Gene structure and regulationRegulatory genes code for a gene product that is involved in the expression of other genes.
Structural genes code for a protein that is involved in everyday cellular metabolism.
Eukaryotic gene structurePromotor: Where RNA polymerase and other transcription factors bind. Where transcription begins. 5’ end. Upstream of the coding region.
Enhancer and silencer: Responsible for increasing or decreasing the rate of transcription. A repressor protein will bind to a silencer or an activator protein will bind to an enhancer, which will decrease/increase the rate of transcription.
Insulator: Stops the RNA polymerase from continuing down the DNA strand to the next gene. Forces it to transcribe each gene separately.
After the RNA polymerase has run along the template strand and transcribed it we end up with pre-mRNA. The pre-mRNA contains the 5’ and 3’ Untranslated Region (UTR) and the Introns and Exons.
Then, during post transcriptional modification (pre-mRNA processing), the introns get cut out, leaving just the UTR’s and exons. A methyl cap is added to the 5’ end and a poly A tail to the 3’ end. It is now mature mRNA. It then leaves the nucleus and travels to a ribosome to be translated.
Lac operonLac: Has to do with the digestion of lactose.
Operon: Found in prokaryotic cells. Cluster of genes that have related functions. They are transcribed together.
Normally a repressor protein is attached to operator region (downstream of promotor), which means the genes cannot be transcribed when there is no lactose present.
When there is lactose, a molecule of it binds to the repressor protein, and changes the proteins shape so it can no longer attach to the operator region, this allows the genes to be transcribed.
Once all of the lactose is digested, the repressor protein goes back to its natural shape and fits back onto the operator, and stops further transcription.
Structure and regulation of biochemical pathwaysInduced fit model: Enzymes changes shape slightly when it bonds with substrate/s which stresses chemical bonds and catalyses a chemical reaction.
Lock and Key model: Substrate/s fit perfectly into the active site of an enzyme, Like a key fits into a lock.
Catalyst: A molecule that speeds up a chemical reaction by reducing the activation energy required.
Biological catalyst: A molecule that catalyses a biologic reaction
Catabolic reaction: One substrate is broken down into two (or more) products.
Anabolic reaction: Two (or more) substrates are built up into one product.
Endergonic: Reaction that requires energy
Exergonic: Reaction that produces energy
Enzyme: A protein that catalyses a biological reaction, by lowering the activation energy required. It is not used up in the reaction.
Temperature:Every enzyme has an optimal temperature where it works the best. Below this temperature it works slow, and above this temperature it can become denatured.
If the temperature gets to high the hydrogen bonds holding the protein in its tertiary (3D) shape break apart. Without its tertiary shape the enzyme cannot function correctly, due to its active site’s shape changing, and therefore no longer being able to bind its substrate. The enzyme is then said to be ‘denatured’. Even if the temperature is cooled down, the enzyme will not return to its original shape (permanent denaturation).
The warmer the environment is, the more the molecules in it move around, and therefore the more the substrate and enzymes interact. Therefore, the optimal temperature is a point just below the point where denaturation occurs. (There is a slight gap, as some enzymes denature first, causing the rate of reaction to slow before it stops all together).
pH:Every enzyme has an optimal pH. If the pH goes above or below optimal, the rate of reaction will slow. In a natural environment it is extremely unlikely that the enzyme will denature due to an unfavourable pH, however it is possible if the enzyme is placed in an extreme pH (either acidic or basic).
Amount of substrate and enzymes: The rate of reaction will increase with the more substrate that is added, until all enzymes are working at maximum speed (they are said to be ‘saturated’).
The more enzymes that are present the faster the rate of reaction, until enzyme concentration is no longer the limiting factor.
Inhibition:Competitive inhibitor: Inhibitor that binds to the active site of an enzyme and prevents substrate from binding, can be dislodged by changing environmental conditions.
Non-competitive inhibitor: Inhibitor that binds to a site other than the active site (called an allostatic site) and in doing so changes the shape of the active site slightly, preventing substrate from binding. Cannot be dislodged by changing environmental conditions.
The cycling of coenzymesCofactors: Help the substrate to fit better in the active site of the enzyme. Increases the rate of reaction.
Coenzyme: Organic cofactors. Damaged in the reaction. A new molecule is needed for each subsequent reaction.
ATP: Adenosine TriPhosphate. A type of coenzyme. An ATP molecule goes into the active site of an enzyme, the substrate/s come in and join/break and in the process the ATP is broken down into ADP.
ADP: Adenosine DiPhosphate. Broken down form of ATP.
NADH: Nicotinamide adenine dinucleotide. Energy carrier molecule involved in cellular respiration. It carries electrons to the electron transport chain, where they are broken off and used to power ATP synthesis.
NAD+: Unloaded form of NADH
NADP+/NADPH: Same as NAD+/NADH except with an additional phosphate. It is involved in photosynthesis.