BIOL 191 Chemistry for Microbiology Students
Take notes on this document while you are watching the recorded chemistry lectures.
08/17/12
I. Atoms, Elements, Molecules, Compounds
II. Chemical Bonds and Chemical Reactions
III. Organic Molecules
IV. Inorganic Molecules
Recorded Lecture Part 1 (16:30)
IMPORTANT: The TEXT referred
to in this document only refers to
the text Microbiology An
Introduction, 11 ed., Tortora,
Funke, and Case. 2013.
Overview
Read Text p. 25
1
Text pp. 26-27
I. Atoms, Elements, Molecules, Compounds
A. Atom: A unit of all matter, the smallest unit of an element (see the periodic table,
next page), having all the characteristics of that element and consisting of a dense,
central, positively charged nucleus (due to the protons) surrounded by a system of
negatively charged electrons. The entire structure has an approximate diameter of 10-8
centimeter and characteristically remains undivided in chemical reactions except for
limited removal, transfer, or exchange of certain electrons. If the atom has not been
influenced by other atoms or molecules, the number of p+ equals the number of e-.
Dictionary: http://education.yahoo.com/reference/dictionary/entry?id=A0501900
Example: Carbon Atom
For the history of the atom go to:
http://www.xtimeline.com/timeline/Discovery-of-the-Atom
AND
http://www.dpgraph.com/janine/electron.html#SMALLER
Each element is an atom with a specific number of protons.
Living organisms only utilize 26 elements.
2
http://www.webelements.com/index.html
3
B. Atoms combine to form MOLECULES
1. Molecule: 2 or more atoms bonded together.
2. Chemical formulas: Symbol(s) of element(s) with a subscript signifying the
number of atoms of each element
Example: glucose
C6H12O6
Text pp. 27-31
II. Chemical Bonds and Reactions
A. Chemical bond: Attractive force between atoms
B. Chemical bonds: We will focus on 3 types of bonds important to living systems.
-Ionic bond-Covalent bond-Hydrogen bond
Keep in mind: Atoms are most stable with 8 electrons in their outer energy level!
Text Fig. 2.2 p. 30 Ionic bond formation
1. Ionic bonds
Formed when two oppositely charged (+ and -) atoms are attracted to one another. This can
occur because some atoms can lose electrons (and are, therefore, positively charged) while other
atoms gain electrons (and are, therefore, negatively charged). The loss/gain of electrons will
result in an electron OCTET (8) in the outer energy level of each atom.
Example: NaCl (sodium chloride)
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NaCl
Text Fig. 2.3 p. 30 Covalent bond formation
Recorded Lecture Part 2 (23:47)
2. Covalent bonds
a. Formed when two atoms share an electron pair (1 electron from each
atom); the shared electrons orbit BOTH atoms’ nuclei
b. Often occurs when the two atoms bonded are the same (e.g., C-C)
c. Ex: Carbon-Carbon bonds
d. Very strong bond
e. Symbols:
1. Single covalent bond (1 e- pair shared): C-C or C:C
Total number of
electrons?
2. Double covalent bond (2 e- pairs shared): C=C or C::C
3. Triple covalent bond (3 e- pairs shared):
f. Examples of Bonding Patterns
number of
element
covalent bonds
H
1
O
2
N
3
C
4
S
5
5
Text Fig. 2.4 p. 31 Hydrogen bond formation in water
(BETWEEN WATER MOLECULES)
3. Hydrogen bonds
a. Formed between an atom which is partially positively (+) charged and a
partially negatively (-) charged atom, especially between a hydrogen (+)
atom and a (-) nitrogen, oxygen, or fluorine atom, often in another
molecule.
b. Hydrogen bonds are weak bonds; they cannot form a completely new
molecule with extensive changes to a molecule’s chemical properties.
However, they can...
1. Weakly bond together more than one molecule (Example: water)
2. Change the shape of one molecule (Example: protein structure)
Example I: Water Molecules
How are partial charges formed?
First let’s look at one water molecule:
H
H
O
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An oxygen atom has 8 protons in its nucleus. Hydrogen only has 1 proton in its nucleus.
Consequently, oxygen has a stronger positive charge than hydrogen, and will exert a stronger
‘pull’ on the shared electrons. Therefore, the shared electrons in the covalent bonds between the
oxygen and the hydrogens are shared UNEQUALLY. The shared electrons spend more time
closer to the oxygen than to the hydrogens. The result is a partial negative charge on the
oxygen and a partial positive charge on the hydrogens.
(+)
(+)
H
H
O
(-)
When two or more water molecules are present, the partial positive charge of the hydrogens in
one water molecule is attracted to the partial negative charge of an oxygen in a different water
molecule. The result is that water molecules ‘stick together’.
Note:
One water molecule (H2O) is bonded to a different water molecule (H2O) by a hydrogen
bond.
Hydrogen bonds are not formed within one individual water molecule.
