RESEARCH SUMMARY SEMESTER 1
All modules
Radboud University, Nijmegen
Made by: Georgia Graat
, Research summary Q1 + Q2
Biochemistry laboratory skills
Enzymes are biological catalysts that control the speed and specificity of almost all reactions in the
body. Their activity as catalysts originates from their ability to provide a highly specific binding site
for biomolecules (substrates). Modification of the binding site enables regulation of enzyme activity
either by the binding of other compounds (ligands; activators or inhibitors) or by enzymatic
alterations, such as phosphorylation. The rate of an enzyme-catalyzed reaction is dependent on the
affinity of the enzyme for the substrates and on the substrate concentration. This relation can be
expressed by the Michaelis-Menten equation:
𝑉𝑚𝑎𝑥 ∗ [𝑆]
𝑣=
𝐾𝑚 + [𝑆]
In this equation, v stands for the velocity. S is the substrate concentration. Km is the Michaelis-
Menten constant and Vmax is the maximum velocity. At a certain time, the enzymes cannot catalyze
faster/more than they already do, so a horizontal asymptote is seen (the Vmax). Km is the substrate
concentration at ½ Vmax. A higher Km will therefor mean a higher Vmax. Km is a measure for the
binding strength between enzyme and substrate.
You can plot the graph ‘absorption against time’. In the graph you can use the first piece of the line
to calculate the initial rate (delta Y/delta X). The unit will be au/s. In this case you have to convert this
initial rate of au/s to mmol/min. If you have calculated multiple initial rates, you can put them all in a
0,12 graph ‘rate against concentration’. Here
you have the different initial rates set
0,1
out against the different substrate
Rate (mmol/min)
0,08 concentrations that you measured with
0,06
and with this information you can draw
the curve that is the Michaelis-Menten
0,04 curve. From this you can estimate/
0,02 obtain the Vmax and Km. In the graph
left the dots are the calculated initial
0
0 0,05 0,1 0,15 0,2 0,25 0,3 0,35
rates and this leads to the estimation of
the Michaelis-Menten curve.
Ethanol (M)
Vmax and Km are the main, biologically
relevant characteristics of an enzyme. Regulation of the activity of key enzymes serves to control
metabolic pathways and cellular and physiological processes in order to maintain homeostasis. At
Vmax, almost all enzyme molecules bind a substrate. The Vmax cannot change, the velocity can until
it reaches Vmax. The rate is only dependent on Vmax, Km has no special effect.
In a spectrophotometer you need to use a blank to set the absorption at zero. This way you make
sure your mixture is measured correctly. The spectrophotometer measures the absorption the whole
time and you can graph this against the time. To quantify an unknown monster, a calibration line
(ijklijn) is used. A calibration line is a set of measurements of standard solutions with a known
concentration of a certain matter/compound. This is used to estimate the concentration of a
compound in a monster. The R-value represents how good points lay on the correct line (with a
maximum of 1).
Made by: Georgia Graat
, A biosafety cabinet is an enclosed, ventilated laboratory workspace for safely working with materials
(potentially) contaminated with pathogens. It protects the workers and the biological specimen from
being contaminated with biomaterial. Mostly tissue, cells and organisms are used here, because they
may not be contaminated. This is achieved by the application of a down-flow of sterile air. In a fume
hood you can work with flammable and toxic chemicals. This is just a safety cabinet, without special
airflow. A centrifuge is a machine with a rapidly rotating container that applies centrifugal force to its
contents, to separate fluids of different densities of fluids from solids. The substances are separated
better with more rotations per minute and a longer centrifugal time.
Enzymes have an optimal pH that is tuned to the pH of their environment. The pH dependence of
enzyme activity is based primarily on the pH dependence of the hydrogen bonds within the enzyme.
