Nucleic Acids and Protein synthesis

Purpose of mRNA - mRNA carries genetic information from the nucleus to the ribosome for translation

Purpose of tRNA - tRNA delivers specific amino acids to the ribosome during translation

Purpose of rRNA - RNA that serves as the key structural component of ribosomes providing the location for protein synthesis from amino acid monomers

Differences between RNA and DNA - Single stranded/Double stranded, Ribose/Deoxyribose sugar, Uracil/Thymine, Temporary short-lived molecules/long term storage

Genome - complete set of DNA housed within the somatic cell of an organism

Proteome - aggregation of all the proteins expressed by a cell/organism at a given time

Peptide bonds - bonds formed between amino acids through condensation polymerisation.

Primary structure - The specific sequence of amino acid monomers in a polypeptide

Secondary structure - The localised coiling and folding of segments of the polypeptide chains (due to formation of hydrogen bonds)

Tertiary structure - The overall 3D structure of a protein composed of a single polypeptide, resulting due to interactions between variable groups

Quaternary Structure - The overall 3D structure of a protein composed of multiple polypeptides with tertiary structure

Degenerate - more than one codon/triplet codes for an amino acid

Unambiguous - one codon can only code for one amino acid

Universal - codons code for the same amino acids in nearly all organisms

Model answer, Transcription - RNA polymerase binds to the promotor region of the gene. DNA unwinds. Complementary free floating nucleotides bind to the template strand of the DNA in a 3' to 5' direction forming a 5' to 3' mRNA strand. Once a termination signal is reached, RNA polymerase detaches and transcription is terminated.

Model answer, RNA processing - Introns are removed, exons are spliced together. poly adenine tail is added to the 3' end to improve stability. methyl guanine cap is added to 5' end to protect the mRNA strand from enzyme attacks.

Model answer, why is the proteome bigger than the genome - During mRNA processing, alternative splicing may occur, where certain exons can be removed and are not present in the mature mRNA strand. This allows multiple different mature mRNA strands to be formed from a singular gene. Each mRNA strand codes for a different protein. Therefore multiple proteins can be created from a single gene.

Model answer, Translation - The mRNA strand goes to a ribosome where it is read by the ribosome in the 5' to 3' direction. The ribosome reads in codons, initiating polypeptide synthesis when a start codon is encountered. tRNA with complementary anticodons to the codons on the mRNA strand, bring the correct amino acid to the ribosome which are joined together through peptide bonds, forming a growing polypeptide chain. Once a stop codon is read, translation terminates.

Model answer, Purpose of gene regulation - To conserve ATP and amino acids by only synthesizing proteins which are absolutely necessary, so that these resources are available for use in more essential situations elsewhere, if applicable.

Gene regulation - the process by which gene expression is inhibited or activated

Structural genes - gene responsible for the production of proteins for cellular structure or function

Regulatory genes - genes that code for products that either inhibit or activate expression of structural genes

Promoter region - upstream binding region for RNA polymerase. Identifies start of gene

Operator region - Binding site for repressor proteins, allowing for gene regulation

Introns - non-coding regions within pre-mRNA

Exons - coding regions within pre-mRNA

Termination sequence - signal for DNA to end transcription

Operon - Linked genes regulated by a common promoter and operator region, transcribed at the same time

Purpose of operon - To conserve ATP by ensuring all proteins that are used together are synthesised at the same time, so ATP is not being consumed by producing one in excess

Function of regulatory genes in gene regulation in prokaryotes - Regulatory genes are separate genes upstream of the operon which code for the repressor protein which binds to the operator region.

Repressor protein - Binds with tryptophan undergoing a conformational shape change allowing it to bind the operator region, obstructing RNA polymerase and preventing transcription.

Tryptophan repression in high trp concentration - Due to high concentration, tryptophan acts as a cofactor and consistently binds to the inactive repressor protein which normally can't bind to the operator region.

Conformational shape change in repressor - Induced in repressor allowing it to bind to operator region, obstructing RNA polymerase.

trp Operon transcription inhibition - Inhibited when repressor binds to operator region.

Purpose of attenuation - Attenuation acts as a secondary inhibitor system for repression of the trp operon, increasing the likelihood that no further trp is produced, conserving energy.

trp operon attenuation in high tryptophan concentration - While transcription and translation occurs concurrently, the ribosome will not stall at the two trp codons in the leader region during translation as there is sufficient tryptophan resulting in the formation of a terminator hairpin.

Terminator hairpin - Causes RNA polymerase to unbind from the DNA and the ribosome to unbind from the mRNA halting transcription and translation before the enzymes for tryptophan synthesis are transcribed.

Genes coding for tryptophan enzymes - Not expressed due to the action of the terminator hairpin.

Ribosome - synthesizes proteins

Rough endoplasmic reticulum - folds and transports proteins

Golgi body - modifies and packages proteins

Transport vesicles - transports proteins inside the cell

Secretory vesicles - contain proteins for export and fuse with the plasma membrane to release the protein into the extracellular environment

Enzyme - organic protein catalyst that catalyses a specific biological reaction by lowering its activation energy

Lock and key model - The substrate is an exact fit into the enzymes active site.

Induced fit model - Substrate is a similar, but not exact, complementary shape to the enzymes active site.

Factors affecting enzymes: High temperature - An increase in temperature above the optimal temperature of the enzyme alters the enzyme's secondary, tertiary (and quaternary, if present) structure, and thus shape, meaning the substrate is no longer specific and complementary and cannot bind, meaning the enzyme is permanently denatured.

Factors affecting enzymes: Low temperature - A decrease in temperature below optimal temperature will result in a decrease in enzymatic activity since the enzyme and substrate molecules collide less frequently.

Factors affecting enzymes: pH - pH higher/lower than the enzymes' optimal pH decreases enzymatic activity by altering the tertiary structure and thus shape of the active site, meaning the substrate is no longer specific and complementary and cannot bind, meaning the enzyme is permanently denatured.

Factors affecting enzymes: Substrate addition - As substrate concentration increases, the amount of substrate molecules available, to bind to the active site of the enzyme, increases, allowing more reactions to occur simultaneously, increasing total enzymatic activity.

Factors affecting enzymes: Enzyme addition - As enzyme concentration increases, the amount of active sites available (for the substrate to bind to) increases, allowing more reactions to occur simultaneously, increasing total enzymatic activity.

Competitive inhibition - competitive inhibitor with a similar shape to the substrate binds to the active site of the enzyme and prevents substrate from binding

Non competitive inhibitor - non competitive inhibitor binds to an allosteric site on the enzyme causing a conformational shape change altering the shape of the active site, preventing the substrate from binding

Cofactor - A molecule that assists enzyme function

Coenzymes - subset of cofactors, non-protein organic cofactor that assists enzyme function