Genetics: DNA, RNA, and Protein Synthesis

Nature of the Genetic Code

• DNA, or deoxyribonucleic acid, serves as the molecule of inheritance.
• DNA allows a species' characteristics to pass through generations, remaining relatively unchanged.
• DNA determines the polypeptides and proteins, especially enzymes, produced by cells.
• Enzymes made under the direction of DNA control cell metabolism.
• DNA includes repeating units of deoxyribose sugar and phosphate.
• Two DNA strands are linked by nitrogenous bases: adenine, guanine, cytosine, and thymine.
• Adenine always pairs with thymine, and cytosine with guanine, through hydrogen bonding.
• The sequence of nitrogenous bases on the template strand creates the DNA code.
• Polypeptides consist of approximately 20 diverse amino acids in various combinations
• The sequence of amino acids is the primary structure and it determines the overall structure of a polypeptide.
• DNA controls the arrangement of amino acids, which makes up the primary structure
• The genetic code determines how DNA codes for specific amino acids in specific locations within a polypeptide or protein.
• The length of DNA needed to code for a specific polypeptide makes up a gene.

The Genetic Code

• A single DNA base cannot code for one of the 20 amino acids.
• Two consecutive bases are also insufficient, as they yield only 16 combinations (4 x 4 = 16).
• Three consecutive bases result in 64 possible combinations (4 x 4 x 4 = 64).
• The genetic code uses three consecutive bases to code for a particular amino acid, known as the triplet code.
• Each group of three bases which code for an amino acids are considered as base triplet.
• The nucleotide sequence AAT codes for leucine and GCG codes for arginine.

Features of the Genetic Code

• The code is non-overlapping, where each base in the DNA sequence is read only once.

• For a DNA sequence of AATGCG, AAT codes for leucine and GCG codes for arginine in consecutive positions.

• The code is degenerate, meaning most amino acids have multiple possible codes.

• With 64 possible base triplets coding for 20 amino acids, this allows for duplication.

• The first two DNA bases in a triplet determine the amino acid produced.

• GGA, GGC, GGG, and GGT all code for the amino acid proline.

• Some base triplets do not code for an amino acid and will act as a terminator instead.

• These types of triplets are called stop base triplets, and signify the end of a sequence.

• TAC codes for methionine and acts as a start triplet, initiating a coding sequence.

• The DNA code is universal, meaning with few exceptions, the code is present in living organisms.

• Protein synthesis occurs in the cytoplasm, while the genetic code resides in the nucleus.

• Messenger RNA (mRNA) must carry the code from the nucleus to the cytoplasm.

• Copying the code from DNA to mRNA is transcription, followed by 'translation' into a polypeptide.

• Protein synthesis involves transcription and translation.

Transcription

• Transcription involves forming complementary mRNA copies from DNA sequences that code for polypeptides or proteins.

Messenger RNA (mRNA)

• Using mRNA instead of DNA has advantages as mRNA is a disposable copy.
• DNA can be copied to produce many mRNA strands which act as the template for many polypeptides to be produced.
• By remaining in the nucleus, the DNA can more easily accessible for transcription
• By remaining in the nucleus, the DNA is less likely to be damaged vs being in more metabolically active cytoplasm.
• mRNA is a single strand compared to DNA's double helix.
• mRNA contains ribose sugar instead of deoxyribose.
• mRNA contains uracil instead of thymine as a nitrogenous base.
• The same coding principles apply to mRNA as to DNA.
• Each sequence of three bases along the mRNA strand codes for an amino acid.
• mRNA is shorter than DNA because it only complements a short section of DNA.

The Process of Transcription

• DNA helicase separates the two DNA strands of the section to be copied by breaking the hydrogen bonds.
• RNA polymerase moves along the template strand, linking the exposed nucleotides to complementary RNA nucleotides.
• mRNA strand building follows complementary base pairing rules, with uracil replacing thymine.
• RNA polymerase links adjacent mRNA nucleotides with phosphodiester bonds.
• The unzipped DNA rejoins behind the assembly area, exposing only around 20 base pairs at a time.
• When RNA polymerase reaches a 'stop' triplet code, it detaches, completing the copying.

Modification of the mRNA

• DNA has coding (exons) and non-coding (introns) sections.
• Introns are often referred to as 'junk' DNA but regulate coding gene activity.
• Prokaryotic DNA does not have introns.
• Transcription copies both exons and introns.
• Introns are removed from pre-mRNA.
• Exons are spliced back to produce the coding sequence.
• Introns are removed following transcription.
• Exons are spliced together to code for the polypeptide or protein.
• Following intron removal, exons can be combined to code for different polypeptides or proteins.
• The flexibility of introns allows 21,000 human genes to code for 100,000 proteins.
• Functional mRNA exits the nucleus through a nuclear pore for translation in the cytoplasm.
• Translation is the process where the mRNA code is translated into a polypeptide.
• Codons are a sequence of three bases on the mRNA that codes for a particular amino acid.

