Lab Exercise 3 - Chemistry of Life
The Chemical Composition of Cells
Introduction:
Cells are the basic structural and functional units of all living organisms. Within these cells are
chemical substances that are of diverse sizes and shapes and that serve a variety of functions. These
substances are constructed from smaller parts called elements. There are 92 naturally occurring
elements, and 25 of these are essential to life. Elements, which are arranged in the periodic table
(Figure 3.1), are composed of atoms.
Figure 3.1 - Periodic Table of Elements
Each atom consists of protons, neutrons, and electrons arranged with the positively charged protons
and uncharged neutrons located in the central core (called a nucleus) of the atom and the negatively
charged electrons outside the nucleus, in constant motion (Figure 3.2 and 3.3).
Figure 3.2 - Atomic Particles
Figure 3.3 - Simplified models of a helium (He) atom
Each atom has a characteristic number of protons and that number is referred to as the atomic number.
Since atoms have the same number of electrons as they have protons, the atomic number can also
indicate the number of electrons. Additionally, because the number of positively charged protons equals
the number of negatively charged electrons, the atom is electrically neutral. The sum of the protons
and neutrons gives the mass number or atomic weight. (Figure 3.4).
Atomic number
Carbon
6
Element symbol
C
12
Element name
Mass number or
Atomic weight
Figure 3.4 - Element
Objectives:
Upon completion of this exercise, you should be able to:
1.
2.
3.
4.
5.
6.
7.
Establish the number of protons, neutrons, and electrons of any given atom of an element.
Accurately diagram a shell model of any given element.
Depict how ionic bonding and covalent bonding occur, in accordance to the octet rule.
Define acid, base, and explain pH scale.
Determine whether a given solution is acidic or basic in nature.
Explain the methods used for chemical testing
Define all the terms that are in bold print and underlined.
Electron Configurations:
Understanding atomic structure is essential to understanding how elements come together to form
chemical bonds. Electrons are distributed within the energy shells. Distribution of the electrons within
the energy shells will help to determine whether an atom is stable or reactive. The first energy shell has
a maximum capacity of two electrons. The second shell can hold up to eight electrons and the third can
hold up to 18 electrons. Placement of the electrons also depends on the octet rule. This rule states that
an atom is most stable when there are eight electrons in the outer most shell (the exception to this rule is
the first shell that is stabilized with just two electrons). The maximum number of electrons for each
shell (energy level) is determined by using the formula 2n2 (where n = shell number with respect to
nucleus). Below is an example for the computation of how to compute the distribution of electrons:
Example:
1st shell
2 electrons ------- low energy
2nd shell 8 electrons ------- more energy
3rd shell up to 18 electrons
Higher shells (up to 7) hold many more electrons
Chemical Bonding:
Atoms that have electron configurations in which the outer shell is incomplete will seek to stabilize
those outer shells by transferring or sharing electrons. The specific arrangement of these stabilized
atoms form larger units called molecules. The molecules are held together by chemical bonds.
Covalent Bonds (Figure 3.5):
A covalent bond is formed when two atoms share one or more pairs of electrons to become more
stable. The two atoms share one, two or three pairs of electrons forming single, double or triple covalent
bonds respectively. An example of this is shown below:
Single bond = share 1 pair; double bond = share 2 pair and triple = share 3 pair
When atoms share electrons, they always try to reach the stable configuration of 8 electrons or whatever
electron number is required to satisfy the outer most shell. When two or more atoms combine in
covalent reaction, the result is a molecule. There are two types of covalent bonds the polar covalent
bond and the non-polar covalent bond. The polar covalent bond is a bond between atoms in which the
outer shell electrons are not shared equally. A non-polar covalent bond is a bond between atoms in
which the outer shell electrons are shared equally.
a. Non-polar Covalent Bond
b. Polar Covalent Bond
Figure 3.5 - Covalent Bonding
Ionic Bonds (Figure 3.6):
Ions are atoms or molecules that have lost or gained electrons. Because of the change in electron
number, ions have either a positive or negative charge. Atoms that have lost electrons are positively
charged (+), and are called cations. Anions are negatively charged (-) atoms that have gained electrons.
