Dna rna and protein synthesis

Mononucleotide Structure

Every mononucleotide is the fundamental building block of nucleic acids and consists of three components linked together through condensation reactions.

A mononucleotide has three parts. These are a pentose sugar (a 5-carbon sugar), a phosphate group, and a nitrogenous base.

The sugar varies between nucleic acids. DNA contains deoxyribose, while RNA contains ribose. Ribose has an extra hydroxyl (-OH) group at carbon 2 that deoxyribose lacks.

Five different bases appear in nucleic acids. DNA uses adenine (A), guanine (G), cytosine (C), and thymine (T). RNA uses the same first three bases but replaces thymine with uracil (U).

Bases fall into two groups based on their ring structure. Adenine and guanine are purines [larger, double-ring molecules]. Cytosine, thymine, and uracil are pyrimidines [smaller, single-ring molecules].

DNA and RNA Polynucleotides

Mononucleotides join together through condensation reactions to form long chains called polynucleotides, which give DNA and RNA their backbone structure.

A condensation reaction joins the phosphate group of one mononucleotide to the sugar of the next. This forms a strong covalent bond called a phosphodiester bond. The bond connects carbon 3 of one sugar to carbon 5 of the next, releasing one water molecule.

Repeated condensation reactions create a long polynucleotide chain. The alternating sugars and phosphates form a sugar-phosphate backbone, with the bases projecting outwards from this backbone.

DNA and RNA differ in several important ways, summarised below.

Examiner InsightExaminers want the precise term phosphodiester bond when describing how mononucleotides join. Writing simply “covalent bond” or “phosphate bond” may not earn the mark. The bond name appears in many short-answer questions.

Exam TipAlways name phosphodiester bonds when explaining DNA or RNA structure.

The DNA Double Helix and Base Pairing

DNA exists as a double helix in which two polynucleotide strands wind around each other, held together by hydrogen bonds between complementary bases.

The two strands run antiparallel, meaning one runs in the opposite direction to the other. The strands are held together by complementary base pairing.

Adenine always pairs with thymine through two hydrogen bonds. Cytosine always pairs with guanine through three hydrogen bonds. A purine always pairs with a pyrimidine, so the width of the helix remains constant along its length.

Each individual hydrogen bond is weak. However, the millions of bonds along a DNA molecule together provide great stability. The sugar-phosphate backbones lie on the outside of the helix, while the bases sit on the inside, protected from chemical damage.

DNA Replication and DNA Polymerase

DNA replication copies the entire DNA molecule before cell division, so each daughter cell receives a complete and identical genome.

The process is semi-conservative: each new DNA molecule contains one original parental strand and one newly synthesised strand.

The process occurs in distinct steps:

1. The DNA double helix unwinds, and hydrogen bonds between complementary base pairs break. This separates the two strands and exposes the bases.
2. Each separated strand acts as a template for a new strand.
3. Free DNA mononucleotides in the nucleus pair with their complementary bases on the template (A with T, C with G), held in place by hydrogen bonding.
4. DNA polymerase catalyses the formation of phosphodiester bonds between adjacent nucleotides, joining them into a continuous new strand.
5. Two identical DNA molecules result, each with one parental strand and one newly synthesised strand.

This semi-conservative mechanism preserves genetic information accurately across cell generations.

Examiner InsightMany students confuse the role of DNA polymerase with the unwinding step. DNA polymerase does not unwind DNA. Instead, it joins nucleotides together by forming phosphodiester bonds.

Exam TipState precisely that DNA polymerase catalyses phosphodiester bond formation between adjacent nucleotides.

The Meselson and Stahl Experiment

In 1958, Meselson and Stahl performed a classic experiment using nitrogen isotopes that confirmed DNA replication occurs by a semi-conservative mechanism.

Three competing hypotheses had been proposed for DNA replication. The conservative model suggested the original double helix stayed intact and a brand-new helix was made alongside it. The semi-conservative model suggested each daughter molecule contained one original and one new strand. The dispersive model suggested fragments of old and new DNA were scattered through both daughter molecules.

The method used heavy nitrogen (¹⁵N) and light nitrogen (¹⁴N):

1. Bacteria (Escherichia coli) were grown for many generations in a medium containing ¹⁵N. Their DNA contained heavy nitrogen.
2. The bacteria were transferred to a medium containing only ¹⁴N. They continued to replicate.
3. DNA samples were extracted after one and two replications.
4. The DNA was centrifuged in caesium chloride solution. Heavier DNA settled lower than lighter DNA.

After one replication, all DNA showed an intermediate density. This single band ruled out the conservative model, which predicted two bands (one heavy, one light).