Transfer RNA (tRNA) and Ribosomes

• tRNA and ribosomes, along with mRNA, translate.
• tRNA is a small molecule, consisting of 70-80 nucleotides and twisted into a clover leaf shape.

tRNA Functions

• Carries a sequence of three bases, which is called an anticodon.
• The anticodon forms complementary base pairs with a mRNA codon.
• Contains an exposed nucleotide section where an amino acids can attach.
• tRNA comes in 20 variants
• The tRNA anticondon is unique to the type of tRNA that is produced.
• Ribosomes are organelles, approximately 30 nm in diameter, and comprised of two sub-units.
• Sub-units made of protein and ribosomal RNA assembled in the nucleolus, then transported to the cytoplasm.
• The two sub-units link together as they lock on to the start of the mRNA strand.
• A ribosome has two sites, the aminoacyl (A) and peptidyl (P) sites.
• tRNA molecules link via complementary anticodons and codons at the A site.
• Adjacent amino acids link together by peptide bonds at the P site.
• The ribosome holds the mRNA, the tRNA and enzymes involved in protein synthesis in place.

The Process of Translation

• A ribosome attaches to the start codon (AUG) on the mRNA by its A site.

• The tRNA molecule with the complementary anticodon (UAC) moves to the ribosome

• With the help of the (UAC) anticodon, the tRNA pairs with it's complementary codon (AUG) sequence.

• The tRNA then carries the amino acid methionine to the ribosome.

• The ribosome shifts to cover two codons, a tRNA molecule with a complementary anticodon pairs with another codon.

• By this stage the AUG (methionine) will now be in the P site, freeing up the A site for the second amino acid.

• A peptide bond links the first two amino acids together to form a dipeptide.

• The ribosome moves along another codon, freeing the tRNA for methionine.

• The tRNA for the second amino acid (serine) occupies the P site which leaves the A site free for the next tRNA.

• The process continues, building a polypeptide sequence.

The End of Translation

• The process continues until a stop codon is reached.
• All polypeptides or proteins needs to go through translation to start, but do not require to AUG.
• The complete complex is called a polyribosome.
• Here are the mRNA condons involved in translation and the amino acids they code for

Key Acids involved in translation

• Polypeptides formed by translation are transported to the Golgi apparatus for processing.
• In the Golgi apparatus, the polypeptides are processed to produce the final proteins.

The One Gene – One Polypeptide Theory

• Established by Francis Crick and James Watson circa 60 years ago, building on prior work done by Chargaff, Franklin and Wilkins.

• Crick's central dogma suggests a key link between DNA, RNA, and protein: DNA → RNA → Protein.

• Retroviruses use reverse transcriptase enzymes and mRNA to make complementary DNA.

• The current revised view is: DNA → DNA → RNA → Protein.

• A gene (DNA sequence) codes for a polypeptide.

• The polypeptide is a sequence of amino acids.

• The amino acids are linked together during translation.

• The concept of a 'one gene one protein' is most usable when the protein only contains one polypeptide

• The term 'one gene one enzyme' is a simplification because enzymes don't make up all proteins and all proteins are not enzymes.

Epigenetics

• Epigenetics studies heritable genome modifications that don't change the DNA sequence.
• It affects gene activity without changing the DNA sequence itself.
• Epigenetics can increase or decrease gene expression, temporarily or permanently, is referred to as epigenetic modification.
• Epigenetic modifications do not alter what a gene codes for, they can only increase or decrease gene coding potential for particular protein.
• Mutations are not epigenetic modifications alter the DNA sequence permanently.
• Two important epigenetic modifications: are DNA methylation and histone modification.
• DNA methylation The chemical group methyl (CH3) can be added to cytosine (C) bases in DNA where C is followed by G (CpG sequences).
• When CpG 'islands' are heavily methylated, the DNA region switches off and transcription can't occur.
• DNA methylation is long term and typically occurs at the regulator of a gene.
• Histone modification is relatively short term and is important for both increasing and decreasing the expression levels of particular genes.
• DNA is wrapped around bundles of eight histone proteins and are usually modified by adding chemical groups.
• Epigenetic modifications remain or passes to progeny.
• Epigenetics allows the environment to influence gene activity and gene expression (nutrition, homrones, age).

Case study winter of Holland 1944-1945

• The winter of 1944-1945 was the last winter of the Second World War where there were near starvation conditions.
• This near starvation affected baby and child birth weights, where subsequent babies were more likely to have lower birth weights.
• Malnourished babies in the early months of pregnancy were very likely to be overweight or obese as adults, a result of genetics.
• Very early child development has long lasting consequences and show how life experience can show how gene expression can be expressed.
• Epigenetic modification increases the flexibility of the genome.