Enzymes
Endergonic reactions
products have more energy than reactants energy is required not spontaneous
Enzymes are large globular
protein molecules
are side reactions leading to harmful waste products are rare or common in enzyme catalysed reactions
rare
allosteric sites
receptor sites located some distance from the active site of certain enzymes that bind substances that may inhibit or stimulate en enzymes activity
co-enzymes are...
small molecules which affect catalytic activity of enzymes -they execute chemical reactions that amino acids cant
inhibitorhttps://www.boundless.com/physiology/human-anatomy-and-physiology-introduction/
substance that binds to an allosteric site which stabilizes the inactive form of an enzyme (keeps active site unavailable)
Do all enzymes function best at the same temperature?
No. Different enzymes have different ideal temperatures. For example, thermophlilic (heat loving) bacteria live in hot environments and have enzymes that function well at very high temperature.
Irreversible inhibitors
-Bind so tightly to the enzyme they cannot be removed -Monoamine oxidase inhibitors (MAOIs) are chemicals which inhibit the activity of the monoamine oxidase enzyme family. They have a long history of use as medications prescribed for the treatment of depression.
Enzyme deficiency diseases
-Hurler syndrome (abnormal bone structure and developmental delay) -build up of glycosaminoglycans (long chain sugar molecule soften found in mucus & fluid around the joints) due to a deficiency of iduronidase -an enzyme responsible for the degradation of mucopolysaccharides in lysosomes -Enzyme replacement therapy & bone marrow replacement
Km
-Km is characteristic for any given enzyme for a specific substrate under defined conditions of pH and temperature. -Km is a measure of the affinity of an enzyme for its substrate. -The lower the Km, the more tightly the substrate is bound. -Km often used to distinguish between different forms of the same enzyme (isoenzymes). -Km of an enzyme for a substrate is often near the concentration of that substrate in a cell, allowing enzymes to be more responsive to substrate concentrations
Un-competitive inhibition
-Lithium is used to treat manic-depressive psychosis -Suggested that it inhibits inositol monophosphatase
Free energy
-Only exergonic reactions can spontaneously happen -The energy required to initiate the conversion of reactants into products can be controlled by enzymes -The free energy difference between products and reactants is not enzyme controlled
Zymogens
-Some enzymes are initially produced as an inactive precursor form known as zymogen. -The zymogen form is typically a longer polypeptide that must be hydrolyzed at a specific location to produce the active form of the enzyme -Cleavage at the activation site(s) may release a polypeptide known as the "pro-sequence", and results in activation of the enzyme
MAOIs
-When ingested orally, MAOIs inhibit the catabolism of dietary amines. -Sufficient intestinal MAO-A inhibition can lead to hypertensive crisis, when foods containing tyramine are consumed (so-called "cheese syndrome"). -The amount required to cause a reaction exhibits great individual variation and depends on the degree of inhibition, which in turn depends on dosage and selectivity.
Activation energy
-When substrates react they have an enriched energy level -This means most reactions require an energy investment to start The energy required to start the reaction is called the activation energy -The reaction proceeds as when the products are formed there is an energy pay back to the cell
ELISA
-detection of Mycobacterium antibodies in tuberculosis -detection of hepatitis B markers in serum -detection of enterotoxin of E. coli in feces -detection of HIV antibodies in blood samples -Hormone levels
Competitive inhibitors
-disulfiram (Antabuse) inhibits the aldehyde oxidase which causes the accumulation of acetaldehyde with subsequent -unpleasant side effects of nausea and vomiting.
co factor groups make
-enzymes fold and create active sites -Enhance the charge in the active site to improve substrate binding
Exorgenic reactions
...
What are some ways that enzymes inhibitors are good for humans?
1. Antibiotics can be used by inhibiting the enzymes in disease causing bacteria. 2. Using feedback inhibition to prevent metabolic reaction pathways from running out of control.
How could you determine whether or not the results of an experiment are reliable?
1. If the results are consistent. 2. Only one variable is being tested once at a time. 3. There is a good control.
What are the steps of the scientific method?
1. Observation 2. previous data 3. formulation of a hypothesis 4. observations and/or experimentation new data 5. conclusion 6. theory
Factors that effect the rate of an enzyme catalyzed reaction.
1. Temperature 2. pH 3.Substrate concentration 4. Enzyme concentration
What are some ways in which enzyme inhibitors can be bad for humans?
