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Biochemistry
Biochemistry
Biochemistry
Overview
Framed by the glowing hands of a forensics laboratory technician, DNA sequences appear
mysterious and intriguing. Although DNA was a mystery for many years, today the interpretation of
DNA sequences can be used to solve mysteries. Through DNA fingerprinting, as the technique is
called, police can often identify a murder based on evidence as small as strand of hair or drop of
blood.
In this module, you will learn how chemists were able to unravel the secrets of many
important molecules – including DNA – by studying the interactions of matter as they occur at the
atomic level. You will learn how atoms join together to form molecules and how molecules interact
with one another. And you will learn how to describe the interactions of matter through the use of
chemical equations. By the time you finish reading the lessons that follow, you may even think that
solving problems in chemistry is as fascinating as solving crimes!
Module Objectives
At the end of the module 3, you should be able to (YSBAT):
1. Define chemical bonds and the 3 main types of chemical bonds and cite examples of each
type.
2. Describe the characteristics of an ionic bond and covalent bonds.
3. State the octet rule.
4. Write names and formula for ionic compounds and molecular compounds.
5. Identify alkanes, alkenes, alkynes, and aromatic compounds.
6. Name a branched hydrocarbon from its structure and draw the structural formula of a branched
hydrocarbon from its name.
7. Define functional group and identify the different functional groups.
8. Identify and name a simple alkyl halide and alcohol.
9. Define the terms monomer and polymer and draw the structure of a polymer from its
monomer.
10. Describe the characteristics of a chemical reaction.
11. Write balanced chemical equation.
12. Classify chemical reactions.
Introduction
The material that makes up a spider web is thin and lightweight, yet strong enough to withstand
wind, rain and other stresses. Why are spider webs so strong, sticky and flexible? The answer lies
with the nature of the chemical bonds that bind the web’s atoms. In this lesson, you will learn all
about chemical bonds – what they are, why atoms form them and why are some bonds are
stronger than others. When you finish this lesson, you may not be able to recreate a spider’s web,
but you should appreciate its qualities all the more.
Activity
Chemistry Journal (10 pts)
In the table below, in the appropriate column, write down as many properties of salt and paper.
SALT PAPER
Analysis (5 pts.; c = 3, org of thought = 2)
1. Based on the properties of salt and paper you have enumerated, in what ways are they alike?
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2. In what ways are they different?
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3. From your learning in module 2, can you describe the elemental composition of table salt and
how it is formed?
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4. Can you describe the elemental composition of paper and how it is produced?
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With the fundamental knowledge on elements and atoms particularly on the arrangement of electrons, you
are now ready to move on to chemical bond, with concepts introduced by the activity starting with its broad
definition.
Abstraction
Chemical bonds are forces of attraction (which are intra or inter-molecular);
among the unit particles of compounds or,
among the atoms comprising a single unit particle of a compound or a molecule of an
element or a compound.
What keeps the molecules (e.g. in the sample of water) stuck to each other?
In chemistry, we generally call these forces the Intermolecular Forces of Attraction (IMFA), that
keep together the many unit particles in a sample of a compound and explain many of the
properties of solids, liquids, gases and plasmas.
Intermolecular Forces of Attraction (IMFA) are the forces of attraction or repulsion which act
between neighboring particles (atoms, molecules, or ions).
There are three types of IMFA namely:
1. Dipole-dipole forces: electrostatic interactions of permanent dipoles in molecules; includes
hydrogen bonding.
2. Ion-dipole forces: electrostatic interaction involving a partially charged dipole of one molecule
and a fully charged ion.
3. London dispersion forces: forces caused by correlated movements of the electrons in
interacting molecules, which are the weakest of intermolecular forces and are categorized as
van der Waals forces.
o For organic compounds, carbon and hydrogen are listed as the first elements in the
molecular formula, and they are followed by the remaining elements in alphabetical order.
For example, for butane, the molecular formula is C 4H10. – to be discussed in details in
lesson 4.
o For ionic compounds, the cation precedes the anion in the molecular formula. For example,
the molecular formula of sodium fluoride is NaF.