The covalent bonds in individual water molecules result in partial charges -This allows
hydrogen bonding between the different water molecules.
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Example II: Hydrogen bonding in protein structure
Proteins are synthesized from amino acids. The covalent bonds in an amino acid also can result
in unequal sharing of electrons and, therefore, partial positive and partial negative charges in
amino acids. These opposite partial charges attract one another and can alter the shape of the
protein (remember, structure determines function).
The following website is a very good overview of bonding:
http://chemsite.lsrhs.net/ChemicalBonds/electronegativity.html
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Recorded Lecture Part 3 (10:45)
Text Chemical Reactions pp. 31-33, p. 112
C. Chemical Reaction (change): Rearrangements of the bonds between atoms/molecules.
A chemical reaction occurs any time a chemical bond is formed or broken. This results
in the formation of new (different) molecules with different properties.
1. A chemical change occurs whenever compounds are formed or decomposed.
o
o
o
Reactants: the starting molecule(s) disappear as chemical change occurs.
Products: the ending molecule(s) appear as chemical change occurs.
Catalysts speed up the rate of the reaction, but aren't produced or consumed. 1
2. Some chemical reactions release energy. Other reactions require energy in order to
proceed. The activation energy is the amount of energy required for a particular
chemical reaction to occur.
a. Most energy in living systems is stored in CHEMICAL BONDS.
b. When chemical bonds are broken, energy is released. When chemical
bonds are formed, energy is stored.
3. In living systems, the catalyst is called an enzyme and is usually a protein.
Text Enzymes
p. 113
Internet readings: Examples of Enzymes
http://www.free-definition.com/Enzyme.html#Digestive_and_metabolic_enzymes
4. Chemical reactions are written in the form of an equation.
ATP synthase
ADP + phosphate
1
ATP
http://antoine.frostburg.edu/chem/senese/101/reactions/index.shtml
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Text Fig. 2.8 p. 38 Dehydration Synthesis and Hydrolysis (Decomposition) reactions
5. Examples of types of chemical reactions important in living systems:
a. Synthesis reactions: 2 or more atoms/molecules are bonded together to
make a larger product.
sucrose 6-phosphate phosphatase2
Glucose + Fructose
Sucrose + Water
Dehydration or condensation synthesis reactions are common in biological systems: Two
molecules are combined and one water molecule is lost.
b. Decomposition reactions: a large molecule is broken down into smaller
products.
sucrase3
Sucrose + Water
Glucose + Fructose
Hydrolysis reactions are common decompositions reactions in biological systems: Water and
another molecule react which breaks bonds in a molecule forming 2 molecules in which the
HOH is added to them, usually H to one and OH to the other.
c. Exchange reactions: 2 or more molecules react and exchange atoms (at
least some atoms) [sometimes called substitution or displacement)
NaOH + HCl
NaCl + HOH
Hydrolysis reactions (see above) can be considered an exchange reaction.
2
Multi-step/multi-enzyme process in plants where several of the molecules are derived from photosynthetic
products. The FINAL enzyme utilized is sucrose 6-phosphate phosphatase.
3
Sucrase is found in yeast and the intestines of animals.
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Several common reaction types. Some reactions can be classified in more than one way, and some
reactions fit into none of these categories.
Type
Definition
Examples
synthesis
a compound forms from simpler reactants
C2H4(g) + H2O(g)
H2(g) + ½ O2(g)
decomposition
a compound breaks down into simpler
products
CaCO3(s)
CaO(s) + CO2(g)
2NH4NO3(s)
2N2(g) + 4H2O(g) + O2(g)
2 H2O(l)
2 H2(g) + O2(g)
displacement
AB + C
Zn(s) + 2 HCl(aq)
Zn(s) + CuCl2(aq)
neutralization
H+ transfer from acid to base
NaOH(aq) + HCl(aq)
KOH + HC2H3O2(aq)
precipitation
a solid product from aqueous reactants
BaCl2(aq) + Na2SO4(aq) = BaSO4(s) + 2 NaCl(aq)
AgNO3(aq) + NaCl(aq) = AgCl(s) + NaNO3(aq)
redox
electron transfer between reactants
2 C2H6(g) + 7 O2(g)
A + BC
C2H5OH(g)
H2O(l)
ZnCl2(aq) + H2(g)
ZnCl2(aq) + Cu(s)
H2O(l) + NaCl(aq)
H2O(l) + KC2H3O2(aq)
4 CO2(g) + 6 H2O(g)
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Text p. 36 Important Biological Molecules- First two Intro paragraphs
only on this page; we’ll come back to inorganic molecules later.
Recorded Lecture Part 4 (14:41)
Text pp. 36-37 Organic compounds
III. Organic Molecules:
The most important (abundant) molecules in living organisms.
Organic molecules always contain carbon bonded to hydrogen.
Carbon forms four covalent bonds with other atoms. Many various bonding patterns result.

