BMOL20060_Practical 1 Manual_2023
BMOL20060_Practical 1 Manual_2023
BMOL20060
Biomolecular Laboratory Skills 1
Practical Introduction & Practical Manual 1
Amount (mole) Mass (gramme) Volume (litre) Concentration
(molar)=(amount/volume)
mol g L 1 M = 1 mol/L
mmol mg mL 1 mM = 1 mmol/L
μmol μg μL 1 μM = μmol/L
nmol ng nL 1 nM = nmol/L
pmol pg pL 1 pM = pmol/L
fmol fg fL 1fM = 1fmol/L
Module Practical’s
It is the policy of the School of Biomolecular and Biomedical Science to safeguard the
health and safety of its undergraduate students during their practical classes.
To achieve this goal it aims to develop and maintain a culture supportive of health and
safety in the undergraduate laboratories.
Before commencing their first practical session in the O’Brien Science Centre
undergraduate laboratories, every student must familiarise their self with the locations of
all relevant fire exits, first aid boxes and emergency showers.
Any student with a health effect that may be adversely affected by working in the
laboratory, or that may affect their ability to carry out their practical work, should
consult in confidence with their academic supervisor.
All practical’s are devised to minimise, as far as reasonably practicable, the risks to
which the students are exposed. This includes minimising exposure to hazardous
chemicals, ensuring that all equipment complies with the correct standards of safety,
segregating any hazardous procedures, providing safety control measures (such as fume
cupboards) and requiring that personal protection equipment be used as appropriate.
IMPORTANT
Students may not attend practical’s without the appropriate personal protective
equipment (PPE) – i.e. lab coat. You MUST bring everything you need to each practical.
BMOL20060 Practical 1 2023
1. All students must wear a clean white lab coat at all times in the laboratory, to
protect themselves and their clothing from contamination and spillages.
2. Safety glasses or over-glasses with side protection must be worn while doing bench work.
3. No unnecessary items, such as coats and bags, may be left on lab benches or on the
floor where they may cause others to trip. There are designated storage spaces
provided for coats and bags.
4. Eating and drinking are strictly forbidden. Students must not place anything in their
mouths and touching the face or hair should also be avoided while in the laboratory.
5. Disposable gloves are provided and should be worn during the practical. Gloves
may become contaminated with potentially hazardous chemicals or biological
materials during routine practical procedures. If so, they should be disposed of
immediately in a yellow waste bag and replaced with clean gloves. This will
prevent spreading the contaminant to people and surfaces within the laboratory.
6. Use of mobile phones is not permitted during the practical. Phones should not be
handled when wearing gloves or left out on the lab bench due to contamination
with potentially hazardous chemicals or biological materials.
8. Students should make note of any hazardous substances they will be using in the
course of each practical.
10. Students should never use an item of equipment before receiving instruction in its
use and being aware of the hazards involved. Any specific notices attached to
individual pieces of equipment must be observed.
11. Students should inform their demonstrator of any fault in electrical or electronic
equipment. No student should attempt to use or repair faulty equipment. A
competent person must carry out any repairs that are required.
BMOL20060 Practical 1 2023
12. Students should familiarise themselves with the different types of waste bins
provided and segregate their waste accordingly:
13. All students must always wash their hands immediately when finished working in
the laboratory, and if they are leaving for a coffee-break, etc. White coats must
never be worn outside the laboratory.
BMOL20060 Practical 1 2023
5. Any splashes of reagents onto a student’s skin must be thoroughly rinsed with water
under a running tap and must be reported immediately to a demonstrator.
6. If a student gets a splash of a chemical into the eye, it must be held under running water
for several minutes at least. The demonstrator must be informed, so that further
appropriate action can be taken.
7. All accidents involving injury, however minor, to persons, damage to property or any
near miss that almost resulted in either must be reported on the official UCD incident
report forms by the demonstrator. Incident report forms can be obtained from the Safety
Officer.
