Nucleic Acids and Protein Synthesis

• Nucleic acids encode instructions for protein synthesis.

Nucleic Acid Structure

• Nucleotides are nucleic acid monomers.
• Nucleotides consist of a phosphate group (negatively charged), a pentose sugar, and a nitrogen-containing base.
• Anabolic reactions, where small molecules join to form a larger one, occur when monomers join to make a polymer
• Endergonic reactions, which require energy for bond formation, occur when monomers join to make a polymer.
• Nucleotides join via a phosphodiester bond between the sugar and the phosphate of the subsequent nucleotide.
• Pentose sugars have a 5’ end to which the phosphate is added and a 3’ end.

Differences in Structure of DNA and RNA

• DNA contains a sugar-phosphate backbone, phosphodiester covalent bonds, hydrogen bonds, and exhibits complementary base pairing.
• DNA has 5’ and 3’ ends and is anti-parallel.
• mRNA has a sugar-phosphate backbone.
• tRNA carries an anticodon and a specific amino acid.
• rRNA is a major component of a ribosome.

Condensation Reactions

• Condensation occurs when monomers are chemically bonded together to form a polymer (polymerisation).
• Polypeptides (proteins) and polysaccharides (large carbohydrates) are also formed by a condensation reaction.
• ATP is needed for condensation polymerisation reactions to proceed
• Water is produced as a waste output
• A peptide bond is produced when amino acids bond together.
• A phosphodiester bond forms when nucleotides join by condensation polymerisation; this bond forms between the sugar and phosphate.

Gene Structure

• A gene is a sequence of DNA nucleotides that codes for the production of a polypeptide.
• The purpose of a gene is to code for the production of a polypeptide that becomes part of a protein.
• A gene includes exons, introns, a promoter region, a termination sequence, a coding region, a template strand, and a non-template strand.
• Transcription starts at the promoter region and stops at the termination sequence.
• The template strand of the gene is read in the 3’ to 5’ direction.
• In eukaryotic cells, both exons and introns are transcribed. However, only exons are translated because introns are spliced out.
• Eukaryotic transcription takes place in the nucleus, while prokaryotic transcription takes place in the cytoplasm.
• Eukaryotic transcription involves transcription of exons and introns, whereas prokaryotic transcription involves exons only.
• The promoter region is where RNA polymerase attaches to begin transcription.
• bp and kbp are units of measurement for DNA, representing base pairs and kilo base pairs (1000 base pairs).
• The operator region is the binding site for a transcription factor that regulates transcription of the gene, however, not all genes have an operator region.
• The termination sequence is where RNA polymerase detaches, stopping transcription.

Genetic Code

• The genetic code is degenerate (redundant), meaning a single amino acid may be coded for by more than one codon.
• The genetic code is non-overlapping, universal and a triplet code.
• The outcome of gene expression is a polypeptide molecule, ultimately becoming a protein.
• The two key processes that make up gene expression are transcription and translation.
• Transcription is the process by which DNA information is copied into mRNA.
• RNA processing involves mRNA capping and tailing, intron splicing, and exon splicing.
• Translation decodes mRNA at a ribosome to produce a specific amino acid chain, or polypeptide.
• Post-translational modifications include folding, interaction with other polypeptides, and conjugation which take place at the endoplasmic reticulum or Golgi apparatus.

Transcription Steps

• RNA polymerase attaches to a promoter sequence of DNA in the upstream region of the template strand.
• The DNA of the gene unwinds and exposes the bases of the template strand.
• The RNA polymerase moves along the DNA template in a 3’ to 5’ direction, building a complementary copy of the mRNA sequence.
• Transcription stops when RNA polymerase encounters a STOP sequence on the DNA template, releasing the mRNA molecule.

RNA Processing

• Modification of pre-mRNA to form mRNA occurs before pre-mRNA leaves the nucleus
• Results in a shorter mRNA molecule than pre-mRNA
• Occurs when a methyl cap is added to the 5’ end and a poly-A tail is added to the 3’ end
• Followed by introns are cut out and remaining exons are spliced together
• Alternate splicing impacts the diversity of possible polypeptides produced, where particular introns may be retained/ particular exons may be removed.

Translation Steps

• mRNA attaches to a ribosome at the START codon (AUG).
• The ribosome “reads” two codons at a time.
• tRNA molecules, carrying anticodons and specific amino acids, come to the ribosome.
• The tRNA anticodon binds to the mRNA codon, and the amino acid forms a peptide bond with the previous amino acid, creating a polypeptide chain.
• The polypeptide chain grows until the ribosome meets a STOP codon (UAA, UAG, or UGA).
• The polypeptide detaches from the ribosome and enters the endoplasmic reticulum (eukaryotes) or remains in the cytoplasm (prokaryotes).
• DNA triplet, mRNA codon and tRNA anticodon names, are specific for the type of nucleic acid being referred to.
• After relinquishing their amino acid, tRNA molecules are recharged with the appropriate amino acid from the cytoplasm.
• A START codon initiates translation and A STOP codon terminates translation on mRNA
• The ribosome recognizes a START codon as the beginning point and A STOP codon as the end point of translation
• A mRNA codon table is used to translate mRNA codons into amino acids
• 5 amino acids exist in the chain translated from AUG AAU CUG UUU GGC UAA

Prokaryotic vs. Eukaryotic Gene Expression

• Prokaryotes do not have introns, so RNA processing is not required.
• In prokaryotes, transcription and translation occur entirely in the cytoplasm as there is no nucleus.