The most important elements which bond to carbon are other carbon atoms, hydrogen
(H), oxygen (O), nitrogen (N), sulfur (S), phosphorus (P).

Carbon acts as a skeleton to many important molecules. Structure determines function.

Biochemistry is the study of the structure and function of cellular components, such as
proteins, carbohydrates, lipids, nucleic acids, and other biomolecules. Although there is a
vast number of different biomolecules, they tend to be composed of the same repeating
subunits (called monomers), in different orders. Each class of biomolecules has a
different set of subunits. Recently, biochemistry has focused more specifically on the
chemistry of enzyme-catalyzed reactions, and on the properties of proteins.

In biological systems, often, small organic molecules, called MONOMERS (mono=one,
mer=unit), serve as the building blocks of other large organic molecules. They join
together to form large macromolecules (polymers- poly=many, mer=unit).
Monomer + Monomer + Monomer + Monomer ….

Polymer
There are 4 major classes of organic molecules:
Carbohydrates
Lipids
Proteins
Nucleic acids
and 1 minor group –Vitamins.
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Text p. 37-38 Carbohydrates
A. Carbohydrates
1. Composed primarily of C, H, and O (other elements may also be bonded
to the carbohydrate)
2. Classified by size
a. Monosaccharides (one sugar, simple sugars): contain 3-7
carbon atoms.
Glucose is the primary
molecule used to acquire
energy.
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Text Fig. 2.8 p. 38 Dehydration Synthesis reaction
b. Disaccharides (2 sugars): formed by bonding together 2
monosaccharides in a synthesis reaction.
c. Polysaccharides (many sugars, complex carbohydrates): Large chains
of eight or more monosaccharides.
1) Not sweet; will not dissolve in water
2) Examples of functions:

Short-term energy storage: glycogen (animals), starches (plants)