8. Any student with a history of an allergic condition should advise their demonstrator and
appropriate personal protective equipment will be provided where necessary.
10. If a large fire occurs or the evacuation alarm sounds, students must follow the directions
of the demonstrators or staff members present. They must not delay to take personal
belongings with them.
BMOL20060 Practical 1 2023
Each chemical has a set of Hazard (H) and Precautionary (P) statements associated with it.
These are typically given in the form of an H or P code e.g. H319, P261. The codes indicate
the type of hazards associated with and precautions necessary when working with that
chemical. A full list of the codes and their meaning are supplied in the appendix of this
manual. The H and P statements replace an older system of Risk (R) and Safety (S) codes,
also in the appendix.
The following warning pictograms are part of a Globally Harmonized System (GHS) of
safety labels found on chemical containers. You should know what they mean. They replace a
similar set of pictograms (see below) which you may also come across and should be familiar
with.
New Pictograms
Old Pictograms
BMOL20060 Practical 1 2023
Amount (mole) Mass (gramme) Volume (litre) Concentration (molar) Relative value of
= (amount/volume) unit prefixes
mol g L 1 M = 1 mol/L 1
mmol mg mL 1 mM = 1 mmol/L milli (m) 10-3
μmol μg μL 1 μM = μmol/L micro (μ) 10-6
nmol ng nL 1 nM = nmol/L nano (n) 10-9
pmol pg pL 1 pM = pmol/L pico (p) 10-12
fmol fg fL 1fM = 1fmol/L femto (f) 10-15
Alternatively
SI unit M/L/g 1 1
milli mM/mL/mg 0.001 1x10-3
micro μM/μL/μg 0.000001 1x10-6
nano nM/pL/ng 0.000000001 1x10-9
pico pM/pL/pg 0.000000000001 1x10-12
femto fM/fL/fg 0.000000000000001 1x1015
BMOL20060 Practical 1 2023
We don’t need to go into a detailed definition of atomic mass here, except to say that it is
very close to the sum of protons and neutrons in the nucleus of the atom.
The terms ‘molecular mass’, ‘molecular weight (MW)’ or ‘formula weight (FW)’ are all
used to describe the mass of a chemical, in grams, that gives 1 mole of that chemical (e.g. the
MW of H2O is 18.015). As another example, the formula weight of NaCl is 58.44, which is
equal to the mass of 1 mole of NaCl ‘molecules’ (strictly speaking NaCl crystals are not made
up of individual molecules but we can treat them as if they are when measuring amounts).
To add to the confusion, another term is sometimes also used; ‘relative molecular mass’
(Mr). This gives the mass of an individual molecule (as opposed to a mol of molecules) and
is usually given in atomic mass units (u) or Daltons (Da). The Mr of H2O is 18.015 Da.
• Note that the Mr of a substance is equal to the sum of the atomic masses of its
constituent atoms, in this case H = 1.008; O=15.999.
You can see that the Mr and MW of H2O have the same value but different units. This is
because of how the unit ‘mol’ is defined. The important point to remember is:
The concentration of smaller molecules like buffers and salts are usually given in Molar
concentrations (M). So for example a 1 M solution of NaCl contains 1 mol of NaCl per litre
of solution. Unless stated otherwise the solution is assumed to be aqueous, i.e. the liquid
(solvent) used to dissolve the NaCl (solute) is water.
Another point to note is the use of square brackets to indicate Molar (M) concentration in
equations
or pH = -log10 [H+] (in this case [H+] = the molar concentration of hydrogen ions)
This is because you are changing the numerator and the denominator by the same amount.
BMOL20060 Practical 1 2023
• Note: the ‘(w/v)’ symbol indicates ‘weight per volume’ (i.e. weight of solute per
volume of solution).