Ionic bonds result from the attraction of ions with unlike charges (cation to anion)
Figure 3.6 - Ionic Bonding
Acids, Bases, and pH (Figure 3.7):
When dissolved in water, some molecules may dissociate (separate) and become ions. Substances that
separate to release hydrogen ions (H+) into a solution are called acids. Conversely, substances that
accept H+ from a solution are called bases (these substances may also release the hydroxide ion, OH-, in
solution). The pH scale, a scale that ranges from 0 to 14, measures acidity by estimating the H+
concentration of a solution. A solution with a high H+ concentration has a pH lower than 7, and is
considered an acid. A solution that has a low H+ concentration has a pH above 7, and is considered a
base (alkaline). Solutions that have a pH of 7 are neutral, because in these solutions the concentration of
H+ and OH- are equal.
Figure 3.7 - pH Scale
Pure water is an example of a neutral solution. Because the pH scale is logarithmic, each change of 1
pH unit on the scale corresponds to a ten-fold difference; therefore, a solution with a pH of 2 is ten times
more acidic than a solution with a pH of 3. Similarly, a solution with pH 9 is ten times more basic than
a solution with pH 8. Examples of acids include hydrochloric acid (HCl) and nitric acid, (HNO3).
When placed in water each of the substances will release H+:
HCl → H+ + ClHNO3 → H+ + NO3Examples of bases include ammonia, NH3, and sodium hydroxide (NaOH). When placed in water these
substances will accept hydrogen ions or release hydroxides ions.
NH3 + H+ → NH4
NaOH → Na+ + OHAcid-base indicators are dyes that are used to distinguish between acidic and basic solutions by means
of color changes. These dyes are common in everyday substances. For example, most teas are amber in
color however, when lemon juice is added (lemon juice contains citric acid) the color lightens.
Anthocynanins are a class of chemicals that are present within the leaves of red cabbage. Red cabbage
contains a large amount of anthocynanins. The red, blue, and purple pigments among the anthocynanins
give the beautiful colors seen in fruits, flowers, and the leaves of trees during the autumn seasons. The
resulting solution can serve as a pH indicator (Table 3.1).
2
4
pH
Red
Purple
Color
Table 3.1 - pH Indicator
6
Violet
8
Blue
10
Bluish green
12
Greenish yellow
Buffering Systems:
All living creatures, even single-celled organisms, must maintain very stable internal environments in
order to survive. As the metabolic environment changes, an organism must sustain physiological
conditions such as temperature, pH, water content, and food intake at healthy levels. This stable level of
metabolic conditions is called homeostasis, and organisms maintain homeostasis in a variety of ways. In
multicellular organisms, complex buffer systems allow the organism to maintain internal pH, avoiding
excessive acidity or excessive alkalinity. Its function is to minimize the change in pH when base or acid
is added to the solution.
Organic Molecules:
Most biological molecules are classified as organic compounds. The key feature of these molecules is
that they are carbon based, and that they contain at least one hydrogen atom and one or more functional
groups that give the molecules specific chemical properties. Organic compounds are held together by
covalent bonds that link small subunits (monomers) to create large molecules (polymers).
There are four classes of biologically important organic molecules. Within the cell each type of
molecule has an important function. The classes of organic molecules are: carbohydrates, lipids,
proteins, and nucleic acids.
Carbohydrates:
Most carbohydrates contain only carbon (C), hydrogen (H), and oxygen (O) and have the general
formula CnH2nOn. They function as energy sources and structural support molecules within a
cell. The simplest forms of carbohydrate molecules are monosaccharides, such as glucose and
fructose. Two monosaccharides can be linked together to form a disaccharide. Common
disaccharides include maltose, sucrose, and lactose. Many carbohydrates linked together form
polysaccharides. Polysaccharides are long chains of monosaccharide subunits linked together.
Common polysaccharides include: glycogen, starch, cellulose, and chitin.
Lipids:
Lipids are a varied group of organic molecules that are insoluble in water. Although they
contain carbon, hydrogen, and oxygen, the amount of oxygen is much less than that which is
found in carbohydrates. They function as energy storage molecules, important components of
biological membranes, and as hormones.
Lipids are subdivided into three groups: fats, phospholipids, and steroids. Fats are lipids that
are composed of fatty acid chains bonded to a molecule of the alcohol glycerol. Phospholipids
are structurally similar to fats except that one of the fatty acid chains is replaced by a group that
contains phosphate. Steroids are a class of structurally distinct lipids, in that they consist of four
interlocking rings.
