BIOL 041 M004 CourseReadings

Biology 041
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Biology 041—Biology, Part 1

Section M004 / .5 Semester hours
Jacob Chalmers, Biology
Copyright © 2021 Brigham Young University. All rights reserved.
Published by
Independent Study
BYU Continuing Education
Brigham Young University
229 HCEB
Provo, Utah 84602-1502
801-422-2868
is.byu.edu
Introduction to This Reading Packet
Thank you for purchasing the lesson packet for BIO 041: Biology, Part 1. These items are
included in this packet:
• this introductory letter

• a copy of the readings from each lesson (the pages following this letter)
• experience activity instructions
Begin your online course by reading the syllabus; it contains the information you need to
successfully complete the course. As you begin, you will notice that each lesson includes les-
son reading material. The reading material for each lesson is included in this packet, as well
as in the online course.
The lessons also have computer-graded assignments, videos, labs, and self-check exercises
associated with them; these are available only through the online course.
This packet is designed to give you the best experience for reading the detailed lesson con-
tent and taking notes. To complete the course, you will need access to the online assignments
and exams.
Best wishes for your success in this course!
Contents
Week 1
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
The Scientific Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
The Characteristics of Life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Levels of Organization of Living Things . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Week 2
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Biotic and Abiotic Factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
About Your Five Biology Experiences Assignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Experiences 1: Sourdough Starter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
The Building Blocks of Life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
The Properties of Water, Part 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
The Properties of Water, Part 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Week 3
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Acids and Bases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Carbohydrates, Part 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Carbohydrates, Part 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Lipids, Part 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Lipids, Part 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Week 4
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Amino Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Protein Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Nucleic Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Week 5
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Enzymes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Week 6
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Cell Theory, Part 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Cell Theory, Part 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Cell Organelles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Cell Organelles, Part 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Week 7
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Types of Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Week 8
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Cell Transport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Experiences 2: Create Your Own Petri Dish . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Week 9
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
Light and Pigments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Products and Processes of Photosynthesis, Part 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
The Calvin Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Week 10
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
Cellular Respiration Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
The Krebs Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Anaerobic Respiration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
Week 11
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Experiences 3: Metabolism of Yeast Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
Week 12
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Introduction to DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
DNA Replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
Week 13
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
Translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
Week 14
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Experiences 4: DNA Extraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Week 15
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Cell Growth Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Mitosis Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
Meiosis, Part 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
Meiosis, Part 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
Week 16
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
Comparing Mitosis and Meiosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
Week 17
Weekly Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
Experiences 5: Making Yogurt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
Week 1
Week 1
Let's Get Started

We e k l y O v e r v i e w
Every discipline has its foundations. In biology, you need to understand the basics of scientific
thinking. Once you have grasped the scientific method and its approach to knowing, you'll begin
your exploration of basic biological principles--the characteristics of life itself.
The content from this week comes from Unit 1: Basics of Biology (Objectives)

Outline
Lessons
Unit 1
The Scientific Method

Objective
(1 part - 15 min.)
The Characteristics of Life

Objective
(2 parts - 20 min.)
Media
Sunflower video (1.5 min.)
7
BIOL 041: Biology, Part 1
Assignments
Scientific Method Activity (5 min.)
Scientific Method Lab (10 min.)
Scientific Method Set-up Assignment (20 min.)
The Characteristics of Life Activity (5 min.)
Levels of Organization of Living Things activity (5 min.)
Self-Checks (15 min.)

Vo c a b u l a r y
Please view this vocabulary deck in your online course.
8
Week 1
Week 1
The Scientific Method1

Reading Section
Sir Francis Bacon (1561–1626) is

credited with being the first to
define the scientific method.
Paul van Somer, Wikimedia Commons
(https://commons.wikimedia.org/wiki/
File:Somer_Francis_Bacon.jpg) ,
public domain.
Biologists study the living world by posing questions about it and seeking science-based
responses. This approach is common to other sciences as well and is often referred to as the
scientific method. The scientific method was used even in ancient times, but it was first
documented by England’s Sir Francis Bacon (1561–1626), who set up inductive methods for
scientific inquiry. The scientific method is not exclusively used by biologists; it can be applied to
almost all fields of study as a logical, rational problem-solving method.
9
Proposing a Hypothesis
A hypothesis is a suggested explanation that can be tested. To solve a problem, several
hypotheses may be proposed. For example, one hypothesis might be, “The classroom is warm
because no one turned on the air conditioning.” But there could be other responses to the
question, and therefore other hypotheses may be proposed. A second hypothesis might be,
“The classroom is warm because there is a power failure, and so the air conditioning doesn’t
work.”
Once a hypothesis has been selected, the student can make a prediction. A prediction is
similar to a hypothesis, but it typically has the format “If . . . then . . . .” For example, the
prediction for the first hypothesis might be, “If the student turns on the air conditioning, then the
classroom will no longer be too warm.”
Te s t i n g a H y p o t h e s i s
A valid hypothesis must be testable. It should also be falsifiable, meaning that it can be
disproven by experimental results. Importantly, science does not claim to “prove” anything,
because scientific understandings are always subject to modification with further information.
This step—openness to disproving ideas—is what distinguishes sciences from non-sciences.
The presence of the supernatural, for instance, is neither testable nor falsifiable.
To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate
one or more of the hypotheses. Each experiment will have one or more variables and one or
more controls. A variable is any part of the experiment that can vary or change during the
experiment. The control group contains every feature of the experimental group except it is not
given the manipulation that is hypothesized about. Therefore, if the results of the experimental
group differ from the control group, the difference must be due to the hypothesized
manipulation, rather than some outside factor.
To test the first hypothesis, the student would find out if the air conditioning is on. If the air
conditioning is turned on but does not work, there should be another reason, and this hypothesis
should be rejected. To test the second hypothesis, the student could check if the lights in the
classroom are functional. If they are, there is no power failure and this hypothesis should be
rejected. Each hypothesis should be tested by carrying out appropriate experiments. Be aware
that rejecting one hypothesis does not determine whether or not the other hypotheses can be
accepted; it simply eliminates one hypothesis that is not valid. Using the scientific method, the
hypotheses that are inconsistent with experimental data are rejected.
10
Week 1
The scientific method consists of a series of well-defined

steps. If a hypothesis is not supported by experimental
data, a new hypothesis can be proposed.
OpenStax Biology, (https://openstax.org/books/biology/pages/1-1-the-science-of-biology) CC BY 4.0
(https://creativecommons.org/licenses/by/4.0/) .
The scientific method consists of a series of well-defined steps. If a hypothesis is not supported
by experimental data, a new hypothesis can be proposed
The scientific method may seem too rigid and structured. It is important to keep in mind that,
although scientists often follow this sequence, there is flexibility. Sometimes an experiment
leads to conclusions that favor a change in approach; often, an experiment brings entirely new
scientific questions to the puzzle. Many times, science does not operate in a linear fashion;
instead, scientists continually draw inferences and make generalizations, finding patterns as
their research proceeds. Scientific reasoning is more complex than the scientific method alone
suggests. Notice, too, that the scientific method can be applied to solving problems that aren’t
necessarily scientific in nature.
11

S e l f-C h e c k
Please complete this self-check exercise in your online course.
References
1. “Chapter 1: Introduction
(https://cnx.org/contents/[email protected]:agVo2CPX@13/The-Science-of-Biology) ,”
OpenStax CNX, CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/) .
12
Week 1
Week 1
The Characteristics of Life1

Reading Section
All living organisms share several key characteristics or functions: order, sensitivity or response
to the environment, reproduction, adaptation, growth and development, regulation, homeostasis,
energy processing, and evolution. When viewed together, these nine characteristics serve to
define life.
Order
A toad represents a highly organized structure consisting of cells,

tissues, organs, and organ systems.
Ivengo(RUS), Bufo viridis, Wikimedia Commons
(https://commons.wikimedia.org/wiki/File:Bufo_viridis.jpg) , public
domain
Organisms are highly organized, coordinated structures that consist of one or more cells. Even
very simple, single-celled organisms are remarkably complex: inside each cell, atoms make up
molecules; these in turn make up cell organelles and other cellular inclusions. In multicellular
organisms, similar cells form tissues. Tissues, in turn, collaborate to create organs (body
structures with a distinct function). Organs work together to form organ systems.
13
Sensitivity or Response to Stimuli
The leaves of this sensitive plant (Mimosa pudica) will instantly droop
and fold when touched. After a few minutes, the plant returns to normal.
Alex Lomas, Mimosa pudica, Wikimedia Commons
(https://commons.wikimedia.org/wiki/File:Mimosa_pudica_(2944467906).
jpg) , CC BY 2.0
(https://creativecommons.org/licenses/by/2.0/deed.en)
Organisms respond to diverse stimuli. For example, plants can bend toward a source of light,
climb on fences and walls, or respond to touch. Even tiny bacteria can move toward or away
from chemicals (a process called chemotaxis) or light (phototaxis). Movement toward a stimulus
is considered a positive response, while movement away from a stimulus is considered a
negative response.
Watch this video to see how sunflowers respond to light.
Please return to the online course to view this video.
Reproduction
Single-celled organisms reproduce by first duplicating their DNA, and then dividing it equally as
the cell prepares to divide to form two new cells. Multicellular organisms often produce
specialized reproductive germline cells that will form new individuals. When reproduction occurs,
genes containing DNA are passed along to an organism’s offspring. These genes ensure that
the offspring will belong to the same species and will have similar characteristics, such as size
and shape.
Growth and Development

Organisms grow and develop following specific instructions coded for by their genes. These
genes provide instructions that will direct cellular growth and development, ensuring that a
species’ young will grow up to exhibit many of the same characteristics as its parents.
14
Week 1
Although no two look alike, these kittens have inherited genes from
both parents and share many of the same characteristics.
Credit: Rocky Mountain Feline Rescue, Wikimedia Commons
(https://commons.wikimedia.org/wiki/File:Figure_01_02_11.jpg) , CC BY
4.0 (https://creativecommons.org/licenses/by/4.0/deed.en)
Regulation
Even the smallest organisms are complex and require multiple regulatory mechanisms to
coordinate internal functions, respond to stimuli, and cope with environmental stresses. Two
examples of internal functions regulated in an organism are nutrient transport and blood flow.
Organs (groups of tissues working together) perform specific functions, such as carrying oxygen
throughout the body, removing wastes, delivering nutrients to every cell, and cooling the body.
Homeostasis
Polar bears (Ursus maritimus) and other mammals living in ice-

covered regions maintain their body temperature by generating heat
and reducing heat loss through thick fur and a dense layer of fat under
their skin.
longhorndave polarbear1, flickr.com
(https://www.flickr.com/photos/cctwebteam/4169335902/in/photolist-
7mqWiL) , CC BY 2.0 (https://creativecommons.org/licenses/by/2.0/)
15
In order to function properly, cells need to have appropriate conditions such as proper
temperature, pH, and appropriate concentration of diverse chemicals. These conditions may,
however, change from one moment to the next. Organisms are able to maintain internal
conditions within a narrow range almost constantly, despite environmental changes,
through homeostasis (literally, “steady state”)—the ability of an organism to maintain constant
internal conditions. For example, an organism needs to regulate body temperature through a
process known as thermoregulation. Organisms that live in cold climates, such as the polar
bear, have body structures that help them withstand low temperatures and conserve body heat.
Structures that aid in this type of insulation include fur, feathers, blubber, and fat. In hot climates,
organisms have methods (such as perspiration in humans or panting in dogs) that help them to
shed excess body heat.
Energy Processing
All organisms use a source of energy for their metabolic activities. Some organisms capture
energy from the sun and convert it into chemical energy in food; others use chemical energy in
molecules they take in as food.
The California condor (Gymnogyps californianus) uses chemical

energy derived from food to power flight. California condors are an
endangered species; this bird has a wing tag that helps biologists
identify the individual.
Pacific Southwest Region U.S. Fish and Wildlife Service, Flying
California condor, flickr.com
(https://www.flickr.com/photos/usfws_pacificsw/5057206247/in/album-
72157628116654501/) , CC BY 2.0
(https://creativecommons.org/licenses/by/2.0/)
16
Week 1

S e l f-C h e c k
References
1. “1.2: Themes and Concepts of Biology
(https://cnx.org/contents/[email protected]:gNLp76vu@13/Themes-and-Concepts-of-
Biology) ,” OpenStax CNX, CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/).
17
Week 1
Levels of Organization of Living Things1

Reading Section
All molecules, including this DNA molecule, are composed of atoms.

