Nucleotides and nucleic acids (2.1.3)
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Nucleotides (or mononucleotides) are monomers that are linked by condensation reactions to form nucleic acids (or polynucleotides; DNA and RNA).
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are information–carrying molecules found in nearly all living cells. They are polymers of nucleotides.
- DNA stores genetic information.
- RNA has several roles, including transferring genetic information from DNA to ribosomes (mRNA), combining with proteins to form ribosomes (rRNA), and being involved in protein synthesis (tRNA).
Nucleotides (mononucleotides) consist of three primary components joined together by condensation reactions:
- a pentose sugar, which is a 5-carbon sugar molecule
- a phosphate group, which is attached to the 5′ carbon of the pentose sugar
- a nitrogenous base (nitrogen-containing organic base), which is attached to the 1′ carbon of the pentose sugar.
By convention, the carbon numbers in the sugar are numbered 1′ to 5′.
DNA and RNA nucleotides differ in the type of pentose sugar they contain:
- DNA (deoxyribonucleic acid) contains the pentose sugar deoxyribose which lacks an oxygen atom on the 2′ carbon.
- RNA (ribonucleic acid) contains the pentose sugar ribose which has a hydroxyl attached to the 2′ carbon.
DNA and RNA nucleotides differ in one of their nitrogenous bases (nitrogen-containing organic bases):
DNA and RNA polynucleotides both contain adenine, cytosine, and guanine.
The fourth nitrogenous base DNA contains is thymine, but in RNA it is uracil.
DNA and RNA have similar structures, but also several important differences.
There are five nitrogenous bases in DNA and RNA nucleotides and they can be split into 2 groups:
- Purines are larger, double carbon ring structures — adenine (A) and guanine (G).
- Pyrimidines are smaller, single carbon ring structures — cytosine (C), thymine (T; only in DNA) and uracil (U; only in RNA).
Di- and polynucleotides are formed when condensation reactions link nucleotides by phosphodiester bonds.
Phosphodiester bonds occur between the phosphate group of one nucleotide and the hydroxyl group on the 3’ carbon of the pentose sugar of another nucleotide.
This linkage forms the sugar–phosphate backbone of DNA and RNA strands.
The breakdown of polynucleotides occurs through the hydrolysis of phosphodiester bonds. This reaction uses water.
ATP (Adenosine triphosphate) is a phosphorylated nucleotide derivative that acts as the immediate energy source in cells. It consists of three key components:
- Adenine: a nitrogenous base.
- Ribose: a five-carbon (pentose) sugar.
- Three phosphate groups: linked with high-energy bonds, which release energy when hydrolysed.
ATP provides an immediate energy source for biological processes. ATP is continuously hydrolysed (by ATP hydrolase) to form ADP + Pi and resynthesised within cells to support metabolic activities such as active transport, muscle contraction and protein synthesis.
The phosphate released from the hydrolysis of ATP can be used to phosphorylate other compounds.
ATP can be (re)synthesised by the condensation of ADP via a phosphorylation reaction requiring energy.
Phosphorylation of ADP is catalysed by the enzyme ATP synthase and occurs in mitochondria, during aerobic respiration (electron transport chain) and in chloroplasts, during photosynthesis (light-dependent reactions).
Adenine (A) pairs with thymine (T) through 2 hydrogen bonds.
Guanine (G) pairs with cytosine (C) through 3 hydrogen bonds.
A DNA molecule is made up of 2 DNA polynucleotide chains.
The two strands run antiparallel to each other; 1 strand runs in the 5’ to 3’ direction, while the other runs in the 3’ to 5’ direction.
Hydrogen bonds between complementary base pairs hold the two chains together.
The two bonded DNA strands twist to form a double helix structure.
DNA can be extracted from cells and purified using DNA precipitation. This method involves a series of chemical treatments to isolate DNA from proteins, lipids, and other cellular components.
- To extract DNA from plant cells, first break down a sample in a pestle and mortar to destroy the cell walls. Transfer all the material to a test tube.
- Add a detergent to break down the cell membranes and release the cell contents.
- Add salt to break the hydrogen bonds between the DNA and water.
- Add proteases to break down the proteins bound to the DNA.
- Carefully add cold ethanol by pouring it down the side of the test tube.
DNA is insoluble in alcohol, so it precipitates as visible, white strands, which form as a layer between the plant tissue and the alcohol. The DNA can be removed from the test tube using a glass rod.
DNA replication is the process by which DNA is copied.
It follows a semi–conservative mechanism; each new DNA molecule consists of one original (parental) strand and one newly synthesised strand.
This ensures that each daughter cell receives an exact copy of the DNA, maintaining genetic continuity between generations of cells.
DNA replication begins with DNA helicase unwinding the DNA double helix, separating the two strands by breaking the hydrogen bonds between complementary bases.
This separation creates two single-stranded templates that can both be used for synthesising new DNA strands. One is called the leading strand and the other, the lagging strand.
The unwound DNA forms a Y–shaped structure called the replication fork.
DNA synthesis on the leading strand occurs continuously.