1.Nerve gases used in war bind to active sites which are needed for nerves to work and thus cause paralysis. 2. Lead and Mercury ions (heavy metals) cause denaturation of the enzymes in the human body and thus lower reaction rate. These heavy metals can be found in our food chain (eg. in tuna).
Catalyst?
A chemical that speeds up a chemical reaction.
Cellular enzymes
1= oxidoreductases 2= transferases 3= hydrolases 4= lyases 5= isomerases 6= ligases
What is a hormone?
A chemical messenger that signals the activity of glands and organs in metabolism, growth, development and homeostasis.
What is thyroxin?
A hormone that is produced by the Thyroid gland?
When does a hypothesis become a scientific theory?
A hypothesis is a statement or prediction based on knowledge where as a scientific theory is supported by a large body of evidence.
Coenzyme?
A molecule that assists the enzyme by binding to the active site and helping the substrate fit better.
Competitive inhibitor?
A molecule that mimics the substrate and therefore competes for the active site on the enzyme causing the reaction to slow down.
Non-competitive inhibitor?
A molecule that slows down the rate of an enzyme catalyzed reaction by changing the shape of the enzymes active site. The non-competitive inhibitor does this by attaching to another site on the enzyme.
What is a metabolic pathway?
A series of reactions that follow each other.
What is the control setup (or control group) in the cucumber experiment?
A set of cucumbers that do not receive any fertilizer.
What molecule do living cells use for reactions that require energy input?
ATP which is hydrolised to release energy from the phosphate bond and makes ADP.
What are the target cells for thyroxin?
All the cells in the body.
What are some of the controlled variable in the cucumber experiment?
Amount of water, amount of sunlight, size of original seed etc.
Control variable?
Any variable factors that you must keep constant so that they do not affect your experiment.
How does temperature effect the rate of an enzyme catalyzed reaction?
As temperature increases, the rate of the enzyme catalyzed reaction also increases because the molecules are moving faster and colliding more frequently. After a certain temperature, the reaction rate decreases because the heat starts to denature the enzyme so that it no longer can function.
Phosphorylation and ATP.
Attachment of phosphate group to ADP to make ATP. Energy is stored in the phosphate bond.
Why is it necessary to have a large sample size?
Better represents the population and therefore the results are more meaningful
Enzyme?
Biological catalysts that speed up a chemical reaction.
Clinical uses for enzymes
Cardiac biomarkers should be measured in all patients who present with chest discomfort consistent with acute coronary syndrome. Elevations of cardiac enzyme levels should be interpreted in the context of clinical and ECG findings.
What is feedback inhibition?
Cells use enzymes to regulate metabolic pathways. This occurs when a product of the metabolic pathway inhibits a previous reaction by inhibiting the enzyme.This is called feedback inhibition (one of the products is inhibiting a previous reaction).
Biochemical reaction in mitochondria?
Cellular Respiration: Glucose + oxygen is turned into ATP (potential energy), carbon dioxide and water.
Endergonic of endothermic reactions?
Chemical reactions that absorb energy.
Exergonic or exothermic reaction?
Chemical reactions that release energy.
What is the ideal temperature for most enzymes in the human body?
Close to 37 oC as this is body temperature.
What is the ideal pH level for enzyme catalyzed reactions for most cells in your body?
Close to neutral (pH 7) because most of our body have a neutral pH.
What is the function of thyroxin?
Controls homeostasis: eg. normal blood pressure, heart rate etc.
True or False: Enzymes start chemical reactions.
FALSE. Eanzymes don't start reactions- they SPEED UP reactions that would occur eventually.
Structure of thyroxin?
Derived from the amino acid called tyrosine. It has 4 iodine atoms attached to it. This is why you need iodine in your diet.
Enzyme Functions
Digestion DNA synthesis Cell signalling Respiration Metabolism Cell movement & growth Cellular digestion Immunology Transport of CO2 Control of vascular tone Control of neuronal pathways ROS Etc.......
Lock and Key Model
Enzymes are specific. The only wok on the substrate that they "fit." Just like a lock has a specific key to open it.
How do enzymes work?
Enzymes work by lower the energy of activation barrier so that the reaction can get started.
True or False: Reactions take place without enzymes
False. Most reactions do not take place if enzymes are not present
Where does the energy for the hydrolysis of ATP come from?
From exergonic reactions.
Where can you get iodine in your diet?