brian0918, DNA_animation, commons.wikimedia.org, Public Domain
Living things are highly organized and structured, following a hierarchy that can be examined on
a scale from small to large. The atom is the smallest and most fundamental unit of matter. It
18
Week 1
consists of a nucleus surrounded by electrons. Atoms form molecules. A molecule is a chemical

structure consisting of at least two atoms held together by one or more chemical bonds. Many
molecules that are biologically important are macromolecules, large molecules that are
typically formed by polymerization (a polymer is a large molecule that is made by combining
smaller units called monomers, which are simpler than macromolecules). An example of a
macromolecule is deoxyribonucleic acid (DNA), which contains the instructions for the structure
and functioning of all living organisms.
Some cells contain aggregates of macromolecules surrounded by membranes; these are

called organelles. Organelles are small structures that exist within cells. Examples of
organelles include mitochondria and chloroplasts, which carry out indispensable functions:
mitochondria produce energy to power the cell, while chloroplasts enable green plants to utilize
the energy in sunlight to make sugars. All living things are made of cells; the cell itself is the
smallest fundamental unit of structure and function in living organisms. (This requirement is why
viruses are not considered living: they are not made of cells. To make new viruses, they have to
invade and hijack the reproductive mechanism of a living cell; only then can they obtain the
materials they need to reproduce.) Some organisms consist of a single cell and others are
multicellular. Cells are classified as prokaryotic or eukaryotic. Prokaryotes are single-celled or
colonial organisms that do not have membrane-bound nuclei; in contrast, the cells
of eukaryotes do have membrane-bound organelles and a membrane-bound nucleus.
In larger organisms, cells combine to make tissues, which are groups of similar cells carrying
out similar or related functions. Organs are collections of tissues grouped together performing a
common function. Organs are present not only in animals but also in plants. An organ
system is a higher level of organization that consists of functionally related organs. Mammals
have many organ systems. For instance, the circulatory system transports blood through the
body and to and from the lungs; it includes organs such as the heart and blood
vessels. Organisms are individual living entities. For example, each tree in a forest is an
organism. Single-celled prokaryotes and single-celled eukaryotes are also considered
organisms and are typically referred to as microorganisms.
Please return to the online course to explore this interaction.
All the individuals of a species living within a specific area are collectively called a population.
For example, a forest may include many pine trees. All of these pine trees represent the
population of pine trees in this forest. Different populations may live in the same specific area.
For example, the forest with the pine trees includes populations of flowering plants and also
insects and microbial populations. A community is the sum of populations inhabiting a
particular area. For instance, all of the trees, flowers, insects, and other populations in a forest
form the forest’s community. The forest itself is an ecosystem. An ecosystem consists of all the
living things in a particular area together with the abiotic, non-living parts of that environment
such as nitrogen in the soil or rain water. At the highest level of organization, the biosphere is
the collection of all ecosystems, and it represents the zones of life on earth. It includes land,
water, and even the atmosphere to a certain extent.
19
The biological levels of organization of living things are shown. From a single
organelle to the entire biosphere, living organisms are parts of a highly structured
hierarchy.2
20
Week 1

S e l f-C h e c k
References
1. “1.2: Themes and Concepts of Biology.
(https://cnx.org/contents/[email protected]:gNLp76vu@13/Themes-and-Concepts-of-
Biology) ” OpenStax CNX, CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/).
2. "Figure 1.16. (https://openstax.org/books/biology/pages/1-2-themes-and-concepts-of-
biology) " OpenStax CNX, CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/).
3. Credit “organelles”: modification of work by Umberto Salvagnin; credit “cells”:
modification of work by Bruce Wetzel, Harry Schaefer/ National Cancer Institute; credit
“tissues”: modification of work by Kilbad; Fama Clamosa; Mikael Häggström; credit
“organs”: modification of work by Mariana Ruiz Villareal; credit “organisms”:
modification of work by "Crystal"/Flickr; credit “ecosystems”: modification of work by US
Fish and Wildlife Service Headquarters; credit “biosphere”: modification of work by
NASA
21
22
Week 2
Week 2
Let's Get Started

Water is a foundational element of life. Acids and bases can have a large effect on living
organisms. Carbohydrates have several functions, but the main one we will focus on is to give
your body energy. Lipids, proteins, nucleic acids, and enzymes all affect our bodies. As we
move from basic biological principles into the key components required for life, you are going to
come to know your body in entirely new ways!
The content from this week comes from Unit 1: Basics of Biology and Unit 2: The Foundations of
Life (Objectives)

Outline
Lessons
Biotic and Abiotic Factors

Objective
(10 min.)
Unit 2
Water and the Building Blocks of Life

Objective
(3 parts — 80 min.)
23
Media
Water and Life video (11 min.)
Assignments
Experiences 1: Sourdough Starter (60 min.)
Properties of Water Lab: Tension (10 min.)
Properties of Water Deep Dive Assignment (30 min.)
Properties of Water Activity (5 min.)

Vo c a b u l a r y
24
Week 2
Week 2
Biotic and Abiotic Factors

Reading Section
Because life doesn’t exist in a vacuum, life both influences and is influenced by its surroundings.
The terms biotic and abiotic factors are used for describing various factors that influence life (in
general and specifically). Biotic factors are other living elements. Abiotic factors are the non-
living ones.
Biotic and abiotic factors not only affect individuals but can also affect the stability of a
population, too. For example, in the 2020 coronavirus outbreak, it was the presence of a biotic
factor—the virus—that caused death in some individual cases, but also caused massive
changes in the way people interacted with each other, traveled, conducted commerce, and
received their education.
An abiotic factor that impacts life is the increasing temperature of our atmosphere caused by
increased carbon dioxide. Pollution, a non-living by-product of the way we live, is affecting how
we live, where we live, and the overall quality of life. Because of the increase in temperature, we
have seen whole species increase in number (southern pine beetles in the United States, for
example) and decrease in number (the northeastern forests decimated by the beetles) because
conditions that previously affected a species (cold winters that limit beetles) have changed.
Watch the following video that discusses biotic and abiotic factors. Look for answers to the
following questions:
How do biotic and abiotic factors influence life positively? How do they impact life negatively?
How likely is it that a biotic or abiotic factor will have an effect so limited that it doesn’t impact our
entire system of life?
Please view this video in your online course.

Self-Check
25
Week 2
About Your Five Biology Experiences Assignments

Reading Section
Introduction to Your Biology Experiences

As noted in the syllabus, throughout this course you will be doing some hands-on activities that
will help you learn about the world of microscopic organisms and apply what you have learned.
We have found that these activities can help contextualize your learning.
As you proceed through these activities, you will need to keep notes about what you observe
(we recommend using a Google Doc so you can copy and paste your work). You will also want
to take photos of your experiments. In the photos, please include a marker that indicates the
date the image was taken. You will also need to answer a series of reflection questions for each
of the activities.
You will submit your reflection assignments for the first three activities in the middle of the
course. The remainder of your work for the subsequent activities will be submitted at the end of
the course.
The image below shows how the experience activities fit into the course.
Experiences Timeline © BYU
26
Week 2
Week 2
Experiences 1: Sourdough Starter
Instructions
To help you get a better idea of microscopic organisms and how they are involved with many of
the foods we eat, please watch the following video:
Please watch this video in your online course.
Now you are going to create a sourdough starter that will be used in a future activity as well. You
will be creating a dough and then allowing bacteria and yeast (which is a fungus) to grow in it.
The bacteria and yeast in the sourdough starter produce different substances that give the
bread its unique flavor. Since it takes some time to grow your sourdough starter, begin making
the starter before studying unit 2 (Chemistry of Life). Then you can learn about the chemistry of
life and apply what you have learned to your sourdough starter.
TAKE CARE OF YOUR SOURDOUGH STARTER AND DON’T THROW IT AWAY. YOU WILL
BE USING IT FOR ACTIVITY 2. (Here are instructions for taking care of a starter.
(https://www.kingarthurflour.com/recipes/feeding-and-maintaining-your-sourdough-starter-recipe) )
Follow the steps below to create your starter:
Water1, wheat flour2, flour3, and plastic wrap4
27
Materials Needed
2½ cups dechlorinated water (read step 1 below on how to remove the chlorine from your
tap water)
½ cup wheat flour
2 cups all-purpose unbleached flour
plastic wrap
Procedure
B E F O R E B E G I N N I N G ( D AY B E F O R E )
1. Since you will be allowing bacteria and yeast to grow, you need to make sure the water
you use does not have chlorine in it, as chlorine will kill the bacteria and yeast. Either you
can buy distilled water OR you can let tap water sit in an open container for 24 hours.
D AY 1
2. In a large container that can hold at least ¾ of a liter, add ½ cup whole-wheat flour and ¼
cup of dechlorinated water. Mix these with a fork until smooth. Cover the jar loosely with
plastic wrap. Let this sit in a warm spot (75°–80°F) for 24 hours.
D AY 2
3. After 24 hours have passed, record in your notebook your observations about how the
starter looks. (Remember that you will be turning in a reflection assignment halfway
through the course and again at the end of the course, so keeping a notebook of these
activities will be very helpful.) Look for things such as small bubbles, odors, and different-
colored layers. These are all signs that the bacteria and yeast in your mixture are growing.
If you do not notice anything yet, that is okay.
4. Nothing else needs to be done at this point. Let the starter sit for another 24 hours.
28
Week 2
D AY 3
5. You may find now that there is a dark liquid either on the surface or slightly below the
surface. This dark liquid shows that the organisms in your starter are growing and need to
be fed. It will also have a strong odor to it. Observe odors, bubbles, and color changes and
record them in your notebook. Even if you do not observe bubbles or dark liquid, you need
to add food to your starter so the organisms are able to grow and reproduce.
6. Remove about half of your starter from the jar and throw that half away. Then add ½ cup
all-purpose flour (which is the food) and ¼ cup dechlorinated water. Mix these with a fork
until smooth. It should be like thick pancake batter, so add more water if needed.
7. Loosely cover with plastic wrap and let sit for another 24 hours.
D AY S 4 , 5 , a n d 6
8. Feed the starter by following the same procedure as day 3 (step 6). Continue to make
observations in your notebook as well. In your notebook, also record the growth each day
of the starter. You could make a mark with a marker where the liquid is and then measure
the increase each day, or you could mark the top of the liquid with a rubber band to see
the growth each day.
9. Your starter is ready when you see many bubbles; the texture will be spongy and fluffy,
kind of like a marshmallow. The odor should be much more pleasant now as well. Since
we are not using the starter to make bread, it is not a big deal if it does not meet all these
requirements. You should at least see bubbles, showing that the bacteria and yeast are
using the flour as a food source and growing.
BE USING IT FOR ACTIVITY 2.
Here's a video that goes through the sourdough creation process:
Questions and Notes

Because the questions for this activity rely on content found in unit 2, they have been placed
after unit 2 in the course. If you kept good notes about what you found, you should be able to
use both the activity and the content to answer the questions.
And remember:
BE USING IT FOR ACTIVITY 2.
29
References
1. Photo (https://www.pexels.com/photo/water-drop-40784/) by Pexel.
2. Photo (https://www.flickr.com/photos/30478819@N08/38037816982) by Marco Verch
(https://www.flickr.com/photos/30478819@N08/) via Flicker. CC BY 2.0.
3. (https://creativecommons.org/licenses/by/2.0/) Photo
(https://www.flickr.com/photos/30478819@N08/45854625462) by Marco Verch
(https://www.flickr.com/photos/30478819@N08/) via Flicker. CC BY 2.0.

4. (https://creativecommons.org/licenses/by/2.0/) Photo
(https://pixabay.com/fr/photos/diapositive-emball%C3%A9s-transparent-967256/) by
Pixabay.
30
Week 2
Week 2
The Building Blocks of Life1

Reading Section
By the end of this section, you will be able to do the following:
Define matter and elements

Describe the interrelationship between protons, neutrons, and electrons
Compare the ways in which electrons can be donated or shared between atoms
Explain the ways in which naturally occurring elements combine to create molecules, cells,
tissues, organ systems, and organisms
At its most fundamental level, life is made up of matter. Matter is any substance that occupies
space and has mass. Elements are unique forms of matter with specific chemical and physical
properties that cannot break down into smaller substances by ordinary chemical reactions.
There are 118 elements, but only 98 occur naturally. The remaining elements are unstable and
require scientists to synthesize them in laboratories.
Each element is designated by its chemical symbol, which is a single capital letter or a
combination of two letters. Some elements follow the English term for the element, such as C for
carbon and Ca for calcium. Other elements’ chemical symbols derive from their Latin names.
For example, the symbol for sodium is Na, referring to natrium, the Latin word for sodium.
The four elements common to all living organisms are oxygen (O), carbon (C), hydrogen (H),
and nitrogen (N). In the nonliving world, elements are found in different proportions, and some
elements common to living organisms are relatively rare on the earth as a whole, as Table 2.1
(https://openstax.org/books/biology-2e/pages/2-1-atoms-isotopes-ions-and-molecules-the-building-
blocks#tab-ch02_01_01) shows. For example, the atmosphere is rich in nitrogen and oxygen but
contains little carbon and hydrogen, while the earth’s crust, although it contains oxygen and a
small amount of hydrogen, has little nitrogen and carbon. In spite of their differences in
abundance, all elements and the chemical reactions between them obey the same chemical and
physical laws regardless of whether they are a part of the living or nonliving world.
31
Table 2.1. Approximate Percentage of Elements in Living Organisms (Humans)

Compared to the Nonliving World
Element Life (Humans) Atmosphere Earth’s Crust
Oxygen (O) 65% 21% 46%
Carbon (C) 18% trace trace
Hydrogen (H) 10% trace 0.1%
Nitrogen (N) 3% 78% trace
Table 2.1
Please review each of the following topics before proceeding.
The Structure of the Atom

To understand how elements come together, we must first discuss the element's smallest
component or building block, the atom. An atom is the smallest unit of matter that retains all
of the element's chemical properties. For example, one gold atom has all the properties of
gold in that it is a solid metal at room temperature. A gold coin is simply a very large number
of gold atoms molded into the shape of a coin and contains small amounts of other
elements known as impurities. We cannot break down gold atoms into anything smaller
while still retaining the properties of gold.
An atom is composed of two regions: the nucleus, which is in the atom's center and
contains protons and neutrons, and the atom's outermost region, which holds electrons in
orbit around the nucleus (as Figure 2.2 (https://openstax.org/books/biology-2e/pages/2-1-
atoms-isotopes-ions-and-molecules-the-building-blocks#fig-ch02_01_01) illustrates). Atoms
contain protons, electrons, and neutrons, among other subatomic particles. The only
exception is hydrogen (H), which is made of one proton and one electron with no neutrons.
32
Week 2
Helium
Figure 2.2. Elements, such as helium, depicted here, are made up of atoms. Atoms are
made up of protons and neutrons located within the nucleus, with electrons in orbitals
surrounding the nucleus.
Protons and neutrons have approximately the same mass, about 1.67 × 10-24 grams.
Scientists define this amount of mass as one atomic mass unit (amu) or one Dalton, as
Table 2.2 (https://openstax.org/books/biology-2e/pages/2-1-atoms-isotopes-ions-and-
molecules-the-building-blocks#tab-ch02_01_02) shows. Although similar in mass, protons
and neutrons differ in their electric charge. A proton is positively charged, whereas a
neutron is uncharged. Therefore, the number of neutrons in an atom contributes
significantly to its mass, but not to its charge. Electrons are much smaller in mass than
protons, weighing only 9.11 × 10-28 grams, or about 1/1800 of an atomic mass unit. Hence,
they do not contribute much to an element’s overall atomic mass. Therefore, when
considering atomic mass, it is customary to ignore the mass of any electrons and calculate
the atom’s mass based on the number of protons and neutrons alone. Although not
significant contributors to mass, electrons do contribute greatly to the atom’s charge, as
each electron has a negative charge equal to the proton's positive charge. In uncharged,
neutral atoms, the number of electrons orbiting the nucleus is equal to the number of
protons inside the nucleus. In these atoms, the positive and negative charges cancel each
other out, leading to an atom with no net charge.
Accounting for the sizes of protons, neutrons, and electrons, most of the atom's volume—
greater than 99 percent—is empty space. With all this empty space, one might ask why so-
called solid objects do not just pass through one another. The reason they do not is that the
electrons that surround all atoms are negatively charged and negative charges repel each
other.
33
Table 2.2. Protons, Neutrons, and Electrons
Charge Mass (amu) Location
Proton +1 1 nucleus
Neutron 0 1 nucleus
Electron –1 0 orbitals
Atomic Number and Mass