A structural formula indicates the number of atoms, their arrangement in space – the relative
positioning of atoms and bonding between atoms. It specifies which atoms are bonded to each
other in a molecule.
There are 3 main types of chemical bonds namely: Ionic (electrostatic), covalent and metallic.
Non-Polar Covalent: identical POLAR Covalent IONIC Bond; electron loss
non-metal atoms bond via co- or donation; electron gain or
Non-identical atoms; most
owning/sharing of electrons acceptance among metal
covalent substances; e.g. H2O,
e.g. O2, N2,diamond and non-metal atoms e.g.
C12H22O11, CO2
NaCl
Special “communal” sharing of bond electrons among metallic
atoms: Metallic Bond e.g. elemental iron bar, steel, metal alloys.
The octet rule is one of the most important rules in chemistry, observed in chemical bonding.
1. Ionic bonds/compounds
Atoms are electrically neutral because the number of protons, which carry a + charge, in the nucleus of an
atom is equal to the number of electrons, which carry a – charge outside the nucleus of an atom.
Ionic bonding involves a transfer of an electron, so one atom gains an electron while one atom
loses an electron. The resulting charged species are called ions. One of the resulting ions carries
a negative charge - anion, and the other ion carries a positive charge - cation. Static electrical
attraction is the basis for ionic bonds. Because opposite charges attract, the atoms bond together
to form a molecule as shown below.
As a general rule of thumb, the main group elements will usually gain or lose electrons in order to
get a full octet of valence electrons. By figuring out how many electrons an element is likely to lose
or gain to reach a full octet, we can predict the charge on the ion. This requires first knowing how
many valence electrons are in the neutral atom.
Elements that form Cations
Groups/columns 1, 2, 13, and 14 elements (except carbon) have one to four valence electrons as
neutral atoms and they will usually give away these valence electrons to become cations (ions with
positive net charge) The magnitude of the charge is equal to the number of electrons lost, which is
equal to the number of valence electrons in the neutral atom.
Elements that form Anions
Groups/columns 15 through 17 elements have five to seven valence electrons as neutral atoms
and they gain electrons to reach a full octet of eight valence electrons and become anions (ions
with negative charge) because the resulting ion has fewer protons than electrons.
Elements that form multiple types of cations
Most transition metals – columns 3 to 12 are polyvalent which literally means "many valued"- they
are able to form cations of different charges like iron; Fe 2+, Fe3+.
Naming cations and anions
When we name monoatomic cations, we name the element and add ions like Na 1+ is sodium ion.
Most often, when we name monatomic anions, we add the suffix -ide to the end of the element's
name. We name polyatomic anions, by adding suffix-ate or - ite to the end of the element’s name.
The following table shows names, formulas and charges of common ions.