1. Mass Percent: the mass percent is used to express the concentration of a solution
when the mass of a solute and the mass of a solution is given:
Introduction
Preparation of tools and reagents are critical components of all laboratory experiments. For
any experiment to succeed, it is essential that you know how to use the basic tools (e.g.
micropipettes), how to make buffers and solutions and how to perform basic statistical
analysis of the results.
When making a solution containing a desired molar concentration of a substance, the first
thing you need to know is the molecular weight (MW) or formula weight (FW) of the
substance. Generally, this is supplied by the manufacturer and may be obtained from the
reagent bottle label. It may also be obtained from the Merck index or online chemistry
dictionaries.
You can also determine the MW from the periodic table (e.g. the atomic mass of Na is
22.98 and Cl is 35.45, so the molecular weight of NaCl is 58.44).
Use the following formula to calculate the mass of substance required per volume required:
BMOL20060 Practical 1 2023
• Note: because M=mol/L and MW (or FW) has units of g/mol, we can see that the
final value us in grams (g).
• Write out every calculation step and ALWAYS include the correct units beside
EACH value. Mixing up units is the most common source of error with these
calculations.
Example 1.
Using the formula above, calculate how much NaCl is needed to make a 300 mL solution of
0.5 M NaCl.
Check Units:
BMOL20060 Practical 1 2023
Example 2.
Calculate how much of each reagent is needed to make 1 L of the following buffer:
1. For NaCl:
a. Required molarity is 150 mM = 0.150 M
b. MW of NaCl is 58.44 g/mol
c. Required volume is 1L
d. Therefore: 0.150 M x 58.44 g/mol x 1 L = 8.766 g of NaCl required
Example 3.
You are given a recipe (see below) to male an 800 mL buffer solution. Using the formula
above, calculate the final concentration of each of the reagents.
1. For NaCl:
Micropipettes
Micropipettes (also referred to as pipettes or pipettors) are probably the most frequently used
piece of equipment in any biochemical or biomolecular laboratory. They are used for
transferring small amounts of liquid accurately, and can be set to any volume of liquid within
the range covered by the pipette. Different sizes of pipette cover different ranges of volumes:
Note: Pipettes are most accurate at pipetting volumes in the upper half of their range, so you
should always keep this in mind when selecting a pipette to use.
BMOL20060 Practical 1 2023
When adjusting the volume, it is extremely important to not go above the maximum or below
the minimum volume. This can damage the inner mechanism, which at best makes the pipette
inaccurate, and at worst breaks the pipette (brand new pipettes are expensive!).
• Note: In the teaching labs there are several brands of pipettes, which means that the
method of adjusting the volume may be different.
BMOL20060 Practical 1 2023
When setting the volume, all pipettes have a display window that allows you to see what
value the volume is set to. For most pipettes there are 3 digits visible in the display window,
but for others there are 4 digits instead.
All pipettes have a system that will allow you to distinguish between units of thousands,
hundreds, tens, single units and smaller.
For some pipettes, there is a dot or line to denote where the decimal point is:
For other pipettes, there is a single number that is a different colour to denote the decimal
point or a change in magnitude (i.e. thousands).
BMOL20060 Practical 1 2023
1. Never rotate the volume adjuster beyond the upper or lower limit.
2. Never use a micropipette without an appropriate tip. Also, make sure the correct tip
match the corresponding pipette.
BMOL20060 Practical 1 2023
3. Never lay a micropipette down or turn upside down when fitted with a tip containing a
liquid.
4. Never let the plunger snap back after withdrawing or ejecting a liquid.
BMOL20060 Practical 1 2023
When it comes to validating micropipettes, to ensure that they are working properly and
fit for purpose, each micropipette is tested at its maximum and minimum volume:
• Accuracy is demonstrated by how close the average weight of the pipetted water is to
the expected weight (i.e. 1000 μL = 1 g).
• Precision is estimated by how closely similar the five weights are for the same volume
(i.e. how small is the standard deviation for the 5 replicate values).
• For good accuracy and precision, the margin of error should not exceed 2% for the
maximum volume and 20% for the minimum volume.
