Enzymes Flashcards
Difference between biochemical reaction and biochemical pathway
Chemical pathway: series of biochemical reactions, each step needing a specific enzyme.
Biochemical reaction: reaction in cells that lead to the formation of a product from a reactant.
Metabolism
All chemical reactions occurring in an organism
Reactant: (substrate)
Molecules that are the input to a chemical reaction, compound on which an enzyme acts
Product:
Molecules that are produced as a result of a chemical reaction.
Active site:
cleft region within an enzyme where a substrate binds. Substrate is complementary to active site.
- where catalysis occurs
- substrate split apart into smaller molecules
- substrate rearranged or reassembled into more complex molecules
Allosteric site:
Cleft regoin within enzyme at a different location where another molecule (not substrate) binds. e.g inhibitor
Enzyme:
Biomolecule that catayses a chemical reaction by decreasing the activation energy needed.
- not consumed in the reaction
less energy needed for reaction to start- more energy for substrate molecules when they collide???
Anabolic pathways:
- simple to complex molecules
- energy-requiring (endergonic) (to form chemical bonds)
- energy level of initial reactant is lower than final product
- e.g photosynthesis, amino acids to proteins, nucelotides to DNA, glucose to glycogen
Catabolic pathways:
- break down complex- simple
- energy-releasing (exergonic) as chemical bonds are broken
- energy level of initial reactant is higher than product (release more energy than they consume)
- e.g cellular respiration
Interactions between anabolic and catabolic: (type of energy)
- do not operate in isolation
- energy released by catabolic pathway transferred as chemical energy in ATP to drive anabolic pathways
activation energy: (Ea)
minimum amount of energy required to initiate chemical reaction
Features of enzymes: (shape, type, number of polypeptide chains, features)
- all enzymes are soluble globular proteins except ribozymes (RNA molecules)
- can consist of one or more polypeptide chains (1 like trypsin)
- active site- unique 3D shape, forms a temporary enzyme-substrate complex
Induced fit model vs lock and key:
Induced fit:
Shape of active site can undergo conformational changes to adjust to fit substrate. (shape of active site is complementary to substrate only after binding)
Lock and key:
portrays enzyme as conformationally rigid and able to bond to substrates that exactly fit the active site.
How do the enzyme and substrate hold together?
substrate forms weak bonds with amino acid residues at active site, holding the e-S complex together, easily broken
Some enzymes have… (specificity)
- absolute/substrate specificity
catalyse 1 substrate (e.g. lactase- lactose- breaks down into glucose and galactose) - bond specificity
act on 1 kind of chemical bond (e.g peptidase act only on peptide bonds) - group specificity
act on particular functional groups part of substrate (e.g carboxyl or hydroxyl group)
how is a substrate broken into 2?
- bonding between substrate and enzyme weakens bonds in substrate
- bond breaks under stress
What is a by product of all catabolic reactions?
Heat
Anabolic or catabolic reactions result in an overall production of ATP?
Catabolic (release energy used for the synthesis of ATP)
Why do catabolic reactions result in heat?
They release energy, some of which is lost as heat. (?)
Is all biological metabolism catalysed by enzymes?
YES
Cofactor def
non-organic molecules (like ions) that improve enzyme active site affinity for substrate
- don’t confuse with coenzymes
What are coenzymes
Organic=contains carbon= contains covalent bonds in their structure
Coenzymes
- loosely bound to enzyme only when enzyme is acting on substrate
What do coenzymes do?
- bind to active site and help enzyme function
- create extra stability
- induce conformational changes
- help to attract substrate or repel product
- shuttle chemical groups, donate and accept electrons and protons
Check flashcard!
2 forms of coenzymes:
loaded- high energy (donate electrons to substrates) (in reductive reactions)
unloaded- low energy (electron acceptors from sustrate) (in oxidised reactions)
What does it mean for a substrate or coenzyme to be reduced/oxidised?