Atoms of each element contain a characteristic number of protons and electrons. The
number of protons determines an element’s atomic number, which scientists use to
distinguish one element from another. The number of neutrons is variable, resulting in
isotopes, which are different forms of the same atom that vary only in the number of
neutrons they possess. Together, the number of protons and neutrons determine an
element’s mass number (as Figure 2.3 (https://openstax.org/books/biology-2e/pages/2-1-
atoms-isotopes-ions-and-molecules-the-building-blocks#fig-ch02_01_02) illustrates). Note that
we disregard the small contribution of mass from electrons in calculating the mass number.
We can use this approximation of mass to easily calculate how many neutrons an element
has by simply subtracting the number of protons from the mass number. Since an element’s
isotopes will have slightly different mass numbers, scientists also determine the atomic
mass, which is the calculated mean of the mass number for its naturally occurring isotopes.
Often, the resulting number contains a fraction. For example, the atomic mass of chlorine
(Cl) is 35.45 because chlorine is composed of several isotopes, some (the majority) with
atomic mass 35 (17 protons and 18 neutrons) and some with atomic mass 37 (17 protons
and 20 neutrons).
Figure 2.3 Carbon has an atomic number of 6, and two stable isotopes with mass numbers
of 12 and 13. Its relative atomic mass is 12.011
How many neutrons do carbon-12 and carbon-13 have, respectively?
34
Week 2
Carbon
OpenStax CNX, CC BY 4.0
Isotopes
Isotopes are different forms of an element that have the same number of protons but a
different number of neutrons. Some elements—such as carbon, potassium, and uranium—
have naturally occurring isotopes. Carbon-12 contains six protons, six neutrons, and six
electrons; therefore, it has a mass number of 12 (six protons and six neutrons). Carbon-14
contains six protons, eight neutrons, and six electrons; its atomic mass is 14 (six protons
and eight neutrons). These two alternate forms of carbon are isotopes. Some isotopes may
emit neutrons, protons, and electrons, and attain a more stable atomic configuration (lower
level of potential energy); these are radioactive isotopes, or radioisotopes. Radioactive
decay (carbon-14 decaying to eventually become nitrogen-14) describes the energy loss
that occurs when an unstable atom’s nucleus releases radiation.
EVOLUTION CONNECTION
Carbon Dating
Carbon is normally present in the atmosphere in the form of gaseous compounds like
carbon dioxide and methane. Carbon-14 (14C) is a naturally occurring radioisotope that is
created in the atmosphere from atmospheric 14N (nitrogen) by the addition of a neutron and
the loss of a proton because of cosmic rays. This is a continuous process, so more 14C is
always being created. As a living organism incorporates 14C initially as carbon dioxide fixed
in the process of photosynthesis, the relative amount of 14C in its body is equal to the
concentration of 14C in the atmosphere. When an organism dies, it is no longer
ingesting 14C, so the ratio between 14C and 12C will decline as 14C decays gradually
35
to 14N by a process called beta decay—electrons or positrons emission. This decay emits
energy in a slow process.
After approximately 5,730 years, half of the starting concentration of 14C will convert back
to 14N. We call the time it takes for half of the original concentration of an isotope to decay
back to its more stable form its half-life. Because the half-life of 14C is long, scientists use it
to date formerly living objects such as old bones or wood. Comparing the ratio of the 14C
concentration in an object to the amount of 14C in the atmosphere, scientists can determine
the amount of the isotope that has not yet decayed. On the basis of this amount, Figure 2.4
(https://openstax.org/books/biology-2e/pages/2-1-atoms-isotopes-ions-and-molecules-the-
building-blocks#fig-ch02_01_03) shows that we can calculate the age of the material, such
as the pygmy mammoth, with accuracy if it is not much older than about 50,000 years.
Other elements have isotopes with different half lives. For example, 40K (potassium-40) has
a half-life of 1.25 billion years, and 235U (Uranium 235) has a half-life of about 700 million
years. Through the use of radiometric dating, scientists can study the age of fossils or other
remains of extinct organisms to understand how organisms have evolved from earlier
species.
Dig Site
Bill Faulkner, NPS, public domain
Figure 2.4. Scientists can determine the age of carbon-containing remains less than
about 50,000 years old, such as this pygmy mammoth, using carbon dating.
36
Week 2
LINK TO LEARNING
To learn more about atoms, isotopes, and how to tell one isotope from another, run the
simulation.
Atom and Isotope Simulation

(https://openstax.or g/l/ato ms_isotopes)
T h e P e r i o d i c Ta b l e
The periodic table organizes and displays different elements. Devised by Russian chemist
Dmitri Mendeleev (1834–1907) in 1869, the table groups elements that, although unique,
share certain chemical properties with other elements. The properties of elements are
responsible for their physical state at room temperature: they may be gases, solids, or
liquids. Elements also have specific chemical reactivity, the ability to combine and to
chemically bond with each other.
In the periodic table in Figure 2.5 (https://openstax.org/books/biology-2e/pages/2-1-atoms-

isotopes-ions-and-molecules-the-building-blocks#fig-ch02_01_04) , the elements are
organized and displayed according to their atomic number and are arranged in a series of
rows and columns based on shared chemical and physical properties. In addition to
providing the atomic number for each element, the periodic table also displays the element’s
atomic mass. Looking at carbon, for example, its symbol (C) and name appear, as well as
its atomic number of six (in the upper left-hand corner) and its atomic mass of 12.01.
Figure 2.5 The periodic table shows each element's atomic mass and atomic number.
The atomic number appears above the symbol for the element and the approximate atomic
mass appears below it. Wikimedia Commons (https://commons.wikimedia.org/wiki/
File:Figure_00_02_01.jpg) , CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/
deed.en)
37
The periodic table groups elements according to chemical properties. Scientists base the
differences in chemical reactivity between the elements on the number and spatial
distribution of an atom’s electrons. Atoms that chemically react and bond to each other form
molecules. Molecules are simply two or more atoms chemically bonded together. Logically,
when two atoms chemically bond to form a molecule, their electrons, which form the
outermost region of each atom, come together first as the atoms form a chemical bond.
Electron Shells and the Bohr Model

Note that there is a connection between the number of protons in an element, the atomic
number that distinguishes one element from another, and the number of electrons it has. In
all electrically neutral atoms, the number of electrons is the same as the number of protons.
Thus, each element, at least when electrically neutral, has a characteristic number of
electrons equal to its atomic number.
In 1913, Danish scientist Niels Bohr (1885–1962) developed an early model of the atom.
The Bohr model shows the atom as a central nucleus containing protons and neutrons, with
the electrons in circular orbitals at specific distances from the nucleus (as Figure 2.6
building-blocks#fig-ch02_01_05) illustrates). These orbits form electron shells or energy
levels, which are a way of visualizing the number of electrons in the outermost shells. These
energy levels are designated by a number and the symbol “n.” For example, 1n represents
the first energy level located closest to the nucleus.
Hydrogen atom
(https://creativecommons.org/licenses/b
y/4.0/deed.en)
Figure 2.6. In 1913, Niels Bohr developed the Bohr model in which electrons exist
within principal shells.
38
Week 2
An electron normally exists in the lowest energy shell available, which is the one closest to
the nucleus. Energy from a photon of light can bump it up to a higher energy shell, but this
situation is unstable, and the electron quickly decays back to the ground state. In the
process, it releases a photon of light.
Electrons fill orbitals in a consistent order: they first fill the orbitals closest to the nucleus,
then they continue to fill orbitals of increasing energy further from the nucleus. If there are
multiple orbitals of equal energy, they fill with one electron in each energy level before
adding a second electron. The electrons of the outermost energy level determine the atom's
energetic stability and its tendency to form chemical bonds with other atoms to form
molecules.
Under standard conditions, atoms fill the inner shells first, often resulting in a variable
number of electrons in the outermost shell. The innermost shell has a maximum of two
electrons but the next two electron shells can each have a maximum of eight electrons. This
is known as the octet rule, which states, with the exception of the innermost shell, that
atoms are more stable energetically when they have eight electrons in their valence shell,
the outermost electron shell. Figure 2.7 (https://openstax.org/books/biology-2e/pages/2-1-
atoms-isotopes-ions-and-molecules-the-building-blocks#fig-ch02_01_06) shows examples of
some neutral atoms and their electron configurations. Notice that in Figure 2.7 (https://
openstax.org/books/biology-2e/pages/2-1-atoms-isotopes-ions-and-molecules-the-
building-blocks#fig-ch02_01_06) , helium has a complete outer electron shell, with two
electrons filling its first and only shell. Similarly, neon has a complete outer 2n shell
containing eight electrons. In contrast, chlorine and sodium have seven and one in their
outer shells, respectively, but theoretically they would be more energetically stable if they
followed the octet rule and had eight.
VISUAL CONNECTION
Bohr Diagram
Figure 2.7 Bohr diagrams indicate how many electrons fill each principal shell. Group
18 elements (helium, neon, and argon) have a full outer, or valence, shell.
39
A full valence shell is the most stable electron configuration. Elements in other groups have
partially filled valence shells and gain or lose electrons to achieve a stable electron
configuration.
An atom may give, take, or share electrons with another atom to achieve a full valence
shell, the most stable electron configuration. Looking at this figure, how many electrons do
elements in group 1 need to lose in order to achieve a stable electron configuration? How
many electrons do elements in groups 14 and 17 need to gain to achieve a stable
configuration?
Understanding that the periodic table's organization is based on the total number of protons
(and electrons) helps us know how electrons distribute themselves among the shells. The
periodic table is arranged in columns and rows based on the number of electrons and their
location. Examine more closely some of the elements in the table’s far right column in
Figure 2.5 (https://openstax.org/books/biology-2e/pages/2-1-atoms-isotopes-ions-and-
molecules-the-building-blocks#fig-ch02_01_04) . The group 18 atoms helium (He), neon (Ne),
and argon (Ar) all have filled outer electron shells, making it unnecessary for them to share
electrons with other atoms to attain stability. They are highly stable as single atoms.
Because they are non reactive, scientists coin them inert (or noble gases). Compare this to
the group 1 elements in the left-hand column. These elements, including hydrogen (H),
lithium (Li), and sodium (Na), all have one electron in their outermost shells. That means
that they can achieve a stable configuration and a filled outer shell by donating or sharing
one electron with another atom or a molecule such as water. Hydrogen will donate or share
its electron to achieve this configuration, while lithium and sodium will donate their electron
to become stable. As a result of losing a negatively charged electron, they become
positively charged ions. Group 17 elements, including fluorine and chlorine, have seven
electrons in their outmost shells, so they tend to fill this shell with an electron from other
atoms or molecules, making them negatively charged ions. Group 14 elements, of which
carbon is the most important to living systems, have four electrons in their outer shell
allowing them to make several covalent bonds (discussed below) with other atoms. Thus,
the periodic table's columns represent the potential shared state of these elements’ outer
electron shells that is responsible for their similar chemical characteristics.
Elect ron Orbitals

