DNA Structure and Protein Synthesis for the ESAT

Chromosomes and Genes

DNA is the genetic material that stores information as a code known as the genetic code. In the nucleus of a cell, DNA is organised into long, thread like structures called chromosomes. These structures are typically visible only when a cell is dividing, at which point they take on a shape similar to the letter $X$.

Each chromosome consists of long molecules of DNA wrapped around proteins to allow for tight packaging within the nucleus. During the majority of the cell cycle, a chromosome consists of a single molecule of DNA. However, just before cell division, this DNA molecule is copied so that the chromosome comprises two identical DNA molecules. This ensures that when the cell divides, one molecule from each chromosome can be passed to each daughter cell.

DNA molecules are extremely large, containing many millions of bases. A specific section of a chromosome that codes for a particular protein is called a gene.

The Structure of DNA

DNA is a polymer, meaning it is a large molecule made of repeating smaller units.

1. Single stranded DNA (ssDNA): This is a polymer formed when individual units called nucleotides are joined together in a single chain.
2. Double stranded DNA (dsDNA): This consists of two such strands of DNA that twist around each other to form a structure known as a double helix.

Each nucleotide unit is composed of three distinct parts: a common sugar, a phosphate group, and one of four different nitrogenous bases. It is the sequence of these bases along the DNA strand that carries the genetic information.

How the Cell Uses the Genetic Code

Proteins are polymers made up of chains of smaller molecules called amino acids, which contain carbon, hydrogen, oxygen, and nitrogen. The process of building these chains is called protein synthesis. A gene acts as a set of instructions for the cell to build one specific protein.

Although DNA is double stranded, the cell only uses the sequence of bases on one of the strands, known as the template strand, to provide the instructions for making a protein. The cell reads this genetic code in groups of three bases called triplets. Each triplet, such as $ACG$ or $ATC$, codes for one specific amino acid in the protein chain.

Worked Example: Using the Genetic Code

Consider a section of a gene with the following base sequence: $TCAAGGGAGGTCTCG$. To understand how the cell reads this, we separate the bases into triplets:

$TCA$, $AGG$, $GAG$, $GTC$, $TCG$

Each of these triplets corresponds to a specific amino acid. For instance, in this sequence, $TCA$ and $TCG$ both code for the same amino acid, while $AGG$, $GAG$, and $GTC$ code for different ones. The specific order of these triplets ensures that the amino acids are joined together in the correct sequence during synthesis.

Protein Synthesis and Functional Proteins

Protein synthesis involves producing chains of amino acids called polypeptides. A functional protein may consist of a single polypeptide or multiple polypeptide chains working together.

Name of functional protein	Structural details	Role in the organism
Amylase	1 polypeptide (approx 496 amino acids)	Digests starch into simple sugars.
Pepsin	1 polypeptide (327 amino acids)	Breaks down proteins in the stomach.
Insulin	2 chains (21 and 30 amino acids)	Decreases blood glucose levels.
Collagen	3 chains twisted in a triple helix	Provides structural support to tissues.
Haemoglobin	4 chains (2 alpha and 2 beta)	Transports oxygen in the blood.

The Importance of Protein Folding

The three dimensional shape of a protein is determined by the sequence of its amino acids. After the polypeptide chain is formed, it folds into a specific shape. One major driver of this is the interaction with water: some amino acids are attracted to water (hydrophilic), while others are repelled (hydrophobic).

This folding creates a functional shape, such as the active site of an enzyme. If the sequence of amino acids were different, the protein would fold into a different shape and may lose its ability to function.

Gene Mutations

A gene mutation is a change in the sequence of nucleotides in the DNA. This change can alter a triplet, potentially causing a different amino acid to be placed in the polypeptide chain. This can change the three dimensional structure of the resulting protein.

The Effects of Mutations on Phenotype

1. No effect: Many mutations occur in non coding sections of DNA between genes or are silent, meaning the new triplet still codes for the same amino acid. These have no effect on the phenotype.
2. Small effect: Some mutations cause a minor change in phenotype. An example is polydactyly, where a mutation results in a cat having extra toes.
3. Significant effect: Occasionally, a mutation can determine the phenotype by making a protein non functional. For example, if a mutation alters the active site of an enzyme that produces flower pigment, the petals may lack colour or appear different.