From iodized salt. Manufacturers add iodine to our salt because we need it in our diet.
Why is it necessary for an experiment to be repeatable?
Gives opportunity for a good average of the results and thus makes the experiment more valid.
The importance of Km
Hexokinase catalyses phosphorylation of gluc to Glc-6-P Has a low Km (0.2mmol/L) and is inhibited allosterically by Glc-6-P Norm blood conc=5mmol/L so in intracellular levels are 0.2-2mmol/L Heokinase is efficient (50-90% Vmax) under normal conditions Hepatocytes, store glucose as glycogen, and pancreatic β cells contain glucokinase Glucokinase has a Km of 10mmol/L & is not inhibited by Glc-6-P Its activity increases after a meal Results in storage of glucose & release of insulin Mice lacking the enzyme die within 3days due to sever hyperglycaemia
HYDROLASES
Hydrolase enzymes catalyse hydrolysis; the breaking of single bonds through the addition of water.
Effect of enzyme concentration and reaction rate in an enzyme catalyzed reaction?
If the enzyme concentration is increased the reaction rate is also increased because there are more active sites for the substrate to attach. Eventually the reaction rate reaches a maximum because all of the substrate is saturated with enzyme and there is no more substrate available.
What happens to reaction rate if pH is too high or too low?
If the pH is too high or too low, the enzyme becomes denatured and the reaction rate slows down because the substrate no longer fits the active site.
Effect of substrate concentration on an enzyme catalyzed reaction.
If the substrate concentration is increased, the reaction rate is also increased because there are more substrates to which the enzymes can attach. Eventually the reaction rate reaches a maximum because the enzyme is saturated and their are no more available.
End product inhibition
Important control for complex multi-step processes
How exactly does feedback inhibition work?
In a metabolic reaction, once a sufficient amount of product has been produced, the end product may bond to the first enzyme. This enzyme is inhibited (inactive) until more product is needs. At this stage the enzyme is "released" and the reaction continues. This is a safeguard against a reaction running out of control and producing excess product.
Induced fit model.
In the induced fit model the active site of the enzyme changes shape to accommodate the substrate.
In what way is the induced fit model different from the lock and key model?
In the induced fit model the enzyme active site changes shape to accommodate the substrate. This does not happen in the lock in key model because the enzyme active site already fits the substrate.
What is the effect of thyroxin on heat generation by cells.
Increases heat generation.
How does thyroxin effect metabolic rate of cells?
Increases metabolic rate.
What is the effect of thryroxin on oxygen consumption by cells?
Increases.
Where do the independent and dependent variables go on a graph?
Independent variable goes on x-axis (horizontal axis) Dependent variable goes on the y-axis (vertical axis).
An experiment is done in which cucumbers are given different amount of fertilizer to see how this effects their growth. What is the independent and dependent variable?
Independent variable is the amount of fertilizer. Dependent variable is the amount they grow.
What is a control setup?
Is the setup that is identical to the experimental setup except that is lacks that factor that you are testing. It is used to compare with the experimental group to see if other factors might be affecting the experiment.
Km
KM (the Michaelis constant) is the substrate concentration at which the reaction velocity is 50% of the Vmax.
Asparaginase
L-Asparagine H2O L-aspartate + NH3 Leukaemia
Some examples of heavy metals?
Lead, Mercury
LIGASES
Ligases are responsible for the catalysis of ligation; the joining of two substrates. Usually chemical potential energy is required, so the reaction is coupled to the hydrolysis of a disphosphate bond in a nucleotide triphosphate such as ATP.
Effect of an enzyme on the energy of activation?
Lowers the energy of activation.
What does it mean to denature an enzyme?
Means the tertiary shape becomes damaged and so it does not function well.
Methanol poisoning
Methanol is oxidized to formaldehyde and formic acid which attack the optic nerve causing blindness. Ethanol is given as an antidote Ethanol competitively inhibits the oxidation of methanol. Ethanol is oxidized in preference to methanol Consequently, the oxidation of methanol is slowed down and the toxic by-products do not have a chance to accumulate.
Do enzymes get used up in a chemical reaction?
NO? They can be used over and over again.
What prevents metabolic reactions from running out of control in a cell?
Negative feedback from the products. When there is a sufficient amount of product it blocks the enzymes at the start of the reactions.
Sample size?
Number of individuals tested.
Enzymes transform energy from ...