After two replications, two bands appeared at intermediate and light densities. This pattern matched the semi-conservative prediction exactly. The dispersive model was ruled out because it predicted a single band of decreasing intermediate density.

The Triplet Genetic Code

The genetic code is the relationship between sequences of DNA bases and the amino acids they encode in a polypeptide chain.

The genetic code has three key features:

1. The code is a triplet code. Three consecutive DNA bases code for one amino acid. With four possible bases and three positions, there are 4³ = 64 possible triplets. This is more than enough to code for all 20 amino acids found in proteins.
2. The code is non-overlapping. Each base is read as part of only one triplet. The bases are read sequentially, three at a time, without sharing.
3. The code is degenerate. Most amino acids are coded for by more than one triplet. For example, leucine has six different triplets that code for it. Degeneracy means some single-base mutations do not change the amino acid produced, reducing harm.

Some triplets serve special functions. Three are stop codons that signal the end of a polypeptide chain. One triplet (AUG on mRNA) is the start codon and also codes for methionine.

Genes and Polypeptides

A gene is a sequence of DNA bases that codes for the amino acid sequence of a single polypeptide chain.

A gene is a length of DNA containing a specific sequence of bases that determines the order of amino acids in one polypeptide. The base sequence of the gene is decoded during protein synthesis to produce the polypeptide chain.

Different genes contain different base sequences, so they code for different polypeptides. The unique amino acid sequence of each polypeptide determines its three-dimensional shape and therefore its function.

A change in the base sequence of a gene (a mutation) can alter the amino acid sequence of the polypeptide. This may change the protein’s shape and function.

Transcription

Transcription is the first stage of protein synthesis in which the base sequence of a gene is copied onto a messenger RNA molecule.

Transcription occurs in the nucleus. The result is a single-stranded messenger RNA (mRNA) molecule that carries the genetic information out of the nucleus to the ribosomes.

Transcription occurs in clear steps:

1. The enzyme RNA polymerase binds to the start of the gene on the DNA.
2. RNA polymerase unwinds the DNA double helix in the region of the gene and breaks the hydrogen bonds between bases.
3. One strand of the DNA acts as the template strand (also called the antisense strand). The other strand (the sense strand) is not used.
4. Free RNA mononucleotides in the nucleus pair with their complementary bases on the template strand. Adenine on the DNA template pairs with uracil on the RNA, because RNA contains uracil instead of thymine. Cytosine pairs with guanine.
5. RNA polymerase joins adjacent RNA nucleotides via phosphodiester bonds, forming a chain of mRNA.
6. When RNA polymerase reaches a stop signal, the mRNA is released and detaches from the DNA.
7. The DNA double helix re-forms.

The completed mRNA leaves the nucleus through a nuclear pore and travels to a ribosome in the cytoplasm.

Translation

Translation is the second stage of protein synthesis in which the base sequence on mRNA is decoded into a chain of amino acids.

Translation takes place at a ribosome in the cytoplasm. The ribosome reads the mRNA in groups of three bases called codons and assembles a polypeptide in the order specified by the mRNA.

Three components are involved:

• mRNA: carries the genetic message as codons
• Ribosome: reads the mRNA and forms peptide bonds between amino acids
• Transfer RNA (tRNA): brings amino acids to the ribosome; each tRNA has a specific anticodon complementary to one mRNA codon, and carries one specific amino acid

Translation occurs in clear steps:

1. The mRNA binds to a small ribosomal subunit, and the large subunit attaches.
2. The ribosome locates the start codon (AUG) on the mRNA. A tRNA with the complementary anticodon (UAC) and carrying methionine attaches by hydrogen bonding.
3. A second tRNA with an anticodon complementary to the next codon binds to the ribosome, bringing its amino acid alongside the first.
4. The ribosome catalyses the formation of a peptide bond between the two amino acids in a condensation reaction.
5. The first tRNA leaves, and the ribosome moves one codon along the mRNA.
6. New tRNAs continue to bind, deliver amino acids, and form peptide bonds. The polypeptide chain grows.
7. When the ribosome reaches a stop codon on the mRNA, no tRNA can bind. Translation stops, and the completed polypeptide is released.

The polypeptide then folds into its final three-dimensional shape and may be modified into a functional protein.

Examiner InsightExaminers want precise vocabulary: codons are on mRNA, anticodons are on tRNA, and triplets are on DNA. Mixing these up costs marks. Always pair the term with the correct molecule.

Exam TipState “codon on mRNA” or “anticodon on tRNA”; never use “code” alone.