Charge Name Formula Charge Name Formula
Ammonium NH41+ Acetate C2H3O21-
Copper I (cuprous) Cu1+ Bromate BrO31-
Hydrogen H1+ Bromide Br1-
1+ Potassium K1+ Chlorate ClO31-
Sodium Na1+ Chlorite ClO21-
Lithium Li1+ Cyanide CN1-
Silver Ag1+ Fluoride F1-
Barium Ba2+ Hydride H1-
Cadmium Cd+2 Bicarbonate(hydrogen carbonate) HCO31-
Calcium Ca+2 Bisulfate(hydrogen sulfate) HSO41-
1-
Cobalt(II) Co+2 Bisulfite(hydrogen sulfite) HSO31-
Copper(II) Cu2+ Hydroxide OH1-
Iron(II) ferrous Fe2+ Hypochlorite ClO1-
2+ Lead(II) Pb2+ Iodate IO31-
Magnesium Mg2+ Iodide I1-
Manganese(II) Mn2+ Nitrate NO31-
Mercury(II)/mercuric Hg2+ Nitrite NO21-
Nickel(II) Ni2+ Perchlorate ClO41-
Tin(II)/stannous Sn2+ Permanganate MnO41-
Zinc Zn2+ Thiocyanate SCN1-
Aluminum Al3+ Carbonate CO32-
Antimony(III) Sb3+ Chromate CrO42-
Arsenic(III) As3+ Dichromate Cr2O72-
3+ Bismuth(III) Bi3+ Oxalate C2O42-
Chromium(III) Cr3+ 2- Peroxide O22-
Iron(III)/ferric Fe3+ Silicate SiO32-
Titanium(III)/titanous Ti3+ Sulfate SO42-
Manganese(IV) Mn4+ Sulfide S2-
4+ Tin(IV)/stannic Sn4+ Sulfite SO32-
Titanium(IV)/titanic Ti4+ Arsenate AsO43-
5+ Antimony(V) Sb5+ Borate BO33-
Arsenic(V) As5+ 3- Phosphate PO43-
Phosphide P3-
Phosphite PO33-
In Agriculture, plants use nutrient elements in the form of ions. In the table below, are nutrient ions
considered essential for use by plants:
Element Symbol Ions used by plants
Nitrogen N NO31- (nitrate); NH41+(ammonium)
H2PO4 1-
(orthophosphate/dihydrogen phosphate); HPO42- (hydrogen
Phosphorous P
phosphate)
Potassium K K (potassium ion)
1+
Molybdenum Mo MoO42-(molybdate)
Chlorine Cl Cl1- (chloride)
Nickel Ni Ni2+ (nicklelous)
Making Formula
The ratio of the ions in an ionic compound is denoted in a chemical formula which uses element
symbols to indicate the atoms or ions in a compound, with subscript added to indicate their ratios.
Remember that the formula for ionic compounds usually give the smallest whole number ratio of
the ions.
Ex. The formula or magnesium oxide; Mg2+ O2- Mg2+O2- Mg2O2 the smallest whole
number ratio for Mg and O is 1:1 by dividing both ions by 2.
Using the crisscross method: compounds formed by monoatomic ion and polyatomic ion.
What is the formula for (a) potassium phosphide (b) aluminum sulfate? Refer to the
table of names, formula of common ions.
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Naming Ionic Compounds
The following guidelines can be used for naming ionic compounds:
Always name the cation before the anion; in the chemical formula, the cation will always appear
first as well.
When naming the cation within an ionic compound, we don't include the word ion or the
charge unless it is a polyvalent cation. That means we only have to name the element that the ion
came from.
o Any ionic compound will have a net charge of zero. The number of cations and anions in the
formula should be written as the lowest possible integer value.
o Hydrates are substances formed when ionic compounds absorb water into their solid
structures. Ex. Copper (II) sulfate pentahydrate – CuSO 4 .5H2O
o Anhydrous substances are water-free substances eg. Anhydrous copper (II) sulfate – CuSO 4
Baking Soda (NaHCO3) is a common household ionic compound which has lots of use,
aside from baking. It can be used as a deodorant, cleaning agent and odor absorber.
Nitrites in Food. Sodium nitrite is used as a raw material in the production of a variety of
organic compounds such as dyes, pharmaceuticals and pesticides. It is also used as part of
the food preservatives in cured meats (such as hot dogs, tocino and ham). Generally, curing
salts are a nitrite and in some, sodium nitrate. The nitrite retards spoilage, preserves the
meat’s flavor & red color and wards off botulism bacteria. But during deep frying, HNO 2 is
formed. HNO2 is also a product when nitrite reacts with stomach acid. HNO 2can react with
amino acids to form nitrosamines, which have been shown to produce cancer in lab animals,
thus the concern on the concentration of nitrites in foods.
II. For each of the listed combinations of elements, compose the chemical formula if they were to
form an ionic bond. Remember to use subscripts to denote the ratio of the metal to non-metal. Also, if the
ratio is 1:1 it does not need to be written. (Please refer to sample/practice problems and tables of ionic
charges). 2 pts each = 10 pts
1. Potassium + Fluorine
Solution:
Required: chemical formula?
