Nucleic Acids (OCR A-Level Biology A): Revision Notes

Nucleic Acids

Introduction to nucleic acids

Nucleic acids are essential biological molecules found in all living organisms. There are two types: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). These molecules are vital because they store genetic information and control cellular processes, particularly protein synthesis.

Nucleic acids consist of five chemical elements: carbon, hydrogen, oxygen, nitrogen, and phosphorus.

A polynucleotide is formed when many nucleotide monomers are covalently bonded together through condensation reactions.

Structure of a nucleotide

Nucleotides are the fundamental monomers of nucleic acids. Unlike other biological monomers, each nucleotide consists of three distinct components joined by covalent bonds formed through condensation reactions:

1. Pentose sugar – a five-carbon ($\text{C}_5$) sugar molecule. This can be either ribose or deoxyribose.
2. Organic nitrogenous base – a nitrogen-containing organic compound. Five bases exist: adenine ($\text{A}$), cytosine ($\text{C}$), guanine ($\text{G}$), thymine ($\text{T}$), and uracil ($\text{U}$).
3. Phosphate group – provides the negative charge on nucleotides.

Organic nitrogenous bases

The five organic nitrogenous bases are nitrogen-containing organic compounds that form part of nucleotides. They can be classified into two categories based on their structure:

Purines

Purines are larger molecules consisting of two carbon–nitrogen rings fused together. The two purines are:

• Adenine (A)
• Guanine (G)

Pyrimidines

Pyrimidines are smaller molecules with a single carbon–nitrogen ring. The three pyrimidines are:

• Cytosine (C)
• Thymine (T) – found only in DNA
• Uracil (U) – found only in RNA

DNA structure – a polynucleotide

Formation of a polynucleotide chain

Nucleotides join together through condensation reactions to form a polynucleotide chain. The phosphate group of one nucleotide bonds covalently to the sugar molecule of the next nucleotide in the sequence. This pattern repeats for each added nucleotide, creating one of the two sugar–phosphate backbones in DNA.

Only nucleotides containing the same type of pentose sugar can join together in a single chain. At this stage, the organic bases project outward from the sugar–phosphate backbone. DNA molecules can contain up to $5$ million nucleotides in a single polynucleotide chain.

The double helix structure

When the nucleic acid contains deoxyribose sugar and the base thymine, the molecule is called DNA. DNA forms its characteristic structure when two polynucleotide chains join together through hydrogen bonds between nitrogenous bases.

Complementary base pairing occurs in a specific manner: a pyrimidine always pairs with a purine. This pairing allows hydrogen bonds to form between bases and maintains constant width along the DNA molecule. The specific pairings are:

• Adenine (A) pairs with Thymine (T) – held by $2$ hydrogen bonds
• Guanine (G) pairs with Cytosine (C) – held by $3$ hydrogen bonds

The two polynucleotide strands run in opposite directions to each other – they are described as antiparallel. The phosphate group connects carbon-3 of one deoxyribose sugar to carbon-5 of the next sugar along the chain.

Once formed, the DNA molecule twists into a helical shape with both backbones spiraling together, creating the double helix structure. This is different from a spiral staircase (where one backbone stays upright while the other twists around it). Instead, both backbones twist simultaneously, similar to a ladder twisted around both uprights.

DNA semi-conservative replication

DNA must replicate to produce exact copies when forming two sister chromatids during cell division. The replication process must be highly accurate to preserve genetic information.

The replication process

1. Unwinding and unzipping: The DNA double helix unwinds and then separates down the center. Hydrogen bonds between base pairs break, leaving two single strands. The enzyme helicase catalyzes this process and holds the separated strands apart.
2. Template formation: The two separated strands act as templates for new DNA molecule synthesis.
3. Nucleotide addition: New DNA nucleotides align with and attach to exposed bases on the original strands through complementary base pairing. Adenine always pairs with thymine, and cytosine always pairs with guanine.
4. Bond formation: Hydrogen bonds form between complementary base pairs. The enzyme DNA polymerase then catalyzes condensation reactions to form covalent phosphodiester bonds between adjacent nucleotides along the sugar–phosphate backbone.
5. Completion: Two identical DNA molecules result. Each contains one original template strand (conserved) and one newly synthesized strand.

The genetic code

DNA functions as an information storage molecule, carrying coded instructions for protein synthesis. The genetic code uses a triplet code system where three consecutive bases specify one amino acid.

There are $20$ different amino acids used in proteins and $64$ possible triplet combinations ($4^3 = 64$). This means multiple triplets can code for the same amino acid.

Some amino acids have only one triplet code (methionine and tryptophan are examples). Three specific codes (AGT, GAT, and AAT) act as stop signals, marking the end of the genetic message.

Genes

DNA is an extremely long molecule containing codes for numerous proteins. A gene is a specific sequence of bases coding for the amino acids that make up a single protein. Gene length varies because proteins differ in length. Some genes may be as short as $50$–$100$ nucleotides, though most are thousands of nucleotides long.