Although useful to explain the reactivity and chemical bonding of certain elements, the Bohr
model does not accurately reflect how electrons spatially distribute themselves around the
nucleus. They do not circle the nucleus like the earth orbits the sun, but we find them
in electron orbitals. These relatively complex shapes result from the fact that electrons
behave not just like particles, but also like waves. Mathematical equations from quantum
mechanics, which scientists call wave functions, can predict within a certain level of
probability where an electron might be at any given time. Scientists call the area where an
electron is most likely to be found its orbital.
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Week 2
Recall that the Bohr model depicts an atom’s electron shell configuration. Within each
electron shell are subshells, and each subshell has a specified number of orbitals containing
electrons. While it is impossible to calculate exactly an electron's location, scientists know
that it is most probably located within its orbital path. The letter s, p, d, and f designate the
subshells. The s subshell is spherical in shape and has one orbital. Principal shell 1n has
only a single s orbital, which can hold two electrons. Principal shell 2n has one s and
one p subshell, and can hold a total of eight electrons. The p subshell has three dumbbell-
shaped orbitals, as Figure 2.8 (https://openstax.org/books/biology-2e/pages/2-1-atoms-
isotopes-ions-and-molecules-the-building-blocks#fig-ch02_01_07) illustrates.
Subshells d and f have more complex shapes and contain five and seven orbitals,
respectively. We do not show these in the illustration. Principal shell 3n has s, p,
and d subshells and can hold 18 electrons. Principal shell 4n has s, p, d and f orbitals and
can hold 32 electrons. Moving away from the nucleus, the number of electrons and orbitals
in the energy levels increases. Progressing from one atom to the next in the periodic table,
we can determine the electron structure by fitting an extra electron into the next available
orbital.
Subshell
OpenStax CNX.
Figure 2.8. The s subshells are shaped like spheres. Both the 1n and 2n principal
shells have an s orbital, but the size of the sphere is larger in the 2n orbital. Each
sphere is a single orbital. Three dumbbell-shaped orbitals comprise p subshells.
Principal shell 2n has a p subshell, but shell 1 does not.
The closest orbital to the nucleus, the 1s orbital, can hold up to two electrons. This orbital is
equivalent to the Bohr model's innermost electron shell. Scientists call it the 1s orbital
because it is spherical around the nucleus. The 1s orbital is the closest orbital to the
nucleus, and it is always filled first, before any other orbital fills. Hydrogen has one electron;
41
therefore, it occupies only one spot within the 1s orbital. We designate this as 1s1, where
the superscripted 1 refers to the one electron within the 1s orbital. Helium has two electrons;
therefore, it can completely fill the 1s orbital with its two electrons. We designate this as 1s2,
referring to the two electrons of helium in the 1s orbital. On the periodic table Figure 2.5
building-blocks#fig-ch02_01_04) , hydrogen and helium are the only two elements in the first
row (period). This is because they only have electrons in their first shell, the 1s orbital.
Hydrogen and helium are the only two elements that have the 1s and no other electron
orbitals in the electrically neutral state.
The second electron shell may contain eight electrons. This shell contains another spherical
s orbital and three “dumbbell” shaped p orbitals, each of which can hold two electrons (as
molecules-the-building-blocks#fig-ch02_01_07) shows). After the 1s orbital fills, the second
electron shell fills, first filling its 2s orbital and then its three p orbitals. When filling
the p orbitals, each takes a single electron. Once each p orbital has an electron, it may add
a second. Lithium (Li) contains three electrons that occupy the first and second shells. Two
electrons fill the 1s orbital, and the third electron then fills the 2s orbital. Its electron
configuration is 1s22s1. Neon (Ne), alternatively, has a total of ten electrons: two are in its
innermost 1s orbital and eight fill its second shell (two each in the 2s and three p orbitals).
Thus it is an inert gas and energetically stable as a single atom that will rarely form a
chemical bond with other atoms. Larger elements have additional orbitals, comprising the
third electron shell. While the concepts of electron shells and orbitals are closely related,
orbitals provide a more accurate depiction of an atom's electron configuration because the
orbital model specifies the different shapes and special orientations of all the places that
electrons may occupy.
LINK TO LEARNING
Watch this visual animation to see the spatial arrangement of the p and s orbitals.
Please return back to the online course to view this video.
Chemical Reactions and Molecules
All elements are most stable when their outermost shell is filled with electrons according to
the octet rule. This is because it is energetically favorable for atoms to be in that
configuration and it makes them stable. However, since not all elements have enough
electrons to fill their outermost shells, atoms form chemical bonds with other atoms
thereby obtaining the electrons they need to attain a stable electron configuration. When
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Week 2
thereby obtaining the electrons they need to attain a stable electron configuration. When
two or more atoms chemically bond with each other, the resultant chemical structure is a
molecule. The familiar water molecule, H2O, consists of two hydrogen atoms and one
oxygen atom. These bond together to form water (as Figure 2.9
building-blocks#fig-ch02_01_08) illustrates). Atoms can form molecules by donating,
accepting, or sharing electrons to fill their outer shells.
Helium
Figure 2.9. Two or more atoms may bond with each other to form a molecule. When
two hydrogens and an oxygen share electrons via covalent bonds it forms a water
molecule.
Chemical reactions occur when two or more atoms bond together to form molecules or
when bonded atoms break apart. Scientists call the substances used in the beginning of a
chemical reaction reactants (usually on the left side of a chemical equation), and we call
the substances at the end of the reaction products (usually on the right side of a chemical
equation). We typically draw an arrow between the reactants and products to indicate the
chemical reaction's direction. This direction is not always a “one-way street.” To create the
water molecule above, the chemical equation would be as follows:
2H + O → H2O
An example of a simple chemical reaction is breaking down hydrogen peroxide molecules,
each of which consists of two hydrogen atoms bonded to two oxygen atoms (H2O2). The
reactant hydrogen peroxide breaks down into water, containing one oxygen atom bound
to two hydrogen atoms (H O), and oxygen, which consists of two bonded oxygen atoms
(O2). In the equation below, the reaction includes two hydrogen peroxide molecules and
43
two water molecules. This is an example of a balanced chemical equation, wherein each
element's number of atoms
2 is the same on each side of the equation. According to the law
of conservation of matter, the number of atoms before and after a chemical reaction should
be equal, such that no atoms are, under normal circumstances, created or destroyed.
2H2O2 (hydrogen peroxide) → 2H2O (water) + O2

(oxygen)
Even though all of the reactants and products of this reaction are molecules (each atom
remains bonded to at least one other atom), in this reaction only hydrogen peroxide and
water are representatives of compounds: they contain atoms of more than one type of
element. Molecular oxygen, alternatively (as Figure 2.10
building-blocks#fig-ch02_01_09) shows) consists of two doubly bonded oxygen atoms and is
not classified as a compound but as a homonuclear molecule.
Figure 2.10. A double bond joins the oxygen atoms in an

O2 molecule.
Some chemical reactions, such as the one above, can proceed in one direction until they
expend all the reactants. The equations that describe these reactions contain a
unidirectional arrow and are irreversible. Reversible reactions are those that can go in
either direction. In reversible reactions, reactants turn into products, but when the product's
concentration goes beyond a certain threshold (characteristic of the particular reaction),
some of these products convert back into reactants. At this point, product and reactant
designations reverse. This back and forth continues until a certain relative balance between
reactants and products occurs—a state called equilibrium. A chemical equation with a
double headed arrow pointing towards both the reactants and products often denote these
reversible reaction situations.
For example, in human blood, excess hydrogen ions (H+) bind to bicarbonate ions (HCO3-)
forming an equilibrium state with carbonic acid (H2CO3). If we added carbonic acid to this
system, some of it would convert to bicarbonate and hydrogen ions.
HCO3−+ H+↔H2CO3
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Week 2
However, biological reactions rarely obtain equilibrium because the concentrations of the
reactants or products or both are constantly changing, often with one reaction's product a
reactant for another. To return to the example of excess hydrogen ions in the blood, forming
carbonic acid will be the reaction's major direction. However, the carbonic acid can also
leave the body as carbon dioxide gas (via exhalation) instead of converting back to
bicarbonate ion, thus driving the reaction to the right by the law of mass action. These
reactions are important for maintaining homeostasis in our blood.
HCO3− + H+ ↔ H2CO3 ↔ CO2 + H2O
Ions and Ionic Bonds

Some atoms are more stable when they gain or lose an electron (or possibly two) and form
ions. This fills their outermost electron shell and makes them energetically more stable.
Because the number of electrons does not equal the number of protons, each ion has a net
charge. Cations are positive ions that form by losing electrons. Negative ions form by
gaining electrons, which we call anions. We designate anions by their elemental name and
change the ending to “-ide”, thus the anion of chlorine is chloride, and the anion of sulfur is
sulfide.
Scientists refer to this movement of electrons from one element to another as electron
transfer. As Figure 2.11 (https://openstax.org/books/biology-2e/pages/2-1-atoms-isotopes-
ions-and-molecules-the-building-blocks#fig-ch02_01_10) illustrates, sodium (Na) only has one
electron in its outer electron shell. It takes less energy for sodium to donate that one
electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an
electron, it now has 11 protons, 11 neutrons, and only 10 electrons, leaving it with an overall
charge of +1. We now refer to it as a sodium ion. Chlorine (Cl) in its lowest energy state
(called the ground state) has seven electrons in its outer shell. Again, it is more energy-
efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an
electron to create an ion with 17 protons, 17 neutrons, and 18 electrons, giving it a net
negative (–1) charge. We now refer to it as a chloride ion. In this example, sodium will
donate its one electron to empty its shell, and chlorine will accept that electron to fill its shell.
Both ions now satisfy the octet rule and have complete outermost shells. Because the
number of electrons is no longer equal to the number of protons, each is now an ion and
has a +1 (sodium cation) or –1 (chloride anion) charge. Note that these transactions can
normally only take place simultaneously: in order for a sodium atom to lose an electron, it
must be in the presence of a suitable recipient like a chlorine atom.
45
Figure 2.11. In the formation of an ionic compound, metals lose

electrons and nonmetals gain electrons to achieve an octet.
Ionic bonds form between ions with opposite charges. For instance, positively charged
sodium ions and negatively charged chloride ions bond together to make crystals of sodium
chloride, or table salt, creating a crystalline molecule with zero net charge.
Physiologists refer to certain salts as electrolytes (including sodium, potassium, and
calcium), ions necessary for nerve impulse conduction, muscle contractions, and water
balance. Many sports drinks and dietary supplements provide these ions to replace those
lost from the body via sweating during exercise.
Covalent Bonds and Other Bonds and Interactions

Another way to satisfy the octet rule is by sharing electrons between atoms to
form covalent bonds. These bonds are stronger and much more common than ionic bonds
in the molecules of living organisms. We commonly find covalent bonds in carbon-based
organic molecules, such as our DNA and proteins. We also find covalent bonds in inorganic
molecules like H2O, CO2, and O2. The bonds may share one, two, or three pairs of
electrons, making single, double, and triple bonds, respectively. The more covalent bonds
between two atoms, the stronger their connection. Thus, triple bonds are the strongest.
The strength of different levels of covalent bonding is one of the main reasons living
organisms have a difficult time in acquiring nitrogen for use in constructing their molecules,
even though molecular nitrogen, N2, is the most abundant gas in the atmosphere. Molecular
nitrogen consists of two nitrogen atoms triple bonded to each other and, as with all
molecules, sharing these three pairs of electrons between the two nitrogen atoms allows for
filling their outer electron shells, making the molecule more stable than the individual
nitrogen atoms. This strong triple bond makes it difficult for living systems to break apart this
nitrogen in order to use it as constituents of proteins and DNA.
Forming water molecules provides an example of covalent bonding. Covalent bonds bind
the hydrogen and oxygen atoms that combine to form water molecules as Figure 2.9
building-blocks#fig-ch02_01_08) shows. The electron from the hydrogen splits its time
between the hydrogen atoms' incomplete outer shell and the oxygen atoms' incomplete
outer shell. To completely fill the oxygen's outer shell, which has six electrons but which
would be more stable with eight, two electrons (one from each hydrogen atom) are needed:
hence, the well-known formula H2O. The two elements share the electrons to fill the outer
shell of each, making both elements more stable.
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Week 2
LINK TO LEARNING
View this short video to see an animation of ionic and covalent bonding.
Please return to the online course to view this video.
Polar Covalent Bonds

There are two types of covalent bonds: polar and nonpolar. In a polar covalent
bond, Figure 2.12 (https://openstax.org/books/biology-2e/pages/2-1-atoms-isotopes-ions-
and-molecules-the-building-blocks#fig-ch02_01_11) shows atoms unequally share the
electrons and are attracted more to one nucleus than the other. Because of the unequal
electron distribution between the atoms of different elements, a slightly positive (δ+) or
slightly negative (δ–) charge develops. This partial charge is an important property of water
and accounts for many of its characteristics.
Water is a polar molecule, with the hydrogen atoms acquiring a partial positive charge and
the oxygen a partial negative charge. This occurs because the oxygen atom's nucleus is
more attractive to the hydrogen atoms' electrons than the hydrogen nucleus is to the
oxygen’s electrons. Thus, oxygen has a higher electronegativity than hydrogen and the
shared electrons spend more time near the oxygen nucleus than the hydrogen atoms'
nucleus, giving the oxygen and hydrogen atoms slightly negative and positive charges,
respectively. Another way of stating this is that the probability of finding a shared electron
near an oxygen nucleus is more likely than finding it near a hydrogen nucleus. Either way,
the atom’s relative electronegativity contributes to developing partial charges whenever one
element is significantly more electronegative than the other, and the charges that these
polar bonds generate may then be used to form hydrogen bonds based on the attraction of
opposite partial charges. (Hydrogen bonds, which we discuss in detail below, are weak
bonds between slightly positively charged hydrogen atoms to slightly negatively charged
atoms in other molecules.) Since macromolecules often have atoms within them that differ
in electronegativity, polar bonds are often present in organic molecules.
Nonpolar Covalent Bonds

Nonpolar covalent bonds form between two atoms of the same element or between
different elements that share electrons equally. For example, molecular oxygen (O2) is
nonpolar because the electrons distribute equally between the two oxygen atoms.
molecules-the-building-blocks#fig-ch02_01_11) also shows another example of a nonpolar
covalent bond—methane (CH4). Carbon has four electrons in its outermost shell and needs
four more to fill it. It obtains these four from four hydrogen atoms, each atom providing one,
making a stable outer shell of eight electrons. Carbon and hydrogen do not have the same
47
making a stable outer shell of eight electrons. Carbon and hydrogen do not have the same
electronegativity but are similar; thus, nonpolar bonds form. The hydrogen atoms each need
one electron for their outermost shell, which is filled when it contains two electrons. These
elements share the electrons equally among the carbons and the hydrogen atoms, creating
a nonpolar covalent molecule.
Polarity
Figure 2.12. Whether a molecule is polar or nonpolar depends both on bond type and
molecular shape. Both water and carbon dioxide have polar covalent bonds, but carbon
dioxide is linear, so the partial charges on the molecule cancel each other out.
Hydrogen Bonds and Van Der Waals Interactions

