Unit 3 AOS1 - Gene Structure, Biochemical Pathways Flashcards
Structure of eukaryotic genes
- Most eukaryotic genes contain segments of coding sequences (exons) interrupted by noncoding sequences (introns).
- Both exons and introns are transcribed to yield a long primary RNA transcript. The introns are then removed by splicing to form the mature mRNA.
Eukaryotic cells
- start and stop instructions
Start codon: the sequence of three nucleotides in mRNA that signals the start of translation
Stop codon: the sequence of three nucleotides in mRNA that signals the end of translation
Eukaryotic cells
- promoter regions
A promoter region:
- The upstream (5’ end) binding site of RNA polymerase, the enzyme responsible for transcription.
- By allowing RNA polymerase to bind to certain genes, promoter regions determine which genes are transcribed, where transcription begins, and the direction of transcription.
- In eukaryotes, the promoter region is often the sequence of bases, commonly known as the TATA box.
Eukaryotic cells
- exons and introns
Exons: sequences of DNA that code for proteins. They make up the mRNA molecule
Introns: sequences of DNA that do not code for proteins. They are spliced out during RNA processing
Enzymes
Enzymes speed up biochemical reactions by lowering the activation energy required to initiate a given reaction.
- Enzymes are organic (carbon-based) catalysts.
- This means that they speed up, or catalyse, chemical reactions that would normally take much longer to occur.
- Enzymes bind to a molecule called a substrate. The substrate is the reactant undergoing a reaction.
Key features of enzymes
• Enzymes are reusable. When an enzyme catalyses a reaction, the enzyme is not consumed, broken down, or turned into a product. Because they are not used up in the reaction, enzymes can catalyse future reactions.
• Most enzymes only bind to one specific substrate. This means that they tend to catalyse just one chemical reaction, although some enzymes are less specialised.
• Most enzyme-catalysed reactions are reversible, with the same enzyme often capable of building up larger molecules (anabolic), or breaking them down into smaller
ones (catabolic).
• Enzymes catalyse reactions, but don’t create new reactions. They speed up reactions that would otherwise occur naturally (given enough time) by lowering the activation energy of a reaction.
• Enzymes have an active site – the one area to which the substrate always binds and the reaction occurs. The corresponding area on a substrate is called a binding site.
The enzyme’s active site and substrate tend to be complementary in shape, so they can roughly fit together.
• Most enzymes are proteins. However, some RNA molecules are capable of acting as enzymes.
• All enzymes are catalysts, but not all catalysts are enzymes. Enzymes are organic catalysts, however, there are also inorganic catalysts (such as metal ions) that speed up reactions.
• Enzymes frequently influence entire biochemical pathways (e.g. Figure 4) by catalysing each step.
• Enzyme names typically end with the suffix ‘-ase’ (e.g. catalase, polymerase, ligase, lactase). When you see ‘-ase’, think of enzymes.
• Enzymes are typically displayed above the reaction arrow.
Enzyme-Catalyzed Reactions
- active site
- substrate
- enzyme
The active site is a pocket-like area of the enzyme’s tertiary structure where the substrate fits and binds into the enzyme
The enzyme’s active site and substrate are complementary in shape.
Together they form an enzyme-substrate concept
- The reaction proceeds and the substrate is converted into the product. The product disassociates from the complex and is released.
- The enzyme is then ready to bind to another substrate and repeat the process
Enzyme components
lock+key model induced fit metabolism anabolic catabolic
lock and key mode: active site exactly complementary to substrate shape
induced fit model: enzymes shape changes to bind the substrate
metabolism: is the overall chemical activity of cells
anabolic: reactions that build things up. require an input of energy, endergonic
catabolic: reactions that break things down. produce energy, exergonic
How do enzymes speed up chemical reactions
★Enzymes lower the activation energy of chemical reactions.
Every chemical reaction requires an input of energy to start, regardless of whether it is anabolic or catabolic
➔The initial requirement is the activation energy, and is defined at the minimum amount of energy requires to promote atoms and molecules to a state where they can undergo a chemical reaction
Inhibiting enzymes
define
4 categories
- Enzymes can be hindered by molecules known as inhibitors
- Enzyme inhibitors are molecules that bind together an enzyme and prevent it from performing its function. When an inhibitor is bound to an enzyme, the enzyme can either no longer catalyse its specific reaction, or its functioning is greatly reduced
- They are categorised as either competitive or non-competitive and reversible or irreversible inhibition
Competitive inhibition (reversible)
- Chemicals that have a similar shape to the substrate can also bind to the enzyme’s active site.
- They ‘block’ substrates from binding, thus slowing down the reaction rate.
- By increasing substrate concentration, you can increase the reaction rate, since the substrate can ‘compete’ better.
The effects of these inhibitors are not permanent and can be reversed - slow down the rate of a given enzyme-catalysed reaction, but do not stop indefinitely.
Non-competitive inhibition (irreversible)
- Binds to a site other than the active site of the enzyme and changes the shape of the active site (the site in which the inhibitor binds is called the allosteric site - can be reversed)
Irreversible inhibition
Will form bonds that are unbreakable
Means that if an irreversible inhibitor binds to an enzyme, it is unable to bind with any substrate or catalyse any reactions indefinitely.
Reactions can never occur
Regulating enzymes
Temperature
- If the enzyme is in an area with too low temperature, its activity is lowered. This is because the enzymes are moving slower, and therefore collide with the substrate less frequently.
- If the temperature is higher than the enzyme’s optimum temperature, the activity is significantly lowered, because excessively high temps break the hydrogen bonds in the secondary and tertiary structures. The active site changes due to this, and the enzyme has been denatured, as it can no longer bind to its complementary substrate
Regulating enzymes
pH
- Altered pH changes the location and strength of the ionic interactions between the R groups.
- This changes the tertiary structure and everything that follows it, causing it not to be able to bind to its complementary substrate