Enzymes have an optimal temperature, because the binding of substrates is dependent on protein
structure. Some enzymes have to be modified to become active, like removing an inhibitory part. A
curve with an inhibitor that is competing with the substrate, will have a low Vmax and suddenly a
very high Vmax (because the substrate concentration is too high). Competitive inhibition means that
the substrate and other complex bind to the same site of the enzyme. Allosteric regulation is the
binding of an inhibitor or activator on the allosteric site, by which the active binding site changes.
Enzymes are proteins specific for certain substrates (lock-key
combination). Enzymes accelerate reactions by lowering the
activation energy. Enzymes bring substrates closer together so they
react with each other. Iso-enzymes accelerate the same reactions,
but in different environments. You have different kinds of enzymes.
Oxidoreductases work with oxidators and reductors. Transferases
change the bonds between molecules. Hydrolases work with H2O.
Lyases/synthases break bonds between a big molecule. Isomerases
make isomers and ligases/synthetases use ATP to establish a bond.
Methods and measures on human based research
Epidemiology is the study and analysis of the distribution (who, when and where), patterns and
determinants of health and disease conditions in defined populations. It identifies risk factors for
disease and targets for preventive healthcare. Major areas of study include disease causation,
transmission, outbreak investigation, disease surveillance, screening and comparisons of treatment
effects.
Epidemics are diseases or plagues that are thrown onto a population. The epidemiology is the
science that studies the frequency at which these diseases appear in the population. The epidemics
include things such as chronic diseases, contagious diseases and injury as a cause of accidents.
Epidemiologist try to prevent these diseases. They also aim at etiologic factors (a cause of the
disease), diagnostic factors (indication of the disease) and prognostic factors (progress of disease).
These factors are called determinants. The disease is here the dependent variable.
The spread of a disease can be seen if the population is divided into subgroups that have the same
features. The factors that have influence on the cause or prognosis of a disease are divided into
genetics, behavior and environment.
A hypothesis or theory is made based on observations, other theories and other results. Induction
and deduction play a big part here in formulating questions and proving a hypothesis is correct.
Made by: Georgia Graat
All modules
Radboud University, Nijmegen
Made by: Georgia Graat
, Research summary Q1 + Q2
Biochemistry laboratory skills
Enzymes are biological catalysts that control the speed and specificity of almost all reactions in the
body. Their activity as catalysts originates from their ability to provide a highly specific binding site
for biomolecules (substrates). Modification of the binding site enables regulation of enzyme activity
either by the binding of other compounds (ligands; activators or inhibitors) or by enzymatic
alterations, such as phosphorylation. The rate of an enzyme-catalyzed reaction is dependent on the
affinity of the enzyme for the substrates and on the substrate concentration. This relation can be
expressed by the Michaelis-Menten equation:
𝑉𝑚𝑎𝑥 ∗ [𝑆]
𝑣=
𝐾𝑚 + [𝑆]
In this equation, v stands for the velocity. S is the substrate concentration. Km is the Michaelis-
Menten constant and Vmax is the maximum velocity. At a certain time, the enzymes cannot catalyze
faster/more than they already do, so a horizontal asymptote is seen (the Vmax). Km is the substrate
concentration at ½ Vmax. A higher Km will therefor mean a higher Vmax. Km is a measure for the
binding strength between enzyme and substrate.
You can plot the graph ‘absorption against time’. In the graph you can use the first piece of the line
to calculate the initial rate (delta Y/delta X). The unit will be au/s. In this case you have to convert this
initial rate of au/s to mmol/min. If you have calculated multiple initial rates, you can put them all in a
0,12 graph ‘rate against concentration’. Here
you have the different initial rates set
0,1
out against the different substrate
Rate (mmol/min)
0,08 concentrations that you measured with
0,06
and with this information you can draw
the curve that is the Michaelis-Menten
0,04 curve. From this you can estimate/
0,02 obtain the Vmax and Km. In the graph
left the dots are the calculated initial
0
0 0,05 0,1 0,15 0,2 0,25 0,3 0,35
rates and this leads to the estimation of
the Michaelis-Menten curve.