Ionic and covalent bonds between elements require energy to break. Ionic bonds are not as
strong as covalent, which determines their behavior in biological systems. However, not all
bonds are ionic or covalent bonds. Weaker bonds can also form between molecules. Two
weak bonds that occur frequently are hydrogen bonds and van der Waals interactions.
Without these two types of bonds, life as we know it would not exist. Hydrogen bonds
provide many of the critical, life-sustaining properties of water and also stabilize the
structures of proteins and DNA, the building block of cells.
When polar covalent bonds containing hydrogen form, the hydrogen in that bond has a
slightly positive charge because hydrogen’s electron is pulled more strongly toward the other
element and away from the hydrogen. Because the hydrogen is slightly positive, it will be
attracted to neighboring negative charges. When this happens, a weak interaction occurs
between the hydrogen's δ+ from one molecule and the molecule's δ– charge on another
molecule with the more electronegative atoms, usually oxygen. Scientists call this interaction
48
Week 2
a hydrogen bond. This type of bond is common and occurs regularly between water
molecules. Individual hydrogen bonds are weak and easily broken; however, they occur in
very large numbers in water and in organic polymers, creating a major force in combination.
Hydrogen bonds are also responsible for zipping together the DNA double helix.
Like hydrogen bonds, van der Waals interactions are weak attractions or interactions
between molecules. Van der Waals attractions can occur between any two or more
molecules and are dependent on slight fluctuations of the electron densities, which are not
always symmetrical around an atom. For these attractions to happen, the molecules need to
be very close to one another. These bonds—along with ionic, covalent, and hydrogen bonds
—contribute to the proteins' three-dimensional structure in our cells that is necessary for
their proper function.
CAREER CONNECTION
Pharmaceutical Chemist
Pharmaceutical chemists are responsible for developing new drugs and trying to determine
the mode of action of both old and new drugs. They are involved in every step of the drug
development process. We can find drugs in the natural environment or we can synthesize
them in the laboratory. In many cases, chemists chemically change potential drugs from
nature chemically in the laboratory to make them safer and more effective, and sometimes
synthetic versions of drugs substitute for the version we find in nature.
After a drug's initial discovery or synthesis, the chemist then develops the drug, perhaps
chemically altering it, testing it to see if it is toxic, and then designing methods for efficient
large-scale production. Then, the process of approving the drug for human use begins. In
the United States, the Food and Drug Administration (FDA) handles drug approval. This
involves a series of large-scale experiments using human subjects to ensure the drug is not
harmful and effectively treats the condition for which it is intended. This process often takes
several years and requires the participation of physicians and scientists, in addition to
chemists, to complete testing and gain approval.
An example of a drug that was originally discovered in a living organism is Paclitaxel

(Taxol), an anti-cancer drug used to treat breast cancer. This drug was discovered in the
bark of the pacific yew tree. Another example is aspirin, originally isolated from willow tree
bark. Finding drugs often means testing hundreds of samples of plants, fungi, and other
forms of life to see if they contain any biologically active compounds. Sometimes, traditional
medicine can give modern medicine clues as to where to find an active compound. For
example, mankind has used willow bark to make medicine for thousands of years, dating
back to ancient Egypt. However, it was not until the late 1800s that scientists and
pharmaceutical companies purified and marketed the aspirin molecule, acetylsalicylic acid,
for human use.
49
Occasionally, drugs developed for one use have unforeseen effects that allow usage in
other, unrelated ways. For example, scientists originally developed the drug minoxidil
(Rogaine) to treat high blood pressure. When tested on humans, researchers noticed that
individuals taking the drug would grow new hair. Eventually the pharmaceutical company
marketed the drug to men and women with baldness to restore lost hair.
A pharmaceutical chemist's career may involve detective work, experimentation, and drug
development, all with the goal of making human beings healthier.

Self-Check
References
1. “2.1: Atoms, Isotopes, Ions, and Molecules: The Building Blocks

(https://cnx.org/contents/[email protected]:vogY0C26@21/Atoms-Isotopes-Ions-and-
Molecules-The-Building-Blocks) ,” OpenStax CNX, CC BY 4.0
(https://creativecommons.org/licenses/by/4.0/deed.en) .
50
Week 2
Week 2
The Properties of Water, Part 11

Reading Section
Why do scientists spend time looking for water on other planets? Why is water so important? It
is because water is essential to life as we know it. Water is one of the more abundant molecules
and the one most critical to life on Earth. Approximately 60–70 percent of the human body is
made up of water. Without it, life as we know it simply would not exist.
The polarity of the water molecule and its resulting hydrogen bonding make water a unique
substance with special properties that are intimately tied to the processes of life. Life originally
evolved in a watery environment, and most of an organism’s cellular chemistry and metabolism
occur inside the watery contents of the cell’s cytoplasm. Special properties of water are its high
heat capacity and heat of vaporization, its ability to dissolve polar molecules, its cohesive and
adhesive properties, and its dissociation into ions that leads to the generation of pH.
Understanding these characteristics of water helps to elucidate its importance in maintaining life.
Wa t e r ’s P o l a r i t y
One of water’s important properties is that it is composed of polar molecules: the hydrogen and
oxygen within water molecules (H O) form polar covalent bonds. While there is no net charge to
a water molecule, the polarity of water creates a slightly positive charge on hydrogen and a
slightly negative charge on oxygen, contributing to water’s properties of attraction. Water’s
charges are generated because oxygen is more electronegative than hydrogen, making it more
likely that a shared electron would be found near the oxygen nucleus than the hydrogen
nucleus, thus generating the partial negative charge near the oxygen.
Oil and water do not mix. As this macro image of oil and water
shows, oil does not dissolve in water but forms droplets instead.
This is due to it being a nonpolar compound
Credit: Gautam Dogra, flikr.
51
As a result of water’s polarity, each water molecule attracts other water molecules because of
the opposite charges between water molecules, forming hydrogen bonds. Water also attracts or
is attracted to other polar molecules and ions. A polar substance that interacts readily with or
dissolves in water is referred to as hydrophilic (hydro- = “water”; -philic = “loving”). In contrast,
non-polar molecules such as oils and fats do not interact well with water and separate from it
rather than dissolve in it, as we see in salad dressings containing oil and vinegar (an acidic
water solution). These nonpolar compounds are called hydrophobic (hydro- = “water”; -phobic
= “fearing”).
Wa t e r ’s S t a t e s : G a s , L i q u i d , a n d S o l i d
The formation of hydrogen bonds is an important quality of liquid water that is crucial to life as
we know it. As water molecules make hydrogen bonds with each other, water takes on some
unique chemical characteristics compared to other liquids and, since living things have a high
water content, understanding these chemical features is key to understanding life. In liquid
water, hydrogen bonds are constantly formed and broken as the water molecules slide past
each other. The breaking of these bonds is caused by the motion (kinetic energy) of the water
molecules due to the heat contained in the system. When the heat is raised as water is boiled,
the higher kinetic energy of the water molecules causes the hydrogen bonds to break
completely and allows water molecules to escape into the air as gas (steam or water vapor). On
the other hand, when the temperature of water is reduced and water freezes, the water
molecules form a crystalline structure maintained by hydrogen bonding (there is not enough
energy to break the hydrogen bonds) that makes ice less dense than liquid water, a
phenomenon not seen in the solidification of other liquids.
Water’s lower density in its solid form is due to the way hydrogen bonds are oriented as it
freezes: the water molecules are pushed farther apart compared to liquid water. With most other
liquids, solidification when the temperature drops includes the lowering of kinetic energy
between molecules, allowing them to pack even more tightly than in liquid form and giving the
solid a greater density than the liquid.
The lower density of ice, an anomaly, causes it to float at the surface of liquid water, such as in
an iceberg or in the ice cubes in a glass of ice water. In lakes and ponds, ice will form on the
surface of the water, creating an insulating barrier that protects the animals and plant life in the
pond from freezing. Without this layer of insulating ice, plants and animals living in the pond
would freeze in the solid block of ice and could not survive. The detrimental effect of freezing on
living organisms is caused by the expansion of ice relative to liquid water. The ice crystals that
form upon freezing rupture the delicate membranes essential for the function of living cells,
irreversibly damaging them. Cells can only survive freezing if the water in them is temporarily
replaced by another liquid like glycerol.
52
Week 2
Hydrogen bonding makes ice less dense than liquid water. The (a)
lattice structure of ice makes it less dense than the freely flowing
molecules of liquid water, enabling it to (b) float on water.
Credit a: modification of work by Jane Whitney, image created using
Visual Molecular Dynamics (VMD) software; credit b: Photo
(https://pl.wikipedia.org/wiki/Plik:Argentino_Lake.jpg) by Calyponte
(https://commons.wikimedia.org/wiki/User:Calyponte) via Wikimedia
Commons.CC BY 3.0
Wa t e r ’ s H i g h H e a t C a p a c i t y
Water’s high heat capacity is a property caused by hydrogen bonding among water molecules.
Water has the highest specific heat capacity of any liquids. Specific heat is defined as the
amount of heat one gram of a substance must absorb or lose to change its temperature by one
degree Celsius. For water, this amount is one calorie. It therefore takes water a long time to
heat and long time to cool. In fact, the specific heat capacity of water is about five times more
than that of sand. This explains why the land cools faster than the sea. Due to its high heat
capacity, water is used by warm blooded animals to more evenly disperse heat in their bodies: it
acts in a similar manner to a car’s cooling system, transporting heat from warm places to cool
places, causing the body to maintain a more even temperature.
Wa t e r ’s H e a t o f Va p o r i z a t i o n
Water also has a high heat of vaporization, the amount of energy required to change one gram
of a liquid substance to a gas. A considerable amount of heat energy (586 cal) is required to
accomplish this change in water. This process occurs on the surface of water. As liquid water
heats up, hydrogen bonding makes it difficult to separate the liquid water molecules from each
other, which is required for it to enter its gaseous phase (steam). As a result, water acts as a
heat sink or heat reservoir and requires much more heat to boil than does a liquid such as
ethanol (grain alcohol), whose hydrogen bonding with other ethanol molecules is weaker than
53
water’s hydrogen bonding. Eventually, as water reaches its boiling point of 100° Celsius (212°
Fahrenheit), the heat is able to break the hydrogen bonds between the water molecules, and the
kinetic energy (motion) between the water molecules allows them to escape from the liquid as a
gas. Even when below its boiling point, water’s individual molecules acquire enough energy from
other water molecules such that some surface water molecules can escape and vaporize. This
process is known as evaporation.

Self-Check
Please complete the self-check exercise in your online course.
References
1. “2.2: Water (https://cnx.org/contents/[email protected]:pPjfgsd4@10/Water) ,”
OpenStax CNX, CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/deed.en) .
54
Week 2
Week 2
The Properties of Water, Part 21

Reading Section
Wa t e r ’s S o l v e n t P r o p e r t i e s
Since water is a polar molecule with slightly positive and slightly negative charges, ions and
polar molecules can readily dissolve in it. Therefore, water is referred to as a solvent, a
substance capable of dissolving other polar molecules and ionic compounds. The charges
associated with these molecules will form hydrogen bonds with water, surrounding the particle
with water molecules. This is referred to as a sphere of hydration, or a hydration shell, and
serves to keep the particles separated or dispersed in the water.
When ionic compounds are added to water, the individual ions react with the polar regions of the
water molecules and their ionic bonds are disrupted in the process of dissociation. Dissociation
occurs when atoms or groups of atoms break off from molecules and form ions. Consider table
salt (NaCl, or sodium chloride): when NaCl crystals are added to water, the molecules of NaCl
dissociate into Na+ and Cl– ions, and spheres of hydration form around the ions. The positively
charged sodium ion is surrounded by the partially negative charge of the water molecule’s
oxygen. The negatively charged chloride ion is surrounded by the partially positive charge of the
hydrogen on the water molecule.
When table salt (NaCl) is mixed in water, spheres of hydration are

formed around the ions.
Wa t e r ’s C o h e s i v e a n d A d h e s i v e P r o p e r t i e s
Have you ever filled a glass of water to the very top and then slowly added a few more drops?
Before it overflows, the water forms a dome-like shape above the rim of the glass. This water
can stay above the glass because of the property of cohesion. In cohesion, water molecules
are attracted to each other (because of hydrogen bonding), keeping the molecules together at
the liquid-gas (water-air) interface, although there is no more room in the glass.
55
The weight of the needle is pulling the surface downward; at the same time, the
surface tension is pulling it up, suspending it on the surface of the water and keeping
it from sinking. Notice the indentation in the water around the needle.
Credit: Cory Zanker
Cohesion allows for the development of surface tension, the capacity of a substance to
withstand being ruptured when placed under tension or stress. This is also why water forms
droplets when placed on a dry surface rather than being flattened out by gravity. When a small
scrap of paper is placed onto the droplet of water, the paper floats on top of the water droplet
even though paper is denser (heavier) than the water. Cohesion and surface tension keep the
hydrogen bonds of water molecules intact and support the item floating on the top. It’s even
possible to “float” a needle on top of a glass of water if it is placed gently without breaking the
surface tension.
Capillary action in a glass tube is caused by the adhesive forces

exerted by the internal surface of the glass exceeding the cohesive
forces between the water molecules themselves.
Modification of work by Pearson-Scott Foresman, The Properties of
Water, Wikimedia Commons
(https://commons.wikimedia.org/wiki/File:Capillary_Attraction_Repulsion
(PSF)_(bjl).svg) , public domain
56
Week 2
These cohesive forces are related to water’s property of adhesion, or the attraction between
water molecules and other molecules. This attraction is sometimes stronger than water’s
cohesive forces, especially when the water is exposed to charged surfaces such as those found
on the inside of thin glass tubes known as capillary tubes. Adhesion is observed when water
“climbs” up the tube placed in a glass of water: notice that the water appears to be higher on the
sides of the tube than in the middle. This is because the water molecules are attracted to the
charged glass walls of the capillary more than they are to each other and therefore adhere to it.
This type of adhesion is called capillary action.
Why are cohesive and adhesive forces important for life? Cohesive and adhesive forces are
important for the transport of water from the roots to the leaves in plants. These forces create a
“pull” on the water column. This pull results from the tendency of water molecules being
evaporated on the surface of the plant to stay connected to water molecules below them, and so
they are pulled along. Plants use this natural phenomenon to help transport water from their
roots to their leaves. Without these properties of water, plants would be unable to receive the
water and the dissolved minerals they require. In another example, insects such as the water
strider use the surface tension of water to stay afloat on the surface layer of water and even
mate there.
Water’s cohesive and adhesive properties allow this water strider

(Gerris sp.) to stay afloat.
Tim Vickers, Water Strider, Wikimedia Commons
(https://commons.wikimedia.org/wiki/File:Water_strider.jpg) , public domain
Review

Self-Check
References
57
58
Week 3
Week 3
Let's Get Started

This week we'll be looking at acids and bases. Why are they so destructive? Why are they so
helpful? We'll also look at the stuff that makes butter and bread so yummy.
The content from this week comes from Unit 2: The Foundations of Life (Objectives)

Outline
Lessons
Acids and Bases

Objective |
(1 part - 10 min.)
Carbohydrates
Objective |
(2 parts - 25 min.)
Lipids
Objective |
(2 parts - 25 min.)
Media
Carbohydrates Interactive Video activity (7 min.)
59
Lipids Interactive Video (8 min.)
Assignments
pH Simulation Lab (20 min.)
pH Simulation Lab Quiz (10 min.)