Protein synthesis

Protein synthesis occurs in two main stages: transcription and translation.

Transcription

Transcription is the process of copying genetic information from DNA to form messenger RNA (mRNA).

Within each gene, one DNA strand is the 'coding' strand and the other is the 'template' strand. When a cell needs to produce a specific protein:

1. The enzyme RNA polymerase binds to the DNA at the gene location and unzips the two strands.
2. RNA polymerase moves along the template strand in the $3'$ to $5'$ direction.
3. As it moves, RNA polymerase pairs free RNA nucleotides with complementary nucleotides on the DNA template strand.
4. These RNA nucleotides are covalently linked with phosphodiester bonds to create a polynucleotide chain growing in the $5'$ to $3'$ direction. This chain is called mRNA.
5. Because the mRNA forms through complementary pairing with the DNA template strand, it has the same base sequence as the DNA coding strand (with uracil replacing thymine).

Translation

Translation converts the genetic code in mRNA into a sequence of amino acids.

Once formed, mRNA exits the nucleus through nuclear pores and travels to ribosomes in the cytoplasm. At ribosomes, mRNA acts as the template for protein synthesis. Each triplet of bases on mRNA is called a codon.

Different transfer RNA (tRNA) molecules exist for each amino acid. Each tRNA molecule has two key regions:

• One end binds to a specific amino acid
• The opposite end contains an anticodon – a triplet of bases complementary to an mRNA codon

RNA – a polynucleotide

RNA is a single-stranded polynucleotide composed of RNA nucleotide monomers joined by covalent bonds formed through condensation reactions. RNA molecules are relatively short, typically containing up to a few thousand nucleotides.

Three types of RNA

Messenger RNA (mRNA)

When DNA 'unzips' during transcription, mRNA forms by attaching RNA bases to the exposed section of the DNA template strand. RNA nucleotides attach through hydrogen bonds with complementary DNA bases, building the new mRNA molecule. Complementary base pairing ensures correct base attachment. The mRNA therefore copies genetic information from DNA – this process is transcription.

Transfer RNA (tRNA)

tRNA molecules are short RNA chains that fold back on themselves, creating a clover-shaped structure with some double-stranded regions. These molecules transport amino acids to mRNA at ribosomes, where enzymes form peptide bonds between amino acids to create polypeptide chains.

Ribosomal RNA (rRNA)

rRNA molecules are short RNA chains that combine with ribosomal proteins to form ribosomes – the sites of protein synthesis.

Comparing DNA and RNA

Structural differences

Feature	DNA	RNA
Strand structure	Double-stranded	Single-stranded
Nitrogenous bases	Adenine, thymine, cytosine, guanine	Adenine, uracil, cytosine, guanine
Pentose sugar	Deoxyribose	Ribose
Helical structure	Double helix of two antiparallel polynucleotide chains	One polynucleotide chain can twist into a helix and fold back on itself (tRNA and rRNA); mRNA is linear
Molecule types	One type with numerous variations in base sequence	Three types – mRNA, tRNA, and rRNA – each with different roles
Length	Extremely long (up to $5$ million nucleotides)	Short (up to a few thousand nucleotides)

Functional differences

Feature	DNA	RNA
Information storage	Base sequence codes for proteins – functions as long-term information storage	Does not store information; copies DNA code by hydrogen bonding RNA nucleotides to DNA bases, forming mRNA
Replication	Complementary base pairing allows exact code copying to form new DNA strands; each new molecule contains one original and one new polynucleotide chain	Complementary base pairing enables mRNA formation by copying from DNA – this is transcription
Information capacity	Large information storage capacity due to extremely long strands	Large amounts can be copied as mRNA, but in small sections; molecules are much shorter (typically a few thousand nucleotides)
Stability	Stable molecule due to covalent bonds within and between nucleotides, hydrogen bonds between all bases, and double helix structure	Less stable; easily forms when RNA nucleotides attach to DNA template and breaks down after use; can reform into different mRNA as needed; tRNA and rRNA are more stable than mRNA
Information copying	Hydrogen bonds between bases allow code unzipping for copying or reading	Hydrogen bonds between complementary DNA and mRNA bases enable exact copying; easily broken to allow mRNA exit through nuclear pores; tRNA and rRNA are not involved in copying
Overall role	Long-term genetic information storage; base sequence codes for amino acid assembly into proteins	Protein synthesis

DNA precipitation practical

Isolating DNA from cells is an important molecular biology technique used as the starting point for various investigations. The 'Marmar preparation' method precipitates and isolates DNA through the following steps:

1. Cell disruption: Cells are disrupted by breaking cell and nuclear membranes using concentrated detergent solution.
2. Filtration: The resulting suspension is filtered to remove cell debris and membrane fragments, leaving soluble proteins and DNA.
3. Protein removal: A protease enzyme digests and removes proteins, leaving only DNA.
4. Precipitation: Ice-cold ethanol is added to precipitate the DNA, producing a white precipitate.
5. Analysis: The precipitated DNA can then be used for analysis or further investigations.