DNA polymerase joins new adjacent nucleotides that are complementary to the template strand via condensation reactions which form phosphodiester bonds.
The addition of nucleotides in the 5’ to 3’ direction means that the newly synthesised strand grows in the direction of the movement of the replication fork.
DNA synthesis on the lagging strand occurs discontinuously because DNA polymerase can only add nucleotides in the 5′ to 3′ direction. As a result, the lagging strand is synthesised in short sections called Okazaki fragments, which are later joined together.
Errors in DNA replication can cause random, spontaneous genetic mutations, which are changes to the base sequence of DNA within a gene.
They are often corrected by DNA repair mechanisms, but those that persist can lead to genetic diversity or, in some cases, diseases.
The genetic code is the set of rules by which the information encoded within DNA or RNA sequences is translated into proteins by living cells.
This code specifies how sequences of nucleotides correspond to specific amino acids, which are the building blocks of proteins.
The genetic code is written in triplet codes, which are sequences of three nucleotides and referred to as codons.
Each DNA codon corresponds to a specific amino acid, or to a ‘start’ or ‘stop’ command during protein synthesis.
For example, the codon AUG codes for the amino acid methionine, which also serves as the start codon.
The genetic code is non-overlapping, meaning that each nucleotide is part of only one codon.
This linear and non-overlapping reading frame is critical. A shift in the reading frame is known as a frameshift mutation. This can lead to the placement of an incorrect amino acid in a polypeptide chain or the incorrect ‘reading’ of a stop codon, resulting in a truncated or non-functional protein.
The genetic code is degenerate, which means that multiple codons can code for the same amino acid.
For example, the amino acid leucine is coded by six different codons (UUA, UUG, CUU, CUC, CUA, CUG).
This redundancy is beneficial because it provides a ‘buffer’ against mutations. A mutation in one nucleotide of a codon might not change the amino acid it codes for, thereby minimising the impact on the protein’s structure and function.
Methionine and tryptophan are the only amino acids that are coded by a single codon (AUG and UGG, respectively).
The genetic code is universal, meaning that the same codons specify the same amino acids across almost all living organisms.
The universality of the genetic code suggests a common evolutionary origin and allows for the possibility of genetic engineering, where genes from one organism can be expressed in another (e.g., using bacterial cells to produce human insulin).
DNA contains the ‘instructions’ for making polypeptides, but is contained in the nucleus of cells. The ribosomes, which assemble polypeptides, are in the cytoplasm.
Protein synthesis, therefore, happens in two stages:
- Transcription – messenger RNA (mRNA) is made from the DNA template. The mRNA takes the instructions from the nucleus to the ribosomes.
- Translation – ribosomes join amino acids together in the order specified by the sequence of bases in the mRNA, forming a polypeptide.
To start transcription, the DNA template of a gene must be exposed.
At the start codon of a gene, the enzyme DNA helicase unzips the DNA double helix, breaking the hydrogen bonds between complementary base pairs.
The sense strand of DNA runs 5’ – 3’ and codes for proteins; the antisense strand is complementary to it.
During transcription, the DNA sequence of a gene is copied into messenger RNA (mRNA):
- To copy the base sequence held on the sense strand, the mRNA is complementary to the antisense strand, which acts as a template.
- Free RNA nucleotides match up with their complementary base pairs on the exposed antisense strand.
- RNA polymerase joins the RNA nucleotides in condensation reactions, forming phosphodiester bonds.
- Transcription stops at the end of a gene, and the mRNA molecule leaves the nucleus through a nuclear pore.
During translation, ribosomes join amino acids together in the order specified by the sequence of bases in the mRNA codons, forming a polypeptide and determining how it will fold and function.
Each codon specifies a particular amino acid, which is delivered to the ribosome by a transfer RNA (tRNA) molecule.
ATP provides energy for an enzyme to join amino acids together by peptide bonds.
Transfer RNA, tRNA is made of RNA nucleotides. It is a small, single-stranded molecule that folds into a clover leaf shape due to complementary base pairing within its single strand.
Each tRNA has an anticodon region that pairs with a complementary codon on the mRNA.
At the other end of the molecule from the anticodon, tRNA molecules have an amino acid attachment site. Each tRNA can only bind to one specific amino acid which is determined by its anti-codon.
Translation is a multistep process involving mRNA, ribosomes, tRNA and amino acids:
- mRNA binds to the small subunit of a ribosome at its start codon.
- A tRNA molecule with the complementary start anticodon binds to the mRNA and the ribosome, bringing with it an amino acid.
- A tRNA molecule with an anticodon complementary to the next codon along on the mRNA molecule and an amino acid binds next.
- Part of the ribosomal RNA, rRNA of the ribosome, the enzyme peptidyl transferase catalyses the formation of a peptide bond, joining the two amino acids together.
- The ribosome moves along the length of the mRNA molecule, repeating the above process until reaching a stop codon. There is no complementary tRNA anticodon for the stop codon, so the polypeptide chain is released.
Multiple ribosomes can simultaneously synthesise multiple polypeptide chains from a single mRNA molecule by following each other along the mRNA.