Vo c a b u l a r y
Please view this interactive vocabulary deck in your online course.
60
Week 3
Week 3
Acids and Bases1

Reading Section
The pH scale is an inverse logarithm and ranges from 0 to 14 (see figure below). Anything
below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is
alkaline, or basic. Extremes in pH in either direction from 7.0 are usually considered inhospitable
to life. The pH inside cells (6.8) and the pH in the blood (7.4) are both very close to neutral.
However, the environment in the stomach is highly acidic, with a pH of 1 to 2. So how do the
cells of the stomach survive in such an acidic environment? How do they homeostatically
maintain the near-neutral pH inside them? The answer is that they cannot do it and are
constantly dying. New stomach cells are constantly produced to replace dead ones, which are
digested by the stomach acids. It is estimated that the lining of the human stomach is
completely replaced every seven to ten days.
The pH scale measures the concentration of hydrogen ions (H+) in a

solution.
Credit: Photo
(https://commons.wikimedia.org/wiki/File:PH_Scale.svg) by Edward
Stevens via Wikimedia Commons.CC BY 3.0
61

Self-Check
References
62
Week 3
Week 3
Carbohydrates, Part 11

Reading Section
Most people are familiar with carbohydrates, one type of macromolecule, especially when it
comes to what we eat. To lose weight, some individuals adhere to “low-carb” diets. Athletes, in
contrast, often “carb-load” before important competitions to ensure that they have enough
energy to compete at a high level. Carbohydrates are, in fact, an essential part of our diet;
grains, fruits, and vegetables are all natural sources of carbohydrates. Carbohydrates provide
energy to the body, particularly through glucose, a simple sugar that is a component
of starch and an ingredient in many staple foods. Carbohydrates also have other important
functions in humans, animals, and plants.
Molecular Structures
Carbohydrates can be represented by the stoichiometric formula (CH2O)n, where n is the
number of carbons in the molecule. In other words, the ratio of carbon to hydrogen to oxygen is
1:2:1 in carbohydrate molecules. This formula also explains the origin of the term
“carbohydrate”: the components are carbon (“carbo”) and the components of water (“hydrate”).
Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and
polysaccharides.
Monosaccharides
Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars, the most common of
which is glucose. In monosaccharides, the number of carbons usually ranges from three to
seven. Most monosaccharide names end with the suffix -ose. If the sugar has an aldehyde
group (the functional group with the structure R-CHO), it is known as an aldose, and if it has a
ketone group (the functional group with the structure RC(=O)R'), it is known as a ketose.
Depending on the number of carbons in the sugar, they also may be known as trioses (three
carbons), pentoses (five carbons), or hexoses (six carbons).
63
Monosaccharides are classified based on the position of their carbonyl group and the number of
carbons in the backbone. Aldoses have a carbonyl group (indicated in green) at the end of the carbon
chain, and ketoses have a carbonyl group in the middle of the carbon chain. Trioses, pentoses, and
hexoses have three, five, and six carbon backbones, respectively. OpenStax CNX, CC BY 4.0
The chemical formula for glucose is C6H12O6. In humans, glucose is an important source of
energy. During cellular respiration, energy is released from glucose, and that energy is used to
help make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and
water, and glucose in turn is used for energy requirements for the plant. Excess glucose is often
stored as starch that is catabolized (the breakdown of larger molecules by cells) by humans and
other animals that feed on plants.
Galactose (part of lactose, or milk sugar) and fructose (found in sucrose, in fruit) are other
common monosaccharides. Although glucose, galactose, and fructose all have the same
chemical formula (C6H12O6), they differ structurally and chemically (and are known as isomers)
64
Week 3
because of the different arrangement of functional groups around the asymmetric carbon; all of
these monosaccharides have more than one asymmetric carbon.
Glucose, galactose, and fructose are isomeric monosaccharides (hexoses), meaning they have
the same chemical formula but have slightly different structures. Glucose and galactose are
aldoses, and fructose is a ketose.
Monosaccharides can exist as a linear chain or as ring-shaped molecules; in aqueous solutions

they are usually found in ring forms (see figure below). Glucose in a ring form can have two
different arrangements of the hydroxyl group (OH) around the anomeric carbon (carbon 1 that
becomes asymmetric in the process of ring formation). If the hydroxyl group is below carbon
number 1 in the sugar, it is said to be in the alpha (α) position, and if it is above the plane, it is
said to be in the beta (β) position.
Five and six carbon monosaccharides exist in equilibrium between linear and ring
forms. When the ring forms, the side chain it closes on is locked into an α or β
position. Fructose and ribose also form rings,
although they form five-membered rings as opposed to the six-
membered ring of glucose.
65
Disaccharides
Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction
(also known as a condensation reaction or dehydration synthesis). During this process, the
hydroxyl group of one monosaccharide combines with the hydrogen of another
monosaccharide, releasing a molecule of water and forming a covalent bond. A covalent bond
formed between a carbohydrate molecule and another molecule (in this case, between two
monosaccharides) is known as a glycosidic bond. Glycosidic bonds (also called glycosidic
linkages) can be of the alpha or the beta type.
Sucrose is formed when a monomer of glucose and a monomer of fructose are

joined in a dehydration reaction to form a glycosidic bond.
In the process, a water molecule is lost. By convention, the carbon atoms in a
monosaccharide are numbered from the terminal carbon
closest to the carbonyl group. In sucrose, a glycosidic linkage is
formed between carbon 1 in glucose and carbon 2 in fructose.

Common disaccharides include lactose, maltose, and sucrose. Lactose is a disaccharide

consisting of the monomers glucose and galactose. It is found naturally in milk. Maltose, or malt
sugar, is a disaccharide formed by a dehydration reaction between two glucose molecules. The
most common disaccharide is sucrose, or table sugar, which is composed of the monomers
glucose and fructose.
66
Week 3
Common disaccharides include maltose (grain sugar),

lactose (milk sugar), and sucrose (table sugar).

Self-Check
References
1. “3.2: Carbohydrates
(https://cnx.org/contents/[email protected]:c7OsVIEc@7/Carbohydrates) ,” OpenStax
CNX, CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/deed.en) .
67
Week 3
Carbohydrates, Part 21

Reading Section
Polysaccharides
A long chain of monosaccharides linked by glycosidic bonds is known as
a polysaccharide (poly- = “many”). The chain may be branched or unbranched, and it may
contain different types of monosaccharides. The molecular weight may be 100,000 daltons or
more depending on the number of monomers joined. Starch, glycogen, cellulose, and chitin are
primary examples of polysaccharides.
Starch is the stored form of sugars in plants and is made up of a mixture of amylose and
amylopectin (both polymers of glucose). Plants are able to synthesize glucose, and the excess
glucose, beyond the plant’s immediate energy needs, is stored as starch in different plant parts,
including roots and seeds. The starch in the seeds provides food for the embryo as it
germinates and can also act as a source of food for humans and animals. The starch that is
consumed by humans is broken down by enzymes, such as salivary amylases, into smaller
molecules, such as maltose and glucose. The cells can then absorb the glucose.
Starch is made up of glucose monomers that are joined by α 1-4 or α 1-6 glycosidic bonds. The
numbers 1-4 and 1-6 refer to the carbon number of the two residues that have joined to form the
bond. Amylose is starch formed by unbranched chains of glucose monomers (only α 1-4
linkages), whereas amylopectin is a branched polysaccharide (α 1-6 linkages at the branch
points).
68
Week 3
Amylose and amylopectin are two different forms of starch. Amylose is composed of
unbranched chains of glucose monomers connected by α 1,4 glycosidic linkages.
Amylopectin is composed of branched chains of glucose monomers connected by α
1,4 and α 1,6 glycosidic linkages. Because of the way the subunits are joined, the
glucose chains have a helical structure. Glycogen (not shown) is similar in structure
to amylopectin but more highly branched.
Glycogen is the storage form of glucose in humans and other vertebrates and is made up of
monomers of glucose. Glycogen is the animal equivalent of starch and is a highly branched
molecule usually stored in liver and muscle cells. Whenever blood glucose levels decrease,
glycogen is broken down to release glucose in a process known as glycogenolysis.
Cellulose is the most abundant natural biopolymer. The cell wall of plants is mostly made of
cellulose; this provides structural support to the cell. Wood and paper are mostly cellulosic in
nature. Cellulose is made up of glucose monomers that are linked by β 1-4 glycosidic bonds.
69
In cellulose, glucose monomers are linked in unbranched chains

by β 1-4 glycosidic linkages. Because of the way the glucose subunits
are joined, every glucose monomer is flipped relative to the next one
resulting in a linear, fibrous structure.
Every other glucose monomer in cellulose is flipped over, and the monomers are packed tightly
as extended long chains. This gives cellulose its rigidity and high tensile strength—which is so
important to plant cells. While the β 1-4 linkage cannot be broken down by human digestive
enzymes, herbivores such as cows, koalas, and buffalos are able, with the help of the
specialized flora in their stomach, to digest plant material that is rich in cellulose and use it as a
food source. In these animals, certain species of bacteria and protists reside in the rumen (part
of the digestive system of herbivores) and secrete the enzyme cellulase. The appendix of
grazing animals also contains bacteria that digest cellulose, giving it an important role in the
digestive systems of ruminants. Cellulases can break down cellulose into glucose monomers
that can be used as an energy source by the animal. Termites are also able to break down
cellulose because of the presence of other organisms in their bodies that secrete cellulases.
Insects have a hard outer exoskeleton made of chitin, a type of

polysaccharide.
Photo (https://commons.wikimedia.org/wiki/File:Louise_Docker_-
_Lift_Off-_Best_Viewed_Large_(by).jpg) by Louise Docker
(https://www.flickr.com/people/14516334@N00) via Wikimedia
Commons. CC BY 2.0 (https://creativecommons.org/licenses/by/2.0/)
.
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Week 3
Carbohydrates serve various functions in different animals. Arthropods (insects, crustaceans,

and others) have an outer skeleton, called the exoskeleton, which protects their internal body
parts. This exoskeleton is made of the biological macromolecule chitin, which is a
polysaccharide-containing nitrogen. It is made of repeating units of N-acetyl-β-d-glucosamine, a
modified sugar. Chitin is also a major component of fungal cell walls; fungi are neither animals
nor plants and form a kingdom of their own in the domain Eukarya.

Self-Check
References
1. “3.2: Carbohydrates
(https://cnx.org/contents/[email protected]:c7OsVIEc@7/Carbohydrates) ,” OpenStax
71
Week 3
Lipids, Part 11

Reading Section
Hydrophobic lipids in the fur of aquatic mammals, such as this river

otter, protect them from the elements.
Photo (https://www.flickr.com/photos/kretyen/2971079375) by Ken
Bosma (https://www.flickr.com/photos/kretyen/) via Flickr. CC BY
2.0 (https://creativecommons.org/licenses/by/2.0/) .
Lipids include a diverse group of compounds that are largely nonpolar in nature. This is
because they are hydrocarbons that include mostly nonpolar carbon–carbon or carbon–
hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”), or insoluble in water.
Lipids perform many different functions in a cell. Cells store energy for long-term use in the form
of fats. Lipids also provide insulation from the environment for plants and animals. For example,
they help keep aquatic birds and mammals dry when forming a protective layer over fur or
feathers because of their water-repellant hydrophobic nature. Lipids are also the building blocks
of many hormones and are an important constituent of all cellular membranes. Lipids include
fats, oils, waxes, phospholipids, and steroids.
Fats and Oils

A fat molecule consists of two main components—glycerol and fatty acids. Glycerol is an
organic compound (alcohol) with three carbons, five hydrogens, and three hydroxyl (OH)
groups. Fatty acids have a long chain of hydrocarbons to which a carboxyl group is attached,
hence the name “fatty acid.” The number of carbons in the fatty acid may range from 4 to 36;
most common are those containing 12–18 carbons. In a fat molecule, the fatty acids are
attached to each of the three carbons of the glycerol molecule with an ester bond through an
oxygen atom.
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Week 3
Triacylglycerol is formed by the joining of three fatty acids to a glycerol backbone in

a dehydration reaction. Three molecules of water are released in the process.

During this ester bond formation, three water molecules are released. The three fatty acids in
the triacylglycerol may be similar or dissimilar. Fats are also
called triacylglycerols or triglycerides because of their chemical structure. Some fatty acids
have common names that specify their origin. For example, palmitic acid, a saturated fatty
acid, is derived from the palm tree. Arachidic acid is derived from Arachis hypogea, the
scientific name for groundnuts or peanuts.
Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there are only single bonds
between neighboring carbons in the hydrocarbon chain, the fatty acid is said to be saturated.
Saturated fatty acids are saturated with hydrogen; in other words, the number of hydrogen
atoms attached to the carbon skeleton is maximized. Stearic acid is an example of a saturated
fatty acid.
Stearic acid is a common saturated fatty acid.