Given:
Analysis:
Answer:
2. Magnesium + Iodine
Solution:
Required: chemical formula?
Given:
Analysis:
Answer:
3. Sodium + Oxygen
Solution:
Required: chemical formula?
Given:
Analysis:
Answer:
4. Sodium + Chlorine
Solution:
Required: chemical formula?
Given:
Analysis:
Answer:
5. Calcium + Chlorine
Solution:
Required: chemical formula?
Given:
Analysis:
Answer:
III. For the list on the left, name the compound. For the list on the right, give the chemical formula
that corresponds to the name. 1 pt. each = 20 pts
Chemical Formula Compound Name Compound Name Chemical Formula
NaF Potassium fluoride
K2CO3 Ammonium sulfate
MgCl2 Magnesium iodide
Be(OH)2 Copper(II) sulfite
Cu2S Lead nitrite
Ca3(PO4)2 Silver cyanide
NH4I Copper(II) carbonate
Mn(NO3)3 Iron(II) oxide
FePO4 Lithium cyanide
CoCO3 Lead(IV) sulfite
I. 30
II. 10
III. 20
Score: 60 pts.
II. Write the formulas of the following acids and bases:1 pt. each = 12 pts.
Inorganic Covalent Compounds are those covalent compounds that do not contain carbon with few
containing carbon as exceptions.
Naming Inorganic Covalent Compounds
Tips in naming binary (two-element) inorganic covalent compounds:
o The first element in the formula is simply listed using the name of the element.
o The second element is named by taking the stem of the element name and adding the suffix -
ide. A system of numerical prefixes is used to specify the number of atoms in a molecule.
Table below lists these numerical prefixes.
o Normally, no prefix is added to the first element’s name if there is only one atom of the first
element in a molecule. *
o If the second element is oxygen, the trailing vowel is usually omitted from the end of a
polysyllabic prefix but not a monosyllabic** one (that is, we would say “monoxide” rather than
“monooxide” and “trioxide” rather than “troxide”).
Number of Atoms in Compound Prefix on the Name of the Element
1 mono-*
2 di-**
3 tri-**
4 tetra-
5 penta-
6 hexa-
7 hepta-
8 octa-
9 nona-
10 deca-
Example 1
Solution: Write carbon for the symbol C of the first element and no prefix because the subscript of
C is understood 1; tetrachloride ∑(chlor- the stem for chlorine plus suffix ide) and prefix tetra to
indicate 4 chlorine atoms in the molecule - for Cl 4. Putting these pieces together gives the
name carbon tetrachloride for this compound.
Example 2
Write the name for each compound whose molecular formula is:
a. BrF5
b. S2F2
c. CO
Solution
a. Write bromine for the symbol Br of the first element and no prefix because the subscript of
Br is understood 1; pentafluoride ∑(fluor- the stem for fluorine plus suffix ide) and prefix
penta to indicate 5 fluorine atoms in the molecule - for F 5. Putting these pieces together
gives the name bromine pentafluoride for this compound BrF5.
b. Write disulfur for the symbol S2 (sulfur for S of the first element and prefix di- because the
subscript of S is 2); difluoride ∑(fluor- the stem for fluorine plus suffix ide) and prefix di- to
indicate 2 fluorine atoms in the molecule - for F 2. Putting these pieces together gives the
name disulfur difluoride for this compound S2F2.
c. Write carbon for the symbol C and no prefix because the subscript of C is understood 1;
monoxide ∑(ox- the stem for oxygen plus suffix ide) and prefix mono- to indicate 1 oxygen
atom in the molecule - for O. Putting these pieces together gives the name carbon
monoxide for the compound CO.
Example 1
Solution
Write the chemical symbol of the element. If there is no numerical prefix on the first and second
element’s name, we can assume that there is only one atom of that element in a molecule. Write
the corresponding subscript of the numerical prefixes of the first and second element’s symbol.
a. Write Cl for the first element chlorine without subscript because chlorine has no prefix; F for
the stem of the second element fluor (for fluorine) and subscript 3 for the prefix tri.