One form to another
How does the optimum pH for the enzymes pepsin and trypsin compare?
Optimal pH for pepsin is around 2. Optimal pH for trypsin is around 8.
Why are the ideal pH levels for pepsin and trypsin different?
Pepsin functions in the stomach to where pH is low (acidic) due to the presence of the acid HCl. Trypsin functions in the small intestine where pH is basic (around 8). For this reason their ideal levels for functioning need to be different.
Biochemical reaction in chloroplasts?
Photosynthesis: Solar energy is transformed in chemical energy glucose.
Enzyme inhibition?
Prevention of enzyme reactions by competitive and non-competitive inhibition.
Biochemical reactions?
Reactions that are carried out by living cells.
Co-enzymes are...
Small organic molecules attach to activate the enzyme and detach when reaction completed to deactivate the enzyme. Most often these are vitamins e.g. Niacin, riboflavin Coenzymes act as transporters of chemical groups from one reactant to another.
What is a target cell for a hormone?
Specific cell on which the hormone will act.
Why can the enzyme Maltase, which breaks down starch into the sugar Maltose, not also be used to break down the sugar sucrose?
Sucrose has a different shape than starch and therefore does not fit the active site in the enzyme Maltase. Each substrate has its own specific enzyme.
Each enzyme has an optimal _________ and _________ in which it can function.
Temperature / pH
An enzyme's activity can be affected by what three factors?
Temperature, pH and Concentration of the Substrate
How does the presence of a heavy metal effect an enzyme catalyzed reaction.
The Heavy metal causes the enzyme to become denatured so the reaction rate is lowered.
Alcohol
The acetaldehyde is processed by aldehyde dehydrogenase Most people have 2 forms of aldehyde dehydrogenase, a low Km mitochondrial and a high Km cytoplasmic form Due to a mutation some people lack the mitochondrial form High concentrations of acetaldehyde need to build before a high rate of catalysis can occur
The active site is a...
The active site is a 3D cleft formed by groups that come from different parts of the amino acid sequence
Metabolism?
The chain of enzyme catalyzed reactions that occur in the human body that maintain life.
Product?
The ending material in a chemical reaction.
Energy of activation (Ea)?
The energy required to start a chemical reaction.
Lock and Key Model of enzymes?
The enzyme and the substrate fit together like a lock that fits a key. this would lower the energy of activation so that the product can form more easily.
The effect of raising temperature above the optimum temperature in an enzyme catalyzed reaction?
The enzyme is a protein and therefore it becomes denatured and the reaction rate slows down.
What is a source gland?
The gland that produces the hormone.
What is the difference between the dependent and independent variable?
The independent variable is the one that the scientist controls and manipulates. The dependent variable is the one that the scientist does not control. It changes as a result of the independent variable.
What effect does the concentration of a coenzyme have on the rate of an enzyme reaction that it helps?
The reaction rate increases as the concentration of the coenzyme increases. Eventually a maximum rate is reached because the active sites all become filled. The reaction rate graph looks the same as and enzyme concentration graph or substrate concentration graph.
Hypothyroidism?
When the thyroid gland is underactive and produces too little thyroxin.
What is the specifity of enzymes due to ?
The specificity is due to precise interaction of the substrate with the enzyme. It is a result of the intricate 3D structure of the enzyme
Substrate or reactant?
The starting material in a chemical reaction.
Michaelis-Menten Enzyme kinetics
The study of the rate of an enzyme controlled reaction E + S <->ES----> E + P With unlimited substrate the rate will depend on [E]
Cellular metabolism?
The sum of all chemical reactions both endergonic and exergonic that take place in a cell.
What provides energy for endergonic reactions?
The synthesis of ATP
Experimental variable?
The variable in the experiment being tested.
Helicases
Their main function is to unpackage an organism's genes. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands (i.e., DNA, RNA, or RNA-DNA hybrid) using energy derived from ATP hydrolysis.
How are coenzymes and vitamins related?
Vitamins are organic coenzymes.
Controlling the variables in a experiment?
This means to keep all variables in an experiment constant except for the one being tested.
Source gland for thyroxin?
Thyroid gland located in the neck region.
TRANSFERASES
Transferases are enzymes that catalyse the movement of a functional group from one molecule to another. These functional groups are very diverse can include phosphate, methyl and glycosyl groups.