73
When the hydrocarbon chain contains a double bond, the fatty acid is said to be unsaturated.
Oleic acid is an example of an unsaturated fatty acid.
Oleic acid is a common unsaturated fatty acid.

Most unsaturated fats are liquid at room temperature and are called oils. If there is one double
bond in the molecule, then it is known as a monounsaturated fat (e.g., olive oil), and if there is
more than one double bond, then it is known as a polyunsaturated fat (e.g., canola oil).
When a fatty acid has no double bonds, it is known as a saturated fatty acid because no more
hydrogen may be added to the carbon atoms of the chain. A fat may contain similar or different
fatty acids attached to glycerol. Long straight fatty acids with single bonds tend to get packed
tightly and are solid at room temperature. Animal fats with stearic acid and palmitic acid
(common in meat) and the fat with butyric acid (common in butter) are examples of saturated
fats. Mammals store fats in specialized cells called adipocytes, where globules of fat occupy
most of the cell’s volume. In plants, fat or oil is stored in many seeds and is used as a source of
energy during seedling development. Unsaturated fats or oils are usually of plant origin and
contain cis unsaturated fatty acids. Cis and trans indicate the configuration of the molecule
around the double bond. If hydrogens are present in the same plane, it is referred to as a cis fat;
if the hydrogen atoms are on two different planes, it is referred to as a trans fat. The cis double
bond causes a bend or a “kink” that prevents the fatty acids from packing tightly, keeping them
liquid at room temperature. Olive oil, corn oil, canola oil, and cod liver oil are examples of
unsaturated fats. Unsaturated fats help to lower blood cholesterol levels whereas saturated fats
contribute to plaque formation in the arteries.
Saturated fatty acids have hydrocarbon chains

connected by single bonds only. Unsaturated
fatty acids have one or more double bonds.
Each double bond may be in a cis or trans
configuration. In the cis configuration, both
hydrogens are on the same side of the
hydrocarbon chain. In the trans configuration,
the hydrogens are on opposite sides. A cis
double bond causes a kink in the chain.

(https://creativecommons.org/licenses/by/4.0/
deed.en)
74
Week 3
Tr a n s F a t s
In the food industry, oils are artificially hydrogenated to make them semi-solid and of a
consistency desirable for many processed food products. Simply speaking, hydrogen gas is
bubbled through oils to solidify them. During this hydrogenation process, double bonds of
the cis- conformation in the hydrocarbon chain may be converted to double bonds in the trans-
conformation.
Margarine, some types of peanut butter, and shortening are examples of artificially
hydrogenated trans fats. Recent studies have shown that an increase in trans fats in the human
diet may lead to an increase in levels of low-density lipoproteins (LDL), or “bad” cholesterol,
which in turn may lead to plaque deposition in the arteries, resulting in heart disease. Many fast
food restaurants have recently banned the use of trans fats, and food labels are required to
display the trans fat content.
Omega Fatty Acids

Essential fatty acids are fatty acids required but not synthesized by the human body.
Consequently, they have to be supplemented through ingestion via the diet. Omega-3 fatty
acids fall into this category and are one of only two known for humans (the other being omega-6
fatty acid). These are polyunsaturated fatty acids and are called omega-3 because the third
carbon from the end of the hydrocarbon chain is connected to its neighboring carbon by a
double bond.
Alpha-linolenic acid is an example of an omega-3 fatty acid. It has three cis

double bonds and, as a result, a curved shape. For clarity, the carbons are not
shown. Each singly bonded carbon has two hydrogens associated with it, also
not shown.
The farthest carbon away from the carboxyl group is numbered as the omega (ω) carbon, and if
the double bond is between the third and fourth carbon from that end, it is known as an omega-3
fatty acid. Nutritionally important because the body does not make them, omega-3 fatty acids
include alpha-linoleic acid (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid
(DHA), all of which are polyunsaturated. Salmon, trout, and tuna are good sources of omega-3
75
fatty acids. Research indicates that omega-3 fatty acids reduce the risk of sudden death from
heart attacks, reduce triglycerides in the blood, lower blood pressure, and prevent thrombosis by
inhibiting blood clotting. They also reduce inflammation, and may help reduce the risk of some
cancers in animals.
Like carbohydrates, fats have received a lot of bad publicity. It is true that eating an excess of
fried foods and other “fatty” foods leads to weight gain. However, fats do have important
functions. Many vitamins are fat soluble, and fats serve as a long-term storage form of fatty
acids: a source of energy. They also provide insulation for the body. Therefore, “healthy” fats in
moderate amounts should be consumed on a regular basis.

Self-Check
References
1. “Chapter 3.3: Lipids (https://cnx.org/contents/[email protected]:I_8zQ2kk@9/Lipids) ,”
76
Week 3
Week 3
Lipids, Part 21

Reading Section
Waxes
Wax covers the feathers of some aquatic birds and the leaf surfaces of some plants. Because of
the hydrophobic nature of waxes, they prevent water from sticking on the surface. Waxes are
made up of long fatty acid chains esterified to long-chain alcohols.
Waxy coverings on some leaves are made of lipids. Roger Griffith,

Highclere Holly, Wikimedia Commons
(http://commons.wikimedia.org) , Public Domain
Phospholipids
Phospholipids are major constituents of the plasma membrane, the outermost layer of animal
cells. Like fats, they are composed of fatty acid chains attached to a glycerol or sphingosine
backbone. Instead of three fatty acids attached as in triglycerides, however, there are two fatty
acids forming diacylglycerol, and the third carbon of the glycerol backbone is occupied by a
modified phosphate group. A phosphate group alone attached to a diaglycerol does not qualify
as a phospholipid; it is phosphatidate (diacylglycerol 3-phosphate), the precursor of
phospholipids. The phosphate group is modified by an alcohol. Phosphatidylcholine and
phosphatidylserine are two important phospholipids that are found in plasma membranes.
77
A phospholipid is a molecule with two fatty acids and a modified phosphate group
attached to a glycerol backbone. The phosphate may be modified by the addition of
charged or polar chemical groups. Two chemical groups that may modify the
phosphate, choline and serine, are shown here. Both choline and serine attach to the
phosphate group at the position labeled R via the hydroxyl group indicated in green.
A phospholipid is an amphipathic molecule, meaning it has a hydrophobic and a hydrophilic

part. The fatty acid chains are hydrophobic and cannot interact with water, whereas the
phosphate-containing group is hydrophilic and interacts with water.
The phospholipid bilayer is the major component of all cellular membranes. The
hydrophilic head groups of the phospholipids face the aqueous solution. The
hydrophobic tails are sequestered in the middle of the bilayer.
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Week 3
The head is the hydrophilic part, and the tail contains the hydrophobic fatty acids. In a
membrane, a bilayer of phospholipids forms the matrix of the structure, the fatty acid tails of
phospholipids face inside, away from water, whereas the phosphate group faces the outside,
aqueous side.
Phospholipids are responsible for the dynamic nature of the plasma membrane. If a drop of
phospholipids is placed in water, it spontaneously forms a structure known as a micelle, where
the hydrophilic phosphate heads face the outside and the fatty acids face the interior of this
structure.
Steroids
Unlike the phospholipids and fats discussed earlier, steroids have a fused ring structure.
Although they do not resemble the other lipids, they are grouped with them because they are
also hydrophobic and insoluble in water. All steroids have four linked carbon rings and several of
them, like cholesterol, have a short tail. Many steroids also have the –OH functional group,
which puts them in the alcohol classification (sterols).
Steroids such as cholesterol and cortisol are composed of four fused hydrocarbon rings.

79
Cholesterol is the most common steroid. Cholesterol is mainly synthesized in the liver and is the
precursor to many steroid hormones such as testosterone and estradiol, which are secreted by
the gonads and endocrine glands. It is also the precursor to Vitamin D. Cholesterol is also the
precursor of bile salts, which help in the emulsification of fats and their subsequent absorption
by cells. Although cholesterol is often spoken of in negative terms by lay people, it is necessary
for proper functioning of the body. It is a component of the plasma membrane of animal cells
and is found within the phospholipid bilayer. Being the outermost structure in animal cells, the
plasma membrane is responsible for the transport of materials and cellular recognition and it is
involved in cell-to-cell communication.
Section Summary
Lipids are a class of macromolecules that are nonpolar and hydrophobic in nature. Major types
include fats and oils, waxes, phospholipids, and steroids. Fats are a stored form of energy and
are also known as triacylglycerols or triglycerides. Fats are made up of fatty acids and either
glycerol or sphingosine. Fatty acids may be unsaturated or saturated, depending on the
presence or absence of double bonds in the hydrocarbon chain. If only single bonds are
present, they are known as saturated fatty acids. Unsaturated fatty acids may have one or more
double bonds in the hydrocarbon chain. Phospholipids make up the matrix of membranes. They
have a glycerol or sphingosine backbone to which two fatty acid chains and a phosphate-
containing group are attached. Steroids are another class of lipids. Their basic structure has four
fused carbon rings. Cholesterol is a type of steroid and is an important constituent of the plasma
membrane, where it helps to maintain the fluid nature of the membrane. It is also the precursor
of steroid hormones such as testosterone.

Self-Check
References
1. “3.3: Lipids (https://cnx.org/contents/[email protected]:I_8zQ2kk@9/Lipids) .”
80
Week 4
Week 4
Let's Get Started

Proteins and nucleic acids are the topics you'll be covering this week. Proteins are probably
familiar to you (since they are one of the building blocks of muscles). However, you probably
didn't know they do most of the work in cells and are required for the structure, function, and
regulation of the body's tissues and organs. Nucleic acids (DNA, RNA) store and express
genetic information. After this week, you're going to take delight in knowing that everything you
do starts with tiny inter-cellular dynamos!

Outline
Lessons
Proteins
Objective |
(5 parts - 50 min.)
Nucleic Acids
Objective |
(3 parts - 30 min.)
Media
Biomolecules video (1 min.)
81
Proteins Interactive Video (5 min.)
Nucleic Acids Interactive Video (10 min.)
Assignments
Proteins Deep Dive Assignment (30 min.)

Vo c a b u l a r y
82
Week 4
Week 4
Proteins1

Reading Section
(You only need to watch 4:09–5:13.)
Proteins are among the most abundant organic molecules in living systems and have the most
diverse range of functions of all macromolecules. Proteins may be structural, regulatory,
contractile, or protective; they may serve in transport, storage, or membranes; or they may be
toxins or enzymes. Each cell in a living system may contain thousands of proteins, each with a
unique function. Their structures, like their functions, vary greatly. They are all, however,
polymers of amino acids, arranged in a linear sequence.
Types and Functions of Proteins

Enzymes, which are produced by living cells, are catalysts in biochemical reactions (like
digestion) and are usually complex or conjugated proteins. Each enzyme is specific for the
substrate (a reactant that binds to an enzyme) it acts on. The enzyme may help in breakdown,
rearrangement, or synthesis reactions. Enzymes that break down their substrates are called
catabolic enzymes, enzymes that build more complex molecules from their substrates are called
anabolic enzymes, and enzymes that affect the rate of reaction are called catalytic enzymes. It
should be noted that all enzymes increase the rate of reaction and, therefore, are considered to
be organic catalysts. An example of an enzyme is salivary amylase, which hydrolyzes its
substrate amylose, a component of starch.
Hormones are chemical-signaling molecules, usually small proteins or steroids, secreted by

endocrine cells that act to control or regulate specific physiological processes, including growth,
development, metabolism, and reproduction. For example, insulin is a protein hormone that
helps to regulate the blood glucose level. The primary types and functions of proteins are listed
in the table below.
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Protein Types and Functions

Type Examples Functions
Digestive Amylase, lipase, pepsin, Help in digestion of food by catabolizing nutrients
Enzymes trypsin into monomeric units
Carry substances in the blood or lymph
Transport Hemoglobin, albumin
throughout the body
Construct different structures, like the
Structural Actin, tubulin, keratin
cytoskeleton
Hormones Insulin, thyroxine Coordinate the activity of different body systems
Defense Immunoglobulins Protect the body from foreign pathogens
Contractile Actin, myosin Effect muscle contraction
Legume storage proteins, egg Provide nourishment in early development of the
Storage
white (albumin) embryo and the seedling
Proteins have different shapes and molecular weights; some proteins are globular in shape
whereas others are fibrous in nature. For example, hemoglobin is a globular protein, but
collagen, found in our skin, is a fibrous protein. Protein shape is critical to its function, and this
shape is maintained by many different types of chemical bonds. Changes in temperature, pH,
and exposure to chemicals may lead to permanent changes in the shape of the protein, leading
to loss of function, known as denaturation. All proteins are made up of different arrangements
of the same 20 types of amino acids.

Self-Check
References
1. “3.4: Proteins (https://cnx.org/contents/[email protected]:2zzm1QG9@8/Proteins) ,”
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Week 4
Amino Acids1

Reading Section
Amino acids are the monomers that make up proteins. Each amino acid has the same
fundamental structure, which consists of a central carbon atom, also known as the alpha (α)
carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom.
Every amino acid also has another atom or group of atoms bonded to the central atom known
as the R group.
Amino acids have a central asymmetric carbon to which an amino group, a carboxyl
group, a hydrogen atom, and a side chain (R group) are attached.
OpenStax Biology, CC BY 4.0
The name "amino acid" is derived from the fact that they contain both amino group and
carboxyl-acid-group in their basic structure. As mentioned, there are 20 amino acids present in
proteins. Nine of these are considered essential amino acids in humans because the human
body cannot produce them and they are obtained from the diet. For each amino acid, the R
group (or side chain) is different.
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There are 20 common amino acids commonly found in proteins, each with a
different R group (variant group) that determines its chemical nature.