Nucleic Acids):
Nucleic acids are complex molecules made from monomers called nucleotides. Each nucleotide
consists of a five-carbon sugar, a nitrogen containing base, and a phosphate group. Nucleic acids
have several functions in the cell including, carriers of genetic information and providing cellular
energy.
Proteins:
All proteins are polymers of amino acids, and thus contain the elements carbon, hydrogen,
oxygen, and nitrogen. The amino acids are covalently bonded in long chains that subsequently,
as a result of hydrogen bonding twist, fold, and coil to form complex shapes that determine the
function of the resulting protein. Proteins have various functions in a cell, including acting as
enzymes, structural components, and transport molecules. Table 3.2 summarizes the organic
molecules, their subgroups, and their functions.
Lab Activity 3 - Chemistry of Life
The Chemical Composition of Cells
Required Materials:
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Periodic Table
pH paper
12 Test Tubes
Test Tube Rack
Test Tube holder
distilled water bottle
Household items (Coffee, Cola, Distilled water, Detergent solution, Baking soda solution
50ml beakers 5 numbers
12 Droppers
Buffered solution, pH 7
1% Hydrochloric acid (HCl)
Bromthymol blue solution
Benedict’s solution
Biuret solution
Iodine solution
Sudan IV solution
20% Sugar Solution
20% Egg albumin solution
20% starch solution
Cooking /Vegetable oil
Hot Plate
Tongs
250ml Beaker 2 Numbers
Potato Juice, Honey, Salad Oil, Egg White
Assignment 1
Use of the Periodic Table
Use the periodic table to determine the atomic number, mass number, number of protons,
neutrons, and electrons for the given elements place your answers in the appropriate area in the
Lab Report portion of this exercise (assignment 1)
Assignment 2
Atomic structure - shell model
Draw the atomic structure (shell model) for the given atoms and place your answers in the
appropriate area of the Lab Report portion of this exercise (assignment 2).
Assignment 3
Ion Formation and Chemical Bonding
a) Determine the number of protons and electrons in the given atoms and ions and place your
answers in the appropriate area of the Lab Report portion of this exercise (assignment 3).
b) Remember, the plus sign (+) indicates the number of electrons that have been lost, while the
minus sign (-) indicates the number of electrons gained.
c) Diagram the bond(s) in the given molecules, name the bond type, and place your answers in the
appropriate area of the Lab Report portion of this exercise (assignment 3).
Assignment 4
pH Measurements
In this experiment, students will measure the pH of various solutions using pH paper and then use
their data to classify those substances as acids, bases, or neutral solutions and place their answers in
the appropriate area of the Lab Report portion of this exercise (assignment 4).
.
Equipment Setup:
a) Using a piece of white paper, label sections in accordance with the sequence of materials in
assignment 4 of your Lab Report and place a small piece of pH paper in each section.
b) Place a drop of the solution to be tested on the pH paper in the appropriate section.
c) Compare the color of the moistened pH paper to the supplied color chart and note the indicated
pH in your Lab Report.
Assignment 5
Investigate the effect of a buffer on pH:
a) Place 25ml of distilled water with pH 7 into a 250 ml beaker labeled “A” and 25ml of a buffered
solution with pH 7 into a 250 ml beaker labeled “B”.
b) Add 6 drops of bromthymol solution to each beaker (6 drops in beaker “A” & 6 drops in beaker
“B”).
c) Mix by swirling the liquid in each beaker. The fluid in each beaker will be pale blue/green in
color. Bromthymol solution is a pH indicator that is blue/green at pH 7.6 and yellow at pH 6.0.
d) Place the beaker with distilled water and bromthymol solution on a piece of white paper. Add
1% HCl drop by drop to the solution in this beaker. Mix thoroughly by swirling the liquid
between each drop. Count and record the number of drops required to turn the solution from
blue/green to yellow, which indicates a pH of 6.
e) Place the beaker with buffer solution and bromthymol solution on a piece of white paper. Add
1% HCl drop by drop to the solution in this beaker. Mix thoroughly by swirling the liquid
between each drop. Count and record the number of drops required to turn the solution from
blue/green to yellow, which indicates a pH of 6. Record your answers under assignment - 5 of
the Lab Report.
Assignment 6
Identifying Biological Molecules
Looking for the biological molecules in specific foods. Each food item must be tested
individually…do not cross contaminated the different foods.