Therefore, the formula is ClF3
b. Write P for the first element phosphorus without subscript because phosphorus has no
prefix; Cl for the stem of the second element chlor (for chlorine) and subscript 5 for the
prefix penta. Therefore, the formula is PCl5.
c. Write S for the first element sulfur without subscript because sulfur has no prefix; O for the
stem of the second element ox (for oxygen) and subscript 2 for the prefix di-. Therefore, the
formula is SO2.
d. Write N for the first element nitrogen with subscript 2 because nitrogen has a prefix di-; O
for the stem of the second element ox (for oxygen) and subscript 5 for the prefix pent-.
Therefore, the formula is N2O5.
II. Write the molecular formula for each compound and show you solution to get your answer:
Explain how you get your answer. 2 pts. Each = 8 pts
a. nitrogen dioxide
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b. dioxygen difluoride
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c. sulfur hexafluoride
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d. selenium monoxide
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III. Write the name for each compound. Explain how you get your answer. 2 pt. each =6 pts.
a. CF4
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b. SeCl2
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c. SO3
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Identify whether each compound has ionic, covalent bonds or both by checking the appropriate
III.
column. 1 pt. each = 11 pts.
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3. What is the name of each of the covalent compound? Write each on the space provided. 1 pt.
each = 5 pts.
a. SiF4 ___________________________________________________
b. NO2 ___________________________________________________
c. P2O5 ___________________________________________________
d. S2O3 ___________________________________________________
e. BF3 ___________________________________________________
4. What is the formula of each covalent compound? Write your answer on the space provided.1
pt. each = 5 pts.
Score= 45
2. Explain why metals, such as copper wires, can conduct electric current.
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3. State the octet rule. Use the octet rule to describe the reaction between elemental chlorine and
sodium.
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4. Vinegar, a sour liquid used in cooking, contains water and acetic acid. What is the molecular
formula of acetic acid? What ions would you expect to find in vinegar?
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5. Sodium chloride (table salt) is a binary ionic compound. Explain how the statement “Donation
can help BOTH the donor and the receiver to attain stability” applies to the compound. Hints:
Which of the elemental composition of sodium chloride is the donor and how it is benefitted and
the receiver and how it is benefitted.
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6. Below are formula of acids and bases. Give the chemical name, classify whether each is an acid
or base and research on at least one commercial product that contains each. 10 pts. (1 pt. each)
Commercial product that
Formula Chemical Name Classify; acid or base?
contains it?
HCl
NaOH
HClO4
Ca(OH)2
H2S
H2SO4
Ba(OH)2
H3PO4
Al2O3
ZnO
7. Cite 1 binary covalent compound. Explain the statement “Co-ownership sharing can help both
owners attain stability” applies to that compound.
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8. Look for and write the formula of the compound in fire extinguisher.
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Based on the rules in writing compound names, write your critical comment on the name and
formula of the compound in the fire extinguisher.
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9. The best analogy of the non-reactive atoms of noble gases are people who are stable being
single. Explain your comparison between the two.
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10. How do ionic bonds and ionic substances differ from covalent bonds and molecules?
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B. Now, reflect on what we have discussed in the lessons of modules 1 and 2 by answering the
questions as follows: 15 pts (3 pts/no.)
1. What concepts have you learned that deepen your understanding on the chemical bonds
formed as atoms and molecules interact to form compounds?
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2. What have you realized about chemical bonding in the formation of compounds and chemical
formula that represent them as defined and discussed ln this lesson?
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3. With your realization about chemical bonding and formula, are you now interested to learn more
about matter? If so, can you cite a specific aspect of matter that we need to tackle?
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Score: A: 65
B: 15
Total: 80
Closure
You now have the knowledge and understanding regarding the connection of the behaviors of
matter at the macroscopic level and the state of the particles of the atoms that comprise matter.
We will move on to organic compounds, covalently bonded compounds containing carbon.