- oxidised substances lose electrons
- reduced substances gain electrons
- when coenzymes accept electrons from substrate, they are being reduced and the substrate is being oxidised
Types of errors:
random errors:
- unpredictable variations in measurements
- cause over or underestimate of true value
- affect precision (how consistent repeated results are)
- increase precision by taking averages of multiple trials
Systematic errors:
- error in the method
- affect accuracy (how close to true value)
- error is unidirectional (always affects results in the same way)
- minimise errors by changing method
e.g measuring a table:
Random Error = You measure a table multiple times and get slightly different lengths each time (e.g. 100.1 cm, 99.8 cm, 100.3 cm).
📏 Systematic Error = Your ruler is misprinted, so every measurement is always 2 cm too short (e.g., you always measure 98 cm instead of 100 cm).
What is the optimum temperature? (def)
- temp at which rate of reaction catalysed by the enzyme is at its highest
What happens as temp decreases from optimum?
- rate of reaction reduces progressively
- molecules move more slowly
- fewer collisions between substrate and enzyme
- may inactivate enzyme
- can reactivate them by increasing temp
NOT denatured , enzymes more slower
What happens as temp increases from optimum?
- rate reduce rapidly
- denaturation due to disruption of bonding (usually breaking of hydrogen bonds)
- permanently inactivated
Define denaturation?
- loss of enzyme structure (secondary, tertiary, quaternary) due to breaking of bonds
- irrevesible change of shape and charge of active site
- enzyme put back into its amino acids, must go through transcription and translation again (lots of energy)
- due to heat, pH change, solvents (alcohol, urea, detergents)
pH: (scale) and what it is based on
based on concentration of hydrogen ions
0-6: acidic
7: neutral (e.g water)
8-14: alkaline/basic
What is optimum pH?
when enzyme displays highest activity
human cells: tytpically 7.0-7.4
Stomach: optimum pH is 2, duodenum- 8.5
How does pH affect enzyme function?
- as pH becomes more alkaline and acidic from optimum, enzyme is denatured (tertiary structure of protein changes due to breaking of bonds)
- bonds in enzyme are altered
- chemically changes conformation/shape of active site
- active site no longer complementary to substrate
Don’t need to know:
- pH alters ionic charges in charged R groups
What happens as you increase substrate concentration?
- increases rate of reaction (as more collisions) up until all active sites are occupied (saturation)
- once all active sites are occupied, no significant change
Enzymes with high affinity vs enzymes with low affinity:
high affinity:
- bind to substrate more tightly
- stronger attraction
- useful when substrate is scarce
- reaches max rate faster
- less affected by substrate concentration
low affinity:
- bind to substrate less tightly/easily
- allows for quick release of substrate (once reach max rate, quicker turnover)
- reaches max rate more slowly
- need more substrates to achieve significant enzyme activity
Effect of enzyme concentration:
- higher concentration- more collisions- greater reaction rate
- if concentration of enzymes is very high, substrate concentration may become rate-limiting, reaction rate flattens out
What are competitive inhibitors?
- bind to active site of enzyme, preventing substrate from binding
- shape and charge is complementary to active site
- reversible
Factors affecting competetive inhibition?
- concentration of inhibitor
- concentration of substrate
- relative affinities of enzyme for inhibitor and substrate
What are non-competitive inhibitors?
- bind to allosteric site, causing conformational change in active site so it cannot properly bind with substrate
- not in competition for active site
- increasing substrate concentration does not remove effect of inhibition
- fixed percentage of enzymes always inactivated
- reaction still occurs (amon active enzymes), but max rate decreases
- reversible
Irreversible inhibition
specific molecule form strong covalent bond with active site, blocks substrate from binding
(many are poisons, lead to death)
Why is regulation of biochemical pathways important?
- conserves energy and substrates for other chemical reactions
- prevents build up of products to harmful levels
How are biochemical pathways regulated?
- up-regulated: increase specific enzyme activity
- down-regulated: decrease specific enzyme activity
allosteric regulation, feedback inhibition, competitive inhibition
What is allosteric regulation?
- regulator molecule binds to allosteric site, conformational change
- allosteric inhibitors (stop enzyme activity)
- allosteric activators (increase enzyme activity)
- reversible
What is end-product inhibition? / feedback inhibition?
- end product of metabolic pathway acts as inhibitor of enzyme that catalyses first step in pathway
(often binds to allosteric site) - occurs when end-product is plentiful
- when end product falls to low levels, inhibition ceases
Explain how an ATP releases energy directly to a cellular reaction and what is formed as a result.