Clinical uses
Troponin is a contractile protein that normally is not found in serum. It is released only when myocardial necrosis occurs.
v=
Vmax [S]/ Km+ [S]
Hyperthyroidism?
When thyroid is over active and produced too much thryroxin.
An ucatalysed reaction requires...
a higher activation energy than a catalysed one
Kinases
a kinase is a type of enzyme that transfers phosphate groups from high-energy donor molecules, such as ATP,to specific substrates, a process referred to as phosphorylation.
feedback inhibition
a method of metabolic control in which a product formed later in a sequence if reactions allosterically inhibits an enzyme that catalyzes a reaction occurring earlier in the process
induced-fit model
a model of enzyme activity that describes an enzyme as a dynamic protein molecule that changes shape to better accommodate the substrate
activator
a substance that binds to an allosteric site which stabilizes the active form of an enzyme
What bonds does papain break ? where is it found ?
all peptide bonds found in papaya
Enzymes w/ot co-factors are called...
apoenzymes
Isozymes are...
are enzymes that differ in amino acid sequence but catalyze the same chemical reaction. -These enzymes usually display different kinetic parameters (e.g. different KM values), or different regulatory properties. -The existence of isozymes permits the fine-tuning of metabolism to meet the particular needs of a given tissue or developmental stage
Oxidoreductases
catalyse oxidation or reduction reactions, where electrons are transferred from one molecule (the reductant) to another molecule (the oxidant).
Enzymes are..
biological Catalysts vast majority reactions in cells are driven by enzymes
What bonds does Trypsin break
bonds between lysine and arginine residues
How do enzymes catalyze reactions?
by lowering the activation energy required for the reaction to occur
The R groups in the active site create ...
charged regions that only appropriate chemical groups can bind to
Endocrine gland?
ductless gland secreting hormones into the blood stream.
A fast, efficient, specific enzyme...
has a high Vmax and a low Km
Enzymes with co-factors are called
holoenzymes
Enzymes are specific
in the reactions they catalyse and in their choice of reactants (substrate)
denaturation
increases in temperature or pH can cause enzymes to lose their shape and function resulting in this process
Co-factors are simple ....
inorganic metal ions that promote enzyme function e.g. Zn Cu,Fe.
allosteric regulation
involves receptor sites located some distance from the active site of certain enzymes that bind substances that either stimulate or inhibit and enzymes activity
Nifedipine- Non-competitive inhibitor
is a calcium channel blocker, it inhibits Ca2+ dependent ATPase Prevents the uptake of calcium into cardiac cells Its main uses are is to treat angina and high blood pressure
Homocystinuria
is an inherited disorder affecting this enzyme. The disease is characterized by nearsightedness (myopia), an increased risk of abnormal blood clotting, and brittle bones that are prone to fracture (osteoporosis) - Less common forms of homocystinuria can cause intellectual disability, failure to grow and gain weight at the expected rate seizures and problems with movement Methylenetetrahydrofolate reductase (MTHFR) converts homocysteine to methionine.
[S]
is the concentration of the substrate S.
How many reactions do enzymes catalyse
just one reaction
Niemann-Pick disease
lack acid sphingomyelinase (ASM). This enzyme is found in lysosomes and is required to metabolise a lipid called sphingomyelin. If ASM is absent or not functioning properly, sphingomyelin cannot be metabolised properly and is accumulated within the cell, eventually causing cell death and the malfunction of major organ systems
Effect of lowering the temperature below the optimum temperature in an enzyme catalyzed reaction.
molecules move more slowly therefore there are fewer collisions and the reaction slows down.
Is there a difference in energy between catalysed and uncatalysed reactions ?
no
Does the active site take up all of the enzyme ?
no, it takes a small proportion of the enzyme. Most enzymes are 100+ amino acids long. only a few create the active site
The specificity of binding depends
on the precisely defined arrangement of atoms in an active site -And can be altered by a change in amino acid away from the binding site.
In mitochondria the free energy in small molecules is converted into...
the energy in an ion gradient, then converted into the stored energy in ATP
Thrombin catalyses
the hydrolysis or Arg- Gly only in a specific chain of residues
Vmax represents ....
the maximum velocity achieved by the system at saturating substrate concentrations.
Where does the catalytic power from enzymes come from ?
their binding substrates together in an orientation that promotes the formation of transition states -They bring together substrates in enzyme-substrate (ES) complexes -Enzymes are selective in the substrate they bind due to the active site of the enzyme