BMOL20060 Practical 1 2023
Results: 3, 7, 7, 19
(3+7+7+19) ÷ 4 = 9
Step 2. Subtract the mean from each of your results value ( χi in the formula):
3-9 = -6
7-9 = -2
7-9 = -2
19-9 = 10
Whether you realise it or not you have just calculated the standard deviation.
This tells us that the 4 samples above (3, 7, 7, 19) have an average (or mean) value of 9,
but that the samples deviate from this mean by an average of ± 6.
BMOL20060 Practical 1 2023
In Microsoft Excel, the average of a group of numbers can be calculates by the formula:
=AVERAGE()
Likewise, the standard deviation (SD) of a group of numbers can be calculated by the
formula:
=STDEV.S( )
BMOL20060 Practical 1 2023
Procedure
b. Calculate how much solute you will need to make 100 ml of a given
concentration. Show this to your demonstrator and record on the sheet
provided.
c. Place a weigh boat on the balance and press the tare button (i.e. set the weight to
zero). Then weigh out the required amount of solute (correct to two decimal
places).
e. Carefully pour the solution into a 100 mL volumetric flask, taking care not to spill
it.
f. Using the same beaker, top up the flask with more distilled water, until the bottom
of the miniscus is level with the line on the neck of the flask.
g. Label the flask with the name and concentration of the chemical. It’s best practice
to also include the date and your initials.
h. Your demonstrator will check (and correct) your calculations and how you
prepared your solution.
BMOL20060 Practical 1 2023
a. Preparation: Hold the pipette in a vertical position. Depress the plunger smoothly
to the first stop position.
b. Aspiration: Immerse the end of the pipette tip in the liquid. Allow the plunger to
move up smoothly to the rest position. Wait one second so that all the liquid has time
to move up into the tip.
c. Distribution: Place the pipette tip at an angle (10-450) against the side wall of the
receiving vessel. Depress the plunger smoothly to the first stop position.
d. Purge: Wait one second, and then depress the plunger to the second stop position.
This blow-out stroke removes any remaining sample from the tip. Keep the plunger
depressed as you carefully move the pipette tip away.
f. Eject the used tip and store the pipette in an upright position: To avoid touching
contaminated tips, hold the pipette over the waste container and press the tip ejector
button.
g. During the practical demonstrators will ask each student to show that they can transfer
a specific volume of liquid using a pipette.
BMOL20060 Practical 1 2023
c. Measure the weights of the maximum and minimum volumes of three different
micropipettes (P5000, P1000 and P200) using distilled water. Record the results in the
sheet provided. Do this 5 times for each volume.
d. Post practical: Before you leave you must submit your completed the Report
Assessment sheet and hand it to your demonstrator. Calculate the average and
standard deviation and recoded it in the sheet provided.
Vol.
Pipette 1 2 3 4 5 Average St.Dev.
(μL)
P5000
P1000
P200
e. Calculate the threshold at which the margin of error is deemed acceptable. Record
this in your practical assessment sheet. You will be asked to do this for one of the
pipettes.
f. E.g. For 5000 µL, which is the maximum volume for a P5000 pipette, the margin of
error should not exceed 2%. 2% of 5000 is 100 µL, so the threshold would be 4900
µL.
3. Do a serial dilution
a) On your bench you will find:
i. A test tube rack containing 6 test tubes
ii. One test tube will contain water with orange dye
iii. Distilled water
iv. Vortex mixer
ii. Take 1 ml of orange dye and add to the first test tube that contains only water
iii. Mix carefully using the vortex mixer (slow-medium speed setting).
iv. Take 1 mL of this solution and add to the next tube that contains only water
c) If the concentration of orange dye started at 100 µM, calculate what the concentration
should be in tube #6.
d) Your demonstrator will check (and correct) your calculations and how you prepared
your serial dilution.
References
Chapter 19 & 20 – Preparing for practical work & Working safely in the lab