Amino Acids and Polypeptide Chains

• Amino acids are the monomers of proteins.
• An amino acid contains an amine group, a carboxyl group, a central carbon atom, and a variable (R group).
• 20 different amino acids exist.
• Amino acids are the same in structure except for their variable R group.
• The characteristics of the R group determine how the amino acid chain folds. For example, Histine is hydrophilic and Methionine is hydrophobic
• Amino acids join in a specific linear sequence to form a polypeptide sequence.
• A protein is considered to be the functional form of the polypeptide that has folded.

Protein Structure Levels

• Primary structure is the specific linear sequence of amino acids joined by peptide bonds.
• Secondary structure involves alpha helices, beta-pleated sheets, and random coils.
• Tertiary structure is determined by interactions between R groups: di-sulphide bridges, hydrogen bonds, attraction between charged side groups.
• Quaternary structure involves multiple polypeptide sequences.
• Hydrophobic R groups are repelled by water and orientate inwards, while hydrophilic and charged R groups are attracted to water and orientate outwards.
• The folding of the polypeptide results in a unique 3D structure
• Not all proteins have a quaternary structure; proteins with only one polypeptide do not have a quaternary structure.
• The shape of a protein dictates how effectively its function can be carried out.
• External factors such as temperature, pH, electric and magnetic fields, and chemicals can disrupt the shape of a protein.
• Denaturation is the disruption of a molecule’s structure by an external factor such as heat, altering the structure of a protein which means that it unable to carry out its function.

Proteins and Proteomes

• A proteome is all the proteins expressed by a cell or organism at a given time.
• A genome is the complete set of DNA housed within an organism.
• Alternate splicing leads to the estimation that humans are thought to have 1000,000 different proteins, yet only 20,000 genes.

Protein function

• Regulation is when signalling molecules that are proteins such as insulin help to regulate the timing of biological processes within the organism
• Immunity is when antibodies (immunoglobulins) are “Y” shaped proteins that attach to disease causing organisms and deactivate them within the body
• Transport is when protein channels and protein carrier molecules carry substances around the body or across membranes.
• Enzymes are the rates of metabolic reactions are increased by organic molecules, such as catalase.
• An enzyme is an organic molecule, typically a protein, that catalyses specific reactions.
• A biochemical pathway is a series of enzyme-catalysed biochemical reactions.

Protein Secretory Pathway

• Protein is manufactured at the ribosome.
• Proteins manufactured on (i) free ribosomes are used within the cell, whereas proteins (ii) on ribosomes attached to the endoplasmic reticulum (ER), are transported from the cell.
• A vesicle is membrane bound organelle often used as transport.
• The mitochondrion is the site of aerobic cellular respiration which produces ATP to fuel processes of the secretory pathway that requires energy
• Exocytosis is the release of hormones from an endocrine gland, or the release of antibodies from a plasma B cell.

Sequence of events in the production of a protein

• Nucleus (site of transcription and RNA processing)
• Ribosomes (site of translation)
• Endoplasmic Reticulum (site of Post translation modification eg folding of the polypeptide into a functional shape)
• Transport vesicles (transports the protein from the endoplasmic reticulum to the Golgi apparatus)
• Golgi apparatus (further post translation modification may take place)
• Secretory vesicles (Secretory vesicle buds off from Golgi apparatus transporting the protein to the plasma membrane)
• Plasma membrane (Secretory vesicle fuses with the plasma membrane and the protein is exported from the cell)

Gene Regulation

• A regulatory gene is a segment of DNA responsible for producing proteins that control the expression of other genes.
• A structural gene is a segment of DNA that codes for proteins that play a role in the structure or function of a cell/organism.
• Mutation in regulatory genes results in more serious effects than in structural genes because regulatory genes control the actions of a number of structural genes
• Structural gene mutations may or may not be harmful depending on whether the amino acid sequence in the expressed protein is altered
• Tryptophan is an essential amino acid.
• An operon is a set of genes transcribed under the control of an operator gene, found in bacteria
• The regulation of the genes in the trp operon is important because it ensures that energy is not wasted.
• The trp operon consists of the promoter, operator, attenuator, and five structural genes.

The components of the trp operon, and their functions

• Regulator gene: produces mRNA that is translated to a protein product that acts as the repressor.
• Promoter it: is where the RNA polymerase attaches to initiate transcription and it identifies the DNA strand which is to be transcribed.
• Operator : the binding site of the transcription factor which in the case of the trp operon is the repressor molecule.
• Structural genes: these five genes are expressed to produce the proteins that are required for production of the amino acid tryptophan, which is a master regulator gene
• Repressor: the expressed protein product of the regulator gene, the repressor,
• Tryptophan: can bind to the repressor molecule which results in repressor molecule undergoing conformational change to become active and can then bind to the operator to block transcription of the structural genes.

Presence of tryptophan

• High levels of tryptophan inhibits unnecessary production of tryptophan.
• Tryptophan binds to the repressor molecule and the repressor molecule is activated and can bind to the operator, preventing RNA polymerase from binding and transcription of the operon cannot occur.

Absence of tryptophan

• The repressor is inactive, thus an unable to bind to the operator. With RNA polymerase able to bind to the promotor region, both transcription and translation of the structural genes can occur.

Moderately high levels of tryptophan

• Repression will not occur.
• Transcription will begin: RNA polymerase will reach the attenuator region.
• Translation will also begin
• Hair pin loops will form in the mRNA transcript which will cause the mRNA transcript to detach from the DNA molecule at the attenuator region.
• RNA polymerase will detach from the DNA and both transcription and translation will cease meaning, the structural genes of the operon will not undergo transcription nor will they undergo translation.

Overview of nucleic acid structure, including nucleotides, phosphodiester bonds, and the 5' and 3' ends of pentose sugars. Differences in the structure of DNA, mRNA, tRNA, and rRNA are explored. Anabolic and endergonic reactions are also mentioned.