Gene expression and protein synthesis

Question 1

Mendel’s Pea Plant experiment -1866

Answer 1

• What it was: Mendel’s pea plant experiment was a series of controlled breeding studies to understand how traits are inherited.
• What he did: He cross-pollinated pea plants with different traits (e.g., tall vs. short, purple flowers vs. white) and tracked how traits appeared over several generations.
• Conclusion: Mendel concluded that traits are inherited as discrete units (genes), leading to his Laws of Inheritance: the Law of Segregation (each parent passes one allele per trait) and the Law of Independent Assortment (different traits are inherited independently).

Question 2

Beadle and Tatum - 1940s

Answer 2

• exposed bread mould (Neurospora crassa) to x rays, creating mutants that were unable to survive on minimal media
• Auxotroph - the inability of an organism to synthesize a particular compound required for its growth
• identified three classes of arginine-deficient mutants (each lacking a different enzyme necessary for synthesizing arginine)
• they developed a gene-one enzyme hypothesis, which states that each gene dictates production of a specific enzyme

Question 3

genome

Answer 3

• complete set of genetic instructions for any organism - typically DNA (sometimes RNA)
• coding system for genetic information is the same in all living organisms

Question 4

transcription

Answer 4

• is the synthesis of RNA using info in genomic DNA
• produces mRNA for protein-coding genes

Question 5

Translation

Answer 5

• synthesis of a polypeptide, using info in the mRNA
• ribosomes are the sites of translation

Question 6

genetic code

Answer 6

• there are 20 amino acids, but there are only four nucleotide bases in DNA

Question 7

the triplet code

Answer 7

• codon: a triplet RNA code
• DNA contains 4 nucleotides: A T - C G
• RNA contains 4 corresponding ribonucleotides: A U - C G
• 64 (4^3) possible codons: 3 stop codons (termination codon), 61 sense codons (code for an amino acid)
• the genetic code is ‘degenerate’ (more than one codon may specify a particular amino acid)
• ….but not ambiguous (no codon specifies more than one amino acid)

Question 8

The codon table for mRNA

Answer 8

• the codons are written 5’→3’, as they appear in the mRNA
• AUG is an initiation codon
• UAA, UAG and UGA are termination (stop) codons
• degeneracy of codons is the redundancy of the genetic code
• 61 codons for only 20 amino acids

Question 9

evolution of the genetic code

Answer 9

• the genetic code is nearly universal, shared by the simplest bacteria to the most complex animals
• genes can be transcribed and translated after being transplanted from one species to another

Question 10

Mutations

Answer 10

• essential but can cause problems
• source of all genetic variation: provides the raw material for evolution
• source of many diseases and disorders
• useful for probing fundamental biological processes
• main types of mutations: - base substitutions, base insertions and deletions

Question 11

What are the effects of base substitution mutations: missense, nonsense, and silent?

Answer 11

• Missense Mutation: Changes one base, resulting in a different amino acid (e.g., Ser → Leu).
• Nonsense Mutation: Changes a base to create a stop codon, ending translation early.
• Silent Mutation: Alters a base but the amino acid remains the same, so the protein is unchanged.

Question 12

How do insertions and deletions affect the reading frame of a DNA sequence?

Answer 12

• Insertion: Adds a base, shifting the reading frame, which changes many downstream codons.
• Deletion: Removes a base, also causing a frameshift and altering the entire protein sequence.
• Both can significantly disrupt protein function by changing multiple amino acids.

Question 13

Phenotypic effects of mutations

Answer 13

• loss of function mutations: results in reduced or abolished protein function
• gain of function mutations: confers new or enhanced activity to a protein
• conditional mutation: a mutant allele causes a mutant phenotype in only a certain environment (restrictive condition), but otherwise retains a wild-type phenotype
• lethal mutation: it affects the survival of the organism

Question 14

oncogene

Answer 14

• any gene that encodes a protein able to induce cancer
• most are derived from normal cellular genes (i.e., proto-oncogenes) that produces protein products that normally enhance cell division or inhibit normal cell death
• conversion of a proto-oncogene into an oncogene involves a gain of function mutation
• gain of function ≠ good
• loss of function ≠ bad

Question 15

What properties of RNA enable it to direct the synthesis of a polypeptide?

Answer 15

• 3D Structure Formation: RNA can fold into complex shapes by base-pairing with itself.
• Catalytic Functional Groups: Some RNA bases have chemical groups that can aid in catalysis.
• Hydrogen Bonding: RNA can form hydrogen bonds with other nucleic acids, which helps in processes like translation.

Question 16

The structure and function of transfer (tRNA)

Answer 16

• there are many tRNA molecules in the cell
• each carries a specific amino acid on one end and has an anticodon on the other end
• the anticodon base-pairs with a complementary codon on mRNA
• hydrogen bond interactions cause the tRNA to fold into a three-dimensional molecule

Question 17

tRNAs in translation

Answer 17

• translation is a complex biochemical and mechanical process, Accurate translation requires two steps:
• a correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetase
• a correct match between the tRNA anticodon and an mRNA codon

Question 18

the tRNA wobble position

Answer 18

this 3rd nucleotide has two major characteristics:
- binding between codon and anti-codon is much ‘looser’. This permits several types of non-Watson-Crick base pairing to occur
- the redundancy of the genetic code is largely specified by the 3rd codon position such that several codons can utilise the same tRNA

Question 19

What is the role of aminoacyl-tRNA synthetase in translation?

Answer 19

Aminoacyl-tRNA synthetase attaches the correct amino acid to its matching tRNA using ATP.
Steps:
1- The amino acid and tRNA enter the enzyme’s active site.
2 - ATP is used to catalyse a covalent bond between the amino acid and tRNA.
3 - The charged tRNA (aminoacyl-tRNA) is released and ready to deliver the amino acid during protein synthesis.

Question 20

Ribosome

Answer 20

• facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis
• the two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rRNA)
• small subunit: info processing (where the mRNA attaches)
• Large subunit: catalytic site, forming bonds between amino acids

Question 21

What are the three binding sites in the ribosome and what are their roles in translation?

Answer 21

• A site (Aminoacyl-tRNA site): Holds the tRNA carrying the next amino acid to be added.
• P site (Peptidyl-tRNA site): Holds the tRNA with the growing polypeptide chain.
• E site (Exit site): Where discharged tRNAs leave the ribosome after delivering their amino acid.

Question 22

Building a polypeptide: 3 stages of translation

Answer 22

• initiation: transitional complex forms, and tRNA brings first amino acid in polypeptide chain to bind to start codon on mRNA
• elongation: tRNAs bring amin acids one by one to add to polypeptide chain
• termination - release factor recognises stop codon, translational complex dissociates, and completed polypeptide is released

Question 23

What happens to polypeptides after translation?

Answer 23

• often translation alone is not sufficient to make a functional protein
• folding may be spontaneous but aften requires chaperone proteins
• polypeptide chains are modified after translation - post-translational modifications (PTMs)
• proteins are often targeted to a certain area of the cell - localisation
• post-translational modifications and localisation are often essential for function