Structural (building materials)
o Cellulose
-Most abundant organic compound on Earth.
-Structural material in plants; found in plant cell
walls and some algae.
-Very tough and difficult for humans to digest.
o Chitin
-Forms the exoskeleton (external skeleton) of
insects and crustaceans.
-Also a major component of fungal cell walls.
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Text pp. 38-41 Lipids
B. Lipids4
1. The lipids are a large and diverse group of naturally occurring organic
compounds that are related by their solubility (will dissolve) in nonpolar5
organic solvents (e.g. ether, chloroform, acetone & benzene) and general
insolubility in water (do not dissolve in water - repel water; hydrophobic).
2. Examples of lipids include fats, oils, waxes, sterols, and triglycerides
One of the simplest fats is butyric acid—found in butter. All fats have a COOH acid at the
beginning of the chain, also known as the "alpha" end. The opposite end is called the
omega (following the Greek alphabet, which begins with alpha and ends with omega).
Butyric acid is a saturated fat, which means that all the carbon bonds in the middle of the
chain are "filled" with hydrogen. It's also one of the shortest fats, with only four carbon
atoms.
http://www.supplementquality.com/news/fatty_acid_structure.html
3. Examples of functions:
a. Long-term energy storage: fatty acids in fats and oils
-Provide twice as much energy as carbohydrates or protein
b. Constituent of biological membranes (phospholipids and terpenes)
c. Steroid hormones: Hormones are produced in one part of the body and
travel to and affect other parts of the body
-Ex: estrogen and testosterone
d. Waterproof coverings
e. Insulation/protection
4
5
http://www.cem.msu.edu/~reusch/VirtualText/lipids.htm
Polar refers to showing difference in charge or electronegativity (the ability to lose or accept electrons).
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Recorded Lecture Part 5 (17:33)
Text pp. 41-44 Proteins
C. Proteins
1. Composed of amino acids6 which contain C, H, O, N, and sometimes sulfur;
often bonded to other types of organic molecules, such as carbohydrates
2. Proteins have MANY functions; examples include:








support: collagen, elastin (found in cartilage, bone, skin, etc...)
immunity (antibodies)
transport: hemoglobin in RBCs transports oxygen to all of the cells of the body
hormones: insulin
muscle contraction: actin, myosin
movement: flagella, cilia
toxins: produced for protection or predation
Enzymes: an example is amylase utilized for digestion
3. Monomers: Amino Acids
a. 20 amino acids are utilized by organisms to form all of the proteins
needed
b. Peptide bonds
4. The structure of a protein depends primarily on the AMINO ACIDS that make
up the protein7
6
7
Amino acid structures and info: http://www.elmhurst.edu/~chm/vchembook/560aminoacids.html
http://biology.clc.uc.edu/courses/bio104/protein.htm
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Text pp. 43-45 Levels of Protein Structure
5. 4 levels of protein structure8
PRIMARY STRUCTURE: sequence of aa
SECONDARY STRUCTURE
Formed by hydrogen bonds between partially charged amino acids in the primary chain.
TERTIARY STRUCTURE:
The overall 3-D structure of the polypeptide after
all of the amino acids have been bonded.
QUATERNARY STRUCTURE
Final 3-D structure after two or more
polypeptides are bonded together.
8
http://en.wikipedia.org/wiki/Protein_structure#Structure_of_the_amino_acids
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6. Denaturation: loss of functional shape due to...
a. Heat
b. Chemicals
c. pH changes
d. Salt concentration changes
7. ENZYMES
a. Very important to the body or cell’s metabolism (total of all of the
chemical reactions occurring in an organism)
Text pp. 113 & Fig. 5.4 p. 116
The Mechanism of Enzymatic
Action

Almost all of these reactions occur in a series of steps.

These sequences of reactions are called METABOLIC or
BIOCHEMICAL PATHWAYS. Each one of the reactions in a
metabolic pathway requires a SPECIFIC ENZYME (one enzymeone reaction).
b. Enzymes function as biological catalysts (function to increase
the rate of chemical reactions without being permanently altered
themselves).

Catalysts lower the activation energy and allow the reaction to proceed
immediately by temporarily binding to the reactant or reactants of a
particular reaction & positioning it or them in a way which allows the
reaction to proceed with a lower energy expenditure.