Ethanol (M)
Vmax and Km are the main, biologically
relevant characteristics of an enzyme. Regulation of the activity of key enzymes serves to control
metabolic pathways and cellular and physiological processes in order to maintain homeostasis. At
Vmax, almost all enzyme molecules bind a substrate. The Vmax cannot change, the velocity can until
it reaches Vmax. The rate is only dependent on Vmax, Km has no special effect.
In a spectrophotometer you need to use a blank to set the absorption at zero. This way you make
sure your mixture is measured correctly. The spectrophotometer measures the absorption the whole
time and you can graph this against the time. To quantify an unknown monster, a calibration line
(ijklijn) is used. A calibration line is a set of measurements of standard solutions with a known
concentration of a certain matter/compound. This is used to estimate the concentration of a
compound in a monster. The R-value represents how good points lay on the correct line (with a
maximum of 1).
Made by: Georgia Graat
, A biosafety cabinet is an enclosed, ventilated laboratory workspace for safely working with materials
(potentially) contaminated with pathogens. It protects the workers and the biological specimen from
being contaminated with biomaterial. Mostly tissue, cells and organisms are used here, because they
may not be contaminated. This is achieved by the application of a down-flow of sterile air. In a fume
hood you can work with flammable and toxic chemicals. This is just a safety cabinet, without special
airflow. A centrifuge is a machine with a rapidly rotating container that applies centrifugal force to its
contents, to separate fluids of different densities of fluids from solids. The substances are separated
better with more rotations per minute and a longer centrifugal time.
Enzymes have an optimal pH that is tuned to the pH of their environment. The pH dependence of
enzyme activity is based primarily on the pH dependence of the hydrogen bonds within the enzyme.
Enzymes have an optimal temperature, because the binding of substrates is dependent on protein
structure. Some enzymes have to be modified to become active, like removing an inhibitory part. A
curve with an inhibitor that is competing with the substrate, will have a low Vmax and suddenly a
very high Vmax (because the substrate concentration is too high). Competitive inhibition means that
the substrate and other complex bind to the same site of the enzyme. Allosteric regulation is the
binding of an inhibitor or activator on the allosteric site, by which the active binding site changes.
Enzymes are proteins specific for certain substrates (lock-key
combination). Enzymes accelerate reactions by lowering the
activation energy. Enzymes bring substrates closer together so they
react with each other. Iso-enzymes accelerate the same reactions,
but in different environments. You have different kinds of enzymes.
Oxidoreductases work with oxidators and reductors. Transferases
change the bonds between molecules. Hydrolases work with H2O.
Lyases/synthases break bonds between a big molecule. Isomerases
make isomers and ligases/synthetases use ATP to establish a bond.
Methods and measures on human based research
Epidemiology is the study and analysis of the distribution (who, when and where), patterns and
determinants of health and disease conditions in defined populations. It identifies risk factors for
disease and targets for preventive healthcare. Major areas of study include disease causation,
transmission, outbreak investigation, disease surveillance, screening and comparisons of treatment
effects.
Epidemics are diseases or plagues that are thrown onto a population. The epidemiology is the
science that studies the frequency at which these diseases appear in the population. The epidemics
include things such as chronic diseases, contagious diseases and injury as a cause of accidents.
Epidemiologist try to prevent these diseases. They also aim at etiologic factors (a cause of the
disease), diagnostic factors (indication of the disease) and prognostic factors (progress of disease).
These factors are called determinants. The disease is here the dependent variable.
The spread of a disease can be seen if the population is divided into subgroups that have the same
features. The factors that have influence on the cause or prognosis of a disease are divided into
genetics, behavior and environment.
A hypothesis or theory is made based on observations, other theories and other results. Induction
and deduction play a big part here in formulating questions and proving a hypothesis is correct.
Made by: Georgia Graat
