3 basic stages:
1. Uptake of substances (for example, across the plasma membrane)
2. Transformation of substances (anabolism or catabolism - explained a bit later!)
3. Release of substances (for example, the elimination of metabolic wastes across the plasma membrane)
- there are lots of interrelated reactions, therefore it is difficult to study
Metabolic pathway- the order in which reactions affecting a starting substance occur. A metabolic pathway may be linear or circular and the product (end substance) of one pathway may be the reactant (starting substance) of another. Often reactions in a pathway are reversible.
All pathways have the following participants:
1. Substrates/reactants (kiindulóanyagok) - substances that enter the reaction
2. Intermediate products (köztestermékek) - compounds formed between the start and the end of the reaction
3. Enzymes (enzímek) - proteins that catalyze (speed up) reactions
4. Energy carriers (energia hordozók) - usually ATP. It donates energy to the reactions that need it and picks up energy from reactions that produce it.
5. End products(végtermékek)/metabolites (anyagcseretermékek) - substances produced at the end of the pathway.
Chemical reactions are basically the release of chemical energy by breaking bonds in one substance and then using it to create new bonds in another substance.
2 Sides of Metabolism: Anabolism and Catabolism
Anabolism (assimilation):
-all the synthesis or "building up" reactions in a cell.
-results in organic compounds (amino acids, lipids, etc) for energy storage, cell growth, repair, reproduction, etc.
-requires energy (endergonic)
What are the energy sources?
1. In autotrophs, they use the energy from the sun (photosynthesis) or from external chemical reactions (chemosynthesis). The cells convert external energy into ATP and then use the ATP to synthesize organic compounds.
2. In hetertrophs, the organisms take in (eat) organic compounds (food) and break it down to synthesize ATP, then use the ATP to synthesize their own organic compounds.
Catabolism (dissimilation):
- this is also called cellular respiration
- organic compounds are broken down to release the energy stored in them and therefore produce energy (exergonic)
-if this process occurs with O2 then it is biological oxidation and the products are CO2, H2O and lots of energy (captured as ATP)
-if this process occurs without O2, then it is fermentation and much less energy is produced (still captured as ATP)
-ATP can be used for various cell activities, such as biosynthesis, transport, cell division, movement, bioluminescence, etc, but some energy is also lost as heat.
B. ENZYMES
- most reactions need the input of energy (E) to get started - this is called the activation energy. In the chemistry lab, we use heat to provide the energy, but most living systems cannot withstand high temperatures, so enzymes are used. We call them catalysts, because they lower the activation energy required for a reaction to occur by forming temporary associations with the substrates.
-without enzymes, most metabolic reactions would be too slow to maintain life.
Properties of enzymes
-they are globular proteins (tertiary or quaternary structure) and can be either simple (just the protein) or complex (protein + cofactor(inorganic, like Mg)/coenzyme(organic, like vitamin B or NAD+))
-they are specific: each enzyme only recognizes one or a few certain substrates and each enzyme can only catalyze one kind of reaction (therefore there are LOTS of different enzymes, we know of over 2000!)
-a cell will only manufacture the enzymes that it needs
-since enzymes are proteins, they can be denatured (structure and function destroyed) by heat or pH changes
-they are not used up by a reaction, they can be reused many times
How enzymes work
-they are globular proteins with a groove or pocket which forms the active site. This is where the substrate(s) fits into it and the reaction is catalyzed.
-when the substrate binds to the enzyme it forms a temporary enzyme-substrate complex
-since the enzyme only binds to specific substrates, it is similar to the way only a specific key fits in each lock, therefore, we call this the lock and key hypothesis of enzyme function
Image from http://hsc.csu.edu.au/biology/core/balance/9_2_1/image1.jpg
Naming Enzymes
- the first enzymes to be discovered were given names which are still used today (traditional names), eg. trypsin, pepsin
-most enzymes have a scientific name: substrate reaction+"ase"
eg. DNA polymerase (the substrate is DNA, the reaction forms a polymer or a long chain of DNA)
Enzyme Activity
1. pH - each enzyme has a "favourite" pH, even a slight change in pH may cause denaturation. In our digestive system, we have various enzymes. Pepsin functions in the stomach, thus "likes" a pH of 2, while trypsin, which is found in the small intestine, prefers a pH of 7.9-9
2. Temperature - for enzymes in our body, 37C is the "favourite" temperature. A lower temperatures, their activity slows, from 37-40C it speeds up, but above 40C H-bonds are broken and their shapes are distorted (denaturation)
3. Enzyme-substrate concentration - with a given amount of enzyme, the reaction rate will increase with an increase in substrate until all the active sites are constantly in use. Here it will reach a maximum and in this case, the enzyme concentration is the limiting factor. If there is an excess of enzyme with respect to the amount of substrate available, then the activity is substrate-limited.
Enzyme Inhibition
Enzymes are unable to function if the active site is block or if the shape of the active site is changed. Different chemicals (or enzyme inhibitors) can do this and so stop the enzyme from functioning. This is called enzyme inhibition and there are 2 types:
1. Competitive inhibition: the inhibitor takes the place of the substrate
2. Non-competitive inhibition: the inhibitor binds to the enzyme and this causes a change to the active site.
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