IB Biology SL Topic D1.2

What does a genome represent for an organism?

The complete set of genetic information (all the DNA) in an organism, including all of its genes and non-coding DNA sequences.

What is a codon?

A sequence of three DNA or RNA nucleotides (a triplet) that codes for a specific amino acid or serves as a start/stop signal during translation.

How many codons are there in total?

There are 64 possible codons in total (4³, since there are 4 different nucleotides taken in combinations of 3).

The genetic code is universal. What does this mean?

It means that virtually all living organisms—from bacteria to humans—use the exact same triplet codons to code for the same amino acids, which provides strong evidence for a common evolutionary ancestry.

How many possible codons exist, and how many amino acids are used in life?

• 64 possible codons exist.

• 20 standard amino acids are used to build proteins in living organisms.

What does it mean that the genetic code is degenerate (redundant)?

It means that most amino acids are specified by more than one codon. For example, multiple codons can code for leucine or serine.

State the flow of information from DNA to protein.

DNA → mRNA → Protein (Transcription followed by Translation, known as the Central Dogma of molecular biology).

What is the metaphor for RNA synthesis, and where does it take place?

• Metaphor: Photocopying or making a working copy of a specific recipe from a master cookbook so it can leave the kitchen safely.

• Location: In the nucleus of eukaryotic cells.

What is the metaphor for protein synthesis, and where does it take place?

• Metaphor: Following the recipe in a factory (the ribosome) to assemble the final product.

• Location: In the cytoplasm at the ribosomes (either free in the cytosol or attached to the rough endoplasmic reticulum).

What is the overall function of mRNA synthesis?

To create a portable, single-stranded copy of a gene (mRNA) that carries the genetic instructions from the DNA in the nucleus to the ribosomes in the cytoplasm.

State the mechanism of RNA polymerase in three steps.

1. Initiation: RNA polymerase binds to the promoter region of a gene, causing the DNA strands to unwind and separate.

2. Elongation: RNA polymerase moves along the template strand, synthesizing a single-stranded mRNA molecule via complementary base pairing (incorporating uracil instead of thymine).

3. Termination: RNA polymerase reaches a terminator sequence, releasing the completed mRNA transcript and detaching from the DNA.

What is the overall function of protein synthesis?

To decode the mRNA sequence into a polypeptide chain (protein) with a specific sequence of amino acids, which determines the structure and function of the cell.

What is the difference between the stability of the genome and proteome?

• The genome is fixed and stable (remains largely identical in almost all cells of an organism throughout its lifetime).

• The proteome is dynamic and variable (constantly changes depending on cell type, developmental stage, and environmental conditions, as different genes are expressed).

State the two types of RNA involved with translation and their functions.

1. mRNA (Messenger RNA): Carries the genetic code from DNA to the ribosome.

2. tRNA (Transfer RNA): Transports specific amino acids to the ribosome and matches its anticodon to the mRNA codon. (Note: rRNA also forms part of the ribosome structure).

What is the function of the ribosome?

To act as the cellular workbench for protein synthesis, coordinating the interaction between mRNA and tRNA, and catalyzing the formation of peptide bonds between amino acids.

How does the tRNA interact with mRNA, ensuring the code is translated correctly?

Each tRNA molecule carries a specific amino acid and possesses a three-nucleotide anticodon that forms complementary base pairs with the corresponding codon on the mRNA strand.

State the mechanism of the ribosome in four steps.

• Initiation: The small ribosomal subunit binds to the mRNA near the start codon (AUG), and the initiator tRNA binds to it. The large ribosomal subunit then joins the complex.

• Elongation: Successful tRNAs enter the A-site carrying amino acids. A peptide bond forms between the amino acid in the P-site and the amino acid in the A-site.

• Translocation: The ribosome shifts three nucleotides down the mRNA. The empty tRNA moves to the E-site and exits, while the tRNA holding the growing peptide chain moves from the A-site to the P-site.

• Termination: When the ribosome reaches a stop codon, a release factor binds, causing the polypeptide chain, mRNA, and ribosomal subunits to dissociate.

What is the relationship between the error rate of transcription and translation and the viability of the cell, and why?

Low error rates are vital for cell survival. While transcription errors affect only a few temporary mRNA copies, translation errors result in misfolded or non-functional proteins. High error rates can disrupt crucial enzymes and structural proteins, leading to cell damage or death.

State an example of a substitution mutation found in the haemoglobin gene.

A single nucleotide substitution in the gene for the beta-globin chain of haemoglobin where adenine is replaced by thymine (changing the DNA triplet from GAG to GTG, resulting in an mRNA codon change from CUC to CAC).

What effect does the mutation have on the haemoglobin protein and red blood cell?

• On the protein: It replaces the amino acid glutamic acid with valine at position 6, making the haemoglobin molecules sticky and prone to forming rigid fibers under low oxygen conditions.

• On the red blood cell: It deforms the normally flexible, disc-shaped red blood cell into a rigid, crescent or "sickle" shape, which can block capillaries, reduce oxygen delivery, and cause the cells to break down prematurely.