segment of DNA that carries the information for one protein is a gene. The relationship between nucleotide triplets and amino acids is the genetic code. With four bases, triplets give $4^3=64$ codons, more than enough for 20 amino acids. So most amino acids have more than one codon (the code is degenerate), and three codons are stop signals.

Every sequence question on this page is solved in the same order, shown as a flowchart:

8. Other Biomolecules: Vitamins and Hormones

8.1 Vitamins

Some organic compounds are needed in the diet in small amounts to carry out particular biological functions, for normal health, growth and nutrition. Their lack causes specific diseases. These compounds are vitamins. Most cannot be made by the body (plants can make almost all of them), so they must come from food. Vitamins are named by letters and subscripts, such as A, ${\mathrm{B}}_1$, ${\mathrm{B}}_2$, ${\mathrm{B}}_6$, ${\mathrm{B}}_{12}$, C, D, E and K. Too much of a vitamin is also harmful, so vitamin pills should be taken only on a doctor's advice.

• Fat-soluble vitamins, A, D, E and K, dissolve in fats and oils but not in water. They are stored in the liver and adipose (fat-storing) tissue.
• Water-soluble vitamins, the B group and C, must be supplied regularly, because they are readily excreted in urine and cannot be stored in the body. Vitamin ${\mathrm{B}}_{12}$ is the exception: it is stored in the liver.

8.2 Hormones

Hormones are molecules that act as messengers between cells. They are made by the endocrine glands and poured directly into the bloodstream, which carries them to the site of action. Chemically they fall into three groups:

• Hormones keep the balance of biological activities in the body. Insulin and glucagon keep blood glucose within a narrow range; epinephrine and norepinephrine drive responses to outside stimuli; growth hormones and sex hormones control growth and development.
• Thyroxine, made in the thyroid gland, is an iodinated derivative of the amino acid tyrosine. Too little thyroxine (hypothyroidism) causes lethargy and obesity; too much (hyperthyroidism) raises the body's activity. Low iodine in the diet causes hypothyroidism and enlargement of the thyroid gland (goitre), which is prevented by adding sodium iodide to table salt (iodised salt).
• The adrenal cortex makes glucocorticoids, which control carbohydrate metabolism, modulate inflammation and help the body cope with stress, and mineralocorticoids, which control how much water and salt the kidneys excrete. Failure of the adrenal cortex causes Addison's disease (hypoglycaemia, weakness, greater sensitivity to stress), which is fatal unless treated with these hormones.
• The gonads make the sex hormones. Testosterone gives male secondary characteristics (deep voice, facial hair, general build); estradiol gives female secondary characteristics and controls the menstrual cycle; progesterone prepares the uterus for the implantation of a fertilised egg.

9. The Whole Topic on One Page: Mind Map

The mind map collects the page: what nucleic acids are made of, how they pair, how the information flows, and the other biomolecules in the chapter.

10. Solved Examples

Common Mistakes to Avoid