Experimental procedure:
Test each food substance provided for you (potato juice, honey, salad oil, egg white, apple juice, and
distilled water) for the presence of starch, sugar, protein, and lipid using experimental procedure
outlined below with the appropriate reagent (Iodine, Benedict’s solution, Sudan IV and Biuret solution),
and record your results in Assignment 6 of the Lab Report.
Equipment setup and experimental procedure:
1. Benedict’s test (test for sugars) - Place I dropper full of food substance into a clean test tube.
Add 6 drops of Benedict’s reagent and then place the tube into a high–temperature water bath
for 5-10 minutes. Benedict’s solution is aqua blue in color. In a positive test reaction, it turns
orange, green, yellow, or red in color (Discard this material in hazardous waste container).
2. Biuret test (test for protein) -. Place I dropper full of food substance into a clean test tube.
Add 6 drops of Biuret reagent (Biuret reagent contains a strong base; avoid contact of this
reagent with your skin) to the tube and then wait 5- 10 minutes. Observe the color of the tube.
Biuret reagent is blue in color. It turns purple in a positive reaction. (Discard this material in
the hazardous waste container.)
3. Iodine test (test for starch) - Place 1 dropper full food substance in a clean test tube. Add 6
drops of Iodine solution to the tube and then wait 5- 10 minutes. The original color of iodine
solution is amber-yellow. In a positive test the resulting solution will turn blue-black or
brownish black in color. (Discard this material in the hazardous waste container).
4. Sudan IV test (test for lipid) - Add one dropper of water into a clean test tube. Add 6 drops of
Sudan IV solution. Shake the tube from side to side to mix well. Add 10 drops food substance
to the same tube. Mix well again. Let the mixture stand for 5-10 minutes. In a positive test
reaction the oil (lipid) will be stained red and will rise to the top of the water or will be
suspended as tiny red globules/droplets. (Discard this material in the hazardous waste
container.)
Lab Report 3 - Chemistry of Life
The Chemical Composition of Cells
Name: ______________________________
Date:
____________________________
Class Index: _________________________
Instructor: __________________________
Before you begin filling out this lab report you must read Exercise 3 - Chemistry of Life in your lab manual.
Complete Assignments 1-7 below. You can use your Lab Manual results and Textbook to complete the
information below.
Assignment 1
Use the period table and write the symbol, atomic number, mass number, number of protons, neutrons,
and electrons for the following atoms:
Element
Symbol
Atomic
Mass
Number
Number
Protons
Neutrons
3
Lithium
3
H
1
39
Potassium
Magnesium
12
12
Draw the atomic structure - shell model of the following atoms
b) F, atomic number 9
c) Al, atomic number 13
1
20
Assignment 2
a) N, atomic number 7
Electrons
d) Ar, atomic number 18
Assignment 3
a) Determine the number of protons and electrons in the following atoms and ions. Remember,
the plus (+) sign indicates the number of electrons that have been lost, while the minus (-)
sign indicates the number of electrons gained.
Atom/Ions
Number of Protons
Number of Electrons
Na
Na+
Mg
Mg2+
ClCl
b) Diagram the bond(s) in the following molecules. Name the bond type.
1. Two atoms of hydrogen with one atom of oxygen.
2. One atom of sodium with one atom of chlorine.
Assignment 4
Acid-base determination: Determine pH using pH paper.
Name of Substance
Color of pH Paper
pH Value
Acidic, basic, or
neutral
1. Coffee
2. Cola
3. Distilled water
4. Detergent
5. Baking soda
Assignment 5
Buffering Systems
a) Indicate the number of drops of 1% HCl required to the decrease pH of the following solutions from
pH 7 to pH 6.
Distilled water ______________________
Buffer solution ______________________
b) What is the function of buffer? _______________________________________________________
________________________________________________________________________________
Assignment 6
Biological Molecules (unknowns): (perform the chemical tests on the substance provided and record
your results) “+” = present; “-” = absent
S.
No.
Test tube
Content
1
Potato Juice
2
Honey
3
Salad Oil
4
Egg White
5
Apple Juice
6
Distilled water
Iodine
Test
(Starch) +/-
Benedicts
Test
(Sugar) +/-
Sudan IV
Test
(Lipid ) +/-
Biuret
Test
(Proteins) + /-
Organic
compound
Present