Explain- cause and effect
3 marks
ATP loses terminal phosphate when bond between 2nd and 3rd phosphate is broken
Breaking bond releases energy to cellular reaction
ADP is formed
Define coenzyme
Non-protein organic molecule, binds to the active site of certain enzymes to increase rate of a reaction
Describe vs explain
Explain: cause and effect, make relationships between things evident. You can integrate the new scenario in brackets after explaining concept to save time.
Describe: describe characteristics, if questions mentions 2 or more concepts, then you need to describe the interrelationships
If process/thing has not been idenitified, first identify!
Effect on reaction rate and effect of increasing substrate concentration: competitive and non competitive inhibitors:
Competitive: slows reaction rate
- if substrate concentration increases, reaction rate will still reach max rate as substrates can overpower inhibitors
non competitive:
- fixed percentage of enzymes inactive
- even if substrate concentration increases, rate will never reach max rate
Control group vs controlled variable
Control group: group that does not have the change condition of the independent variable affecting it and serves as a standard for the results to be compared to.
Controlled variable: a factor kept constant throughout the experiment to ensure that any change in the dependent variable is caused only by the independent variable.
Reproducibility definition
obtaining consistent results using the same input variables, methodological and computational steps, and analysis conditions.
- how consistent the results are of the measurements of the same quantity under changed conditions of measurement.
accuracy def
How close a measurement is to a known or expected value or scientific method.
meaning of “error”
Difference between the measured value and the true value of what is being measured.
importance of collecting class data and averaging the results
- increase sample size
- minimise impact of random errors on data, and increase precision
check!
EXPLAIN tertiary structure of proteins
- overall 3D shape
- achieved due to further folding of secondary structure and interactions between variable groups
- functional at this level of structure
Ribosomes contain rRNA which can act as a ribozyme. Describe how this molecule is produced for the ribosome.
- genome contains gene that encodes for rRNA
- RNA polymerase catalyses formation of pre-rRNA molecule
- pre rRNA undergoes post-transcriptional modifications/RNA processing
- rRNA molecules combine with ribosomal subunits
Explain: Enzyme-catalysed reactions operate at much faster rates than non-catalysed reactions.
- If reactants do not have sufficient energy, no reaction can occur.
- Enzymes lower the activation energy level
- They do this by binding to the reactant molecules and positioning or bending them in a way that enables the breaking of existing bonds and the formation of new ones to occur more readily.
What stabilises a substrate in the active site of an enzyme?
-weak bonds
- hydrogen bonds or ionic bonds
why are 2 mechanisms needed to regulate trp operon?
If repressor protein was not functional (eg. mutation in the regulatory gene) then there would be a back up mechanism to regulate production of Trp in bacteria.
AND/OR
having mechanisms in different locations and stages makes regulation mrore responsive to changes
(eg. if RNA polymerase is already transcribing and then there are higher levels of Trp then translation can still be stopped) - important as Trp is energetically expensive to produce.
compare repression and attentuation when trp is high (6 marks)
- In repression, two trp amino acids bind to repressor, causing a conformational change, allowing it to bind to the operator WHEREAS
- in attenuation, RNA polymerase begins transcription of the leader or attenuator sequence. within sequence, there are 2 trp codons. As ribosome does not stall here, terminator hairpin loop is formed, causing RNA polymerase to detach from DNA.
- In repression, RNA polymerase is prevented from binding to promoter to transcribed structural genes. transcription is not initiated WHILE
- in attenutation transcription of structural genes is not completed.
- both result in no/little trp produdction and conserve cellular energy
- both occur in gene’s regulatory region
Suggest, by referring to cellular function, how aggregates of amyloid beta proteins could result in death of neurons. (2 marks)
- loss of cell contents, disrupting metabolic acivitiy
- loss of mitochondria- no ATP to maintain life
- loss of ribosomes- no protein synthesis, meaning no enzymes are produced and chemical reactions cannot occur fast enough to maintain life
- piercing membrane intiates apoptosis
- disrupts cell’s osmotic gradient