The enzyme is then released and can catalyze another reaction (with the
same reactants); it is not changed.9
Molecules collide… They will come together with a certain amount of energy, and only those collisions that have
enough energy will result in a reaction. An analogy to billiards is useful: two billiard balls can collide with various
amounts of energy depending on how fast they are moving. Slower balls will collide with lower amounts of energy
9
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
The reactants are called the enzyme’s SUBSTRATE.
LOCK AND KEY MODEL OF ENZYME ACTION
as evidenced by the less noise created by their impact. Likewise, a chemical reaction consists of two molecules
coming together at a certain speed and colliding; in order for this collision to lead to anything, however, the
molecules must have enough energy. http://www.sciwrite.caltech.edu/journal03/yeganeh.html
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Recorded Lecture Part 6 (25:08)
Text pp. 44-48
Foundation Figure 2.16 p. 46 The Structure of DNA
D. Nucleic Acids
1. Functions of nucleic acids
a. Store the genetic (hereditary) information for future generations
(primarily DNA) and manage the synthesis of proteins (DNA and RNA)
2. Types of nucleic acid polymers:
-DNA (deoxyribonucleic acid)
-RNA (ribonucleic acid)
3. DNA and RNA are composed of NUCLEOTIDE monomers
5-C sugar:
-RNA (ribose; oxygen is bonded to this carbon*)
-DNA (deoxyribose, no oxygen is bonded to this carbon*)
Each nucleotide
building block is, itself,
composed of 3 smaller
molecules.
Nitrogen base: split into 2 groups (see molecular structures on next page)
-Purines: A (adenine) and G (guanine)
-Pyrimidines: C (cytosine), T (thymine), and U (uracil)
Phosphate group: PO4
4. DNA and RNA are formed when many complete nucleotides are bonded
together, one immediately adjacent to the next

RNA: 1 strand of connected nucleotides

DNA: 2 strands of connected nucleotides
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One Nucleotide
21
5 Nitrogen Bases
22
6. DNA “Ladder” structure
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7. Double helix
8. Sequence of DNA:
Genetic information determines what proteins the cell can produce. The
SEQUENCE of the N bases in the DNA is a code for the amino acids in a
polypeptide.
If you have been reading the text, I KNOW you’re concerned because we haven’t
discussed ATP! 
Don’t worry we will. Read the info on p. 47-48 and take a look at Fig. 2.18 p. 48 The
structure of ATP. We’ll come back to this hugely important molecule later in the
course (pp. 112-113)
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Recorded Lecture Part 7 (3:19)
E. Vitamins
Vitamins are discussed in many places in the text, for example, p. 115 Table 5.2
Selected Vitamins and Their Coenzymatic Functions. Many enzymes need other
molecules in order to allow the enzyme to speed up the rate of its particular
reaction. These are ‘cofactors’. If the cofactor is an organic molecule, like a
vitamin, you call it a ‘coenzyme’. Some cofactors change the shape of the enzyme
so it is functional or form a bridge between the enzyme and the reactant.
1. Minor organic molecules.
2. Essential in small amounts for growth and function but cannot be synthesized
by the organism (must be acquired in the diet).
3. One function: help enzymes function in catalyzing chemical reactions
4. Categories:
a. Fat soluble: A, D, E, K
b. Water soluble: B complex vitamins and C
Text pp. 33-35 Inorganic Molecules
IV. Inorganic Molecules:
A list of important minerals for humans can be found
here: http://yourdoctor.com/patient_info/nutrition_supplements/minerals.
html
A. Minerals: Are defined depending on the context. Any natural, inorganic molecule
might be defined as a mineral (therefore, some include water and phosphate). However, most
often, when we discuss minerals in nutrition, we are talking about those inorganic substances in
pure, or elemental, form (Calcium, Zinc, Iron, etc.), or their ions, that are required in small
amounts and cannot be produced by the organism. Some minerals are needed in a relatively
greater quantity (Calcium, Iron) than others. Minerals needed in very small amounts are also
referred to as ‘trace elements’ (Copper, for example).
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B. Water: Many important properties for living organisms. Examples:


Necessary in order for many chemical reactions to proceed (physical properties,
partial charges)
May take part in the reaction as a reactant
6 CO2 + 6 H2O  C6H12O6 + 6 O2
The oxygen liberated during the light reactions of photosynthesis comes from water
C. Acids, Bases, Salts: There is no recorded discussion of acids, bases, and salts, but
students should be able to distinguish between the three.
See Text pp. 34-35 and Fig. 2.6 p. 34 Acids, bases, and salts
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Exam Review
Chap. 2 Chemical Principles (all)
a. Be able to interpret Table & 2.1 & 2.2, Table 2.3
b. Fig. 2.1, 2.2, 2.3, 2.4, 2.6, 2.8, 2.10, 2.16 (Foundation Figure), 2.18
c. LOs: 2-1 through 2-12
d. CYUs: 2-1 through 2-6, 2-8 through 2-12
e. Chap. 2 – Additional concepts: polarity, solute, solvent, ionization, pH, buffer,
carbon skeleton, functional groups, monomers vs. polymers vs.
macromolecules, saturated vs. unsaturated fatty acids, amino acids vs.
proteins, peptide bonds, DNA vs. RNA
1. Know the definitions of the terms in the lecture guide.
2. Understand the three basic subatomic particles of an atom and be able to use the periodic
table to determine the symbol and the number of protons of an atom.
3. Understand chemical formulas.
4. What are the 6 most important/common elements in living things?
5. Ionic, Covalent and Hydrogen chemical bonds: How is each formed? Know the
importance of an octet (8) of electrons in the outer energy level of an atom. What
symbols are used for the bonds? What are the relative strengths of the bonds? How is a
hydrogen bond different from the other two types of bonds? Be able to compare/contrast
ionic vs. hydrogen bonding. Give examples (be specific) of hydrogen bonding. Why is it
called a ‘hydrogen’ bond?
6. What is a chemical reaction? What are the 3 common chemical reaction categories in
living organisms? Describe each of the three types of chemical bonds discussed in
lecture.
7. How do you write a chemical equation?
8. Describe the covalent bonding in carbon and why it is important.
9. List the 4 major groups and 1 minor group of organic molecules.
10. Define monomer and polymer.
11. List examples and functions of carbohydrates. How are they classified? What are the
monomers of carbohydrates?
12. Describe the properties of a lipid. List examples and functions of lipids.
13. What are proteins composed of (what are the monomers of proteins)? List examples of
functions of proteins. Describe the 4 levels of protein structure. How does DNA
contribute to the structure of proteins? What is denaturation, and how may it occur?
14. Describe the role of enzymes in chemical reactions. What is their function? Describe the
Lock and Key Model of enzyme action.
15. List 3 functions of nucleic acids.
16. What are the monomers of RNA and DNA? What are the 3 components of a nucleotide?
What are the differences/similarities between DNA and RNA?
17. Be able to label and describe, in detail, all components of the ladder structure of DNA
and how the components are bonded together (see last page). If using abbreviations,
include a legend.
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18. What is the overall three-dimensional structure of DNA?
19. What does the genetic information determine? What is the ‘sequence’ of DNA?
20. Define one function of vitamins. What are two categories of vitamins (as described in
lecture)?
21. List one mineral.
22. Describe one reason water is important to living organisms.
23. What is the difference between an acid, a base, and a salt?
Ladder Structure of DNA
Be able to recognize or label the following:
A.
Bonding:
-Strong bonds between the sugar of one nucleotide and the phosphate of
the next nucleotide
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- Weak bonds between the nitrogen bases of opposing strands (A-T & CG).
B. Legend:
S (5C sugar -deoxyribose)
N nitrogen bases: A (adenine), T (thymine), C (cytosine), G (guanine)
P (phosphate group: PO4)
Nucleotide labeled
Base pair labeled
C.
Correct positions of S, N and P
P
Weak hydrogen bonds between
the complementary nitrogen
bases of opposing strands (A-T
& C-G).
S
N
N
S
P
Strong covalent bonds between the
sugar of one nucleotide and the
phosphate of the next nucleotide
P
S
N
N
S
P
One base pair (bp): 2
nitrogen bases bonded
together.
P
One
nucleotide
P
S
N
N
S
S
N
P
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