The chemical nature of the side chain determines the nature of the amino acid (that is, whether
it is acidic, basic, polar, or nonpolar). For example, the amino acid glycine has a hydrogen atom
as the R group. Amino acids such as valine, methionine, and alanine are nonpolar or
hydrophobic in nature, while amino acids such as serine, threonine, and cysteine are polar and
have hydrophilic side chains. The side chains of lysine and arginine are positively charged, and
therefore these amino acids are also known as basic amino acids. Proline has an R group that
is linked to the amino group, forming a ring-like structure. Proline is an exception to the standard
structure of an amino acid since its amino group is not separate from the side chain.
Amino acids are represented by a single upper case letter or a three-letter abbreviation. For
example, valine is known by the letter V or the three-letter symbol val. Just as some fatty acids
are essential to a diet, some amino acids are necessary as well. They are known as essential
amino acids, and in humans they include isoleucine, leucine, and cysteine. Essential amino
acids refer to those necessary for construction of proteins in the body, although not produced by
the body; which amino acids are essential varies from organism to organism.
The sequence and the number of amino acids ultimately determine the protein's shape, size,
and function. Each amino acid is attached to another amino acid by a covalent bond, known as
a peptide bond, which is formed by a dehydration reaction. The carboxyl group of one amino
acid and the amino group of the incoming amino acid combine, releasing a molecule of water.
The resulting bond is the peptide bond.
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Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of

one amino acid is linked to the amino group of the incoming amino acid. In the
process, a molecule of water is released.
The products formed by such linkages are called peptides. As more amino acids join to this
growing chain, the resulting chain is known as a polypeptide. Each polypeptide has a free amino
group at one end. This end is called the N terminal, or the amino terminal, and the other end has
a free carboxyl group, also known as the C or carboxyl terminal. While the terms polypeptide
and protein are sometimes used interchangeably, a polypeptide is technically a polymer of
amino acids, whereas the term protein is used for a polypeptide or polypeptides that have
combined together, often have bound non-peptide prosthetic groups, have a distinct shape, and
have a unique function. After protein synthesis (translation), most proteins are modified. These
are known as post-translational modifications. They may undergo cleavage, phosphorylation, or
may require the addition of other chemical groups. Only after these modifications is the protein
completely functional.
Here's a video to help clarify what you have learned about amino acids.

Self-Check
References
1. “3.4: Proteins (https://cnx.org/contents/[email protected]:2zzm1QG9@8/Proteins) ,”
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Week 4
Protein Structure1

Reading Section
As discussed earlier, the shape of a protein is critical to its function. For example, an enzyme
can bind to a specific substrate at a site known as the active site. If this active site is altered
because of local changes or changes in overall protein structure, the enzyme may be unable to
bind to the substrate. You should be aware that there are four levels of protein structure:
primary, secondary, tertiary, and quaternary. To understand how the protein gets its final shape
or conformation, we will discuss the first: primary structure.
Primary Structure
The unique sequence of amino acids in a polypeptide chain is its primary structure. For
example, the pancreatic hormone insulin has two polypeptide chains, A and B, and they are
linked together by disulfide bonds. The N terminal amino acid of the A chain is glycine, whereas
the C terminal amino acid is asparagine. The sequences of amino acids in the A and B chains
are unique to insulin.
Bovine serum insulin is a protein hormone made of two peptide chains, A (21 amino
acids long) and B (30 amino acids long). In each chain, primary structure is
indicated by three-letter abbreviations that represent the names of the amino acids
in the order they are present. The amino acid cysteine (cys) has a sulfhydryl (SH)
group as a side chain. Two sulfhydryl groups can react in the presence of oxygen to
form a disulfide (S-S) bond. Two disulfide bonds connect the A and B chains
together, and a third helps the A chain fold into the correctshape. Note that all
disulfide bonds are the same length, but are drawn different sizes for clarity.
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The unique sequence for every protein is ultimately determined by the gene encoding the
protein. A change in nucleotide sequence of the gene’s coding region may lead to a different
amino acid being added to the growing polypeptide chain, causing a change in protein structure
and function. In sickle cell anemia, the hemoglobin β chain has a single amino acid substitution,
causing a change in protein structure and function. Specifically, the amino acid glutamic acid is
substituted by valine in the β chain. What is most remarkable to consider is that a hemoglobin
molecule is made up of two alpha chains and two beta chains that each consist of about 150
amino acids. The molecule, therefore, has about 600 amino acids. The structural difference
between a normal hemoglobin molecule and a sickle cell molecule—which dramatically
decreases life expectancy—is a single amino acid of the 600. What is even more remarkable is
that those 600 amino acids are encoded by three nucleotides each, and the mutation is caused
by a single base change (point mutation), 1 in 1800 bases.
The beta chain of hemoglobin is 147 residues in length, yet a single amino acid substitution
leads to sickle cell anemia. In normal hemoglobin, the amino acid at position seven is
glutamate. In sickle cell hemoglobin, this glutamate is replaced by a valine.
Because of this change of one amino acid in the chain, hemoglobin molecules form long fibers
that distort the biconcave, or disc-shaped, red blood cells and assume a crescent or “sickle”
shape, which clogs arteries. This can lead to myriad serious health problems such as
breathlessness, dizziness, headaches, and abdominal pain for those affected by this disease.
In this blood smear, visualized at 535x magnification using bright field microscopy,
sickle cells are crescent shaped, while normal cells are disc-shaped.
Credit: modification of work (https://openstax.org/books/biology/pages/3-4-proteins)
by Ed Uthman
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
Self-Check
References
1. “3.4: Proteins (https://cnx.org/contents/[email protected]:2zzm1QG9@8/Proteins) .”
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Week 4
Nucleic Acids1

Reading Section
Nucleic acids are the most important macromolecules for the continuity of life. They carry the
genetic blueprint of a cell and carry instructions for the functioning of the cell.
DNA and RNA

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA). DNA is the genetic material found in all living organisms, ranging from single-celled
bacteria to multicellular mammals. It is found in the nucleus of eukaryotes and in the organelles,
chloroplasts, and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous
envelope.
The entire genetic content of a cell is known as its genome, and the study of genomes is
genomics. In eukaryotic cells but not in prokaryotes, DNA forms a complex with histone proteins
to form chromatin, the substance of eukaryotic chromosomes. A chromosome may contain tens
of thousands of genes. Many genes contain the information to make protein products; other
genes code for RNA products. DNA controls all of the cellular activities by turning the genes “on”
or “off.”
The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules
never leave the nucleus but instead use an intermediary to communicate with the rest of the
cell. This intermediary is the messenger RNA (mRNA). Other types of RNA—like rRNA, tRNA,
and microRNA—are involved in protein synthesis and its regulation.
DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with
each other to form a polynucleotide, DNA or RNA. Each nucleotide is made up of three
components: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group. Each
nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or
more phosphate groups.
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A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and one or more phosphate
groups. Carbon residues in the pentose are numbered 1′ through 5′ (the prime distinguishes these residues from
those in the base, which are numbered without using a prime notation). The base is attached to the 1′ position of
the ribose, and the phosphate is attached to the 5′ position. When a polynucleotide is formed, the 5′ phosphate of
the incoming nucleotide attaches to the 3′ hydroxyl group at the end of the growing chain. Two types of pentose are
found in nucleotides, deoxyribose (found in DNA) and ribose (found in RNA). Deoxyribose is similar in structure to
ribose, but it has an H instead of an OH at the 2′ position. Bases can be divided into two categories: purines and
pyrimidines. Purines have a double ring structure, and pyrimidines have a single ring.
OpenStax Biology, CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/) .
The nitrogenous bases, important components of nucleotides, are organic molecules and are so
named because they contain carbon and nitrogen. They are bases because they contain an
amino group that has the potential of binding an extra hydrogen, and thus, decreases the
hydrogen ion concentration in its environment, making it more basic. Each nucleotide in DNA
contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and
thymine (T).
Adenine and guanine are classified as purines. The primary structure of a purine is two carbon-
nitrogen rings. Cytosine, thymine, and uracil are classified as pyrimidines which have a single
carbon-nitrogen ring as their primary structure. Each of these basic carbon-nitrogen rings has
different functional groups attached to it. In molecular biology shorthand, the nitrogenous bases
are simply known by their symbols A, T, G, C, and U. DNA contains A, T, G, and C whereas
RNA contains A, U, G, and C.
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The pentose sugar in DNA is deoxyribose, and in RNA, the sugar is ribose. The difference
between the sugars is the presence of the hydroxyl group on the second carbon of the ribose
and hydrogen on the second carbon of the deoxyribose. The carbon atoms of the sugar
molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”). The phosphate residue
is attached to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′
carbon of the sugar of the next nucleotide, which forms a 5′–3′ phosphodiester linkage. The
phosphodiester linkage is not formed by simple dehydration reaction like the other linkages
connecting monomers in macromolecules: its formation involves the removal of two phosphate
groups. A polynucleotide may have thousands of such phosphodiester linkages.

Self-Check
References
1 “3.5: Nucleic Acids (https://cnx.org/contents/[email protected]:yxeAKc4X@9/Nucleic-

Acids) ,” OpenStax CNX, CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/deed.en)
.
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Week 5
Week 5
Let's Get Started

This week concludes the Foundations of Life unit. But, your unit quiz won't be the highlight of the
week; your first scientific thinking assignment series is coming up. This week's assignment is
about observation and inference. You might infer from this that it's time for some biological
application.

Outline
Lessons
Enzymes
Objective
(4 parts - 55 min.)
Fact, Inference, and Classification

Objective
(1 part - 40 min.)
Media
Enzymes Interactive Video (5 min.)
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Assignments
Enzyme Potato Lab (25 min.)
Enzyme Potato Lab Quiz (5 min.)
Unit 2 Quiz (25 min.)
Reflection Questions for Experiences 1 (20 min.)
Observations and Inference Activity (40 min.)

Vo c a b u l a r y
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Week 5
Week 5
Enzymes1

Reading Section
A substance that helps a chemical reaction to occur is a catalyst, and the special molecules that
catalyze biochemical reactions are called enzymes. Almost all enzymes are proteins, made up
of chains of amino acids, and they perform the critical task of lowering the activation energies of
chemical reactions inside the cell. Enzymes do this by binding to the reactant molecules, and
holding them in such a way as to make the chemical bond-breaking and bond-forming
processes take place more readily. It is important to remember that enzymes don’t change the
∆G of a reaction. In other words, they don’t change whether a reaction is exergonic
(spontaneous) or endergonic. This is because they don’t change the free energy of the
reactants or products. They only reduce the activation energy required to reach the transition
state.
Enzymes lower the activation energy of the reaction but do not change the
free energy of the reaction.

Enzyme Active Site and Substrate Specificity

The chemical reactants to which an enzyme binds are the enzyme’s substrates. There may be
one or more substrates, depending on the particular chemical reaction. In some reactions, a
single-reactant substrate is broken down into multiple products. In others, two substrates may
come together to create one larger molecule. Two reactants might also enter a reaction, both
become modified, and leave the reaction as two products. The location within the enzyme where
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the substrate binds is called the enzyme’s active site. The active site is where the “action”
happens, so to speak. Since enzymes are proteins, there is a unique combination of amino acid
residues (also called side chains, or R groups) within the active site. Each residue is
characterized by different properties. Residues can be large or small, weakly acidic or basic,
hydrophilic or hydrophobic, positively or negatively charged, or neutral. The unique combination
of amino acid residues, their positions, sequences, structures, and properties, creates a very
specific chemical environment within the active site. This specific environment is suited to bind,
albeit briefly, to a specific chemical substrate (or substrates). Due to this jigsaw puzzle-like match
between an enzyme and its substrates (which adapts to find the best fit between the transition
state and the active site), enzymes are known for their specificity. The “best fit” results from the
shape and the amino acid functional group’s attraction to the substrate. There is a specifically
matched enzyme for each substrate and, thus, for each chemical reaction; however, there is
flexibility as well.
The fact that active sites are so perfectly suited to provide specific environmental conditions also
means that they are subject to influences by the local environment. It is true that increasing the
environmental temperature generally increases reaction rates, enzyme-catalyzed or otherwise.
However, increasing or decreasing the temperature outside of an optimal range can affect
chemical bonds within the active site in such a way that they are less well suited to bind
substrates. High temperatures will eventually cause enzymes, like other biological molecules, to
denature, a process that changes the natural properties of a substance. Likewise, the pH of the
local environment can also affect enzyme function. Active site amino acid residues have their
own acidic or basic properties that are optimal for catalysis. These residues are sensitive to
changes in pH that can impair the way substrate molecules bind. Enzymes are suited to function
best within a certain pH range, and, as with temperature, extreme pH values (acidic or basic) of
the environment can cause enzymes to denature.
Induced Fit and Enzyme Function

For many years, scientists thought that enzyme-substrate binding took place in a simple “lock-
and-key” fashion. This model asserted that the enzyme and substrate fit together perfectly in
one instantaneous step. However, current research supports a more refined view
called induced fit. The induced-fit model expands upon the lock-and-key model by describing a
more dynamic interaction between enzyme and substrate. As the enzyme and substrate come
together, their interaction causes a mild shift in the enzyme’s structure that confirms an ideal
binding arrangement between the enzyme and the transition state of the substrate. This ideal
binding maximizes the enzyme’s ability to catalyze its reaction.
When an enzyme binds its substrate, an enzyme-substrate complex is formed. This complex
lowers the activation energy of the reaction and promotes its rapid progression in one of many
ways. On a basic level, enzymes promote chemical reactions that involve more than one
substrate by bringing the substrates together in an optimal orientation. The appropriate region
(atoms and bonds) of one molecule is juxtaposed to the appropriate region of the other molecule
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with which it must react. Another way in which enzymes promote the reaction of their substrates
is by creating an optimal environment within the active site for the reaction to occur. Certain
chemical reactions might proceed best in a slightly acidic or non-polar environment. The
chemical properties that emerge from the particular arrangement of amino acid residues within
an active site create the perfect environment for an enzyme’s specific substrates to react.
You’ve learned that the activation energy required for many reactions includes the energy
involved in manipulating or slightly contorting chemical bonds so that they can easily break and
allow others to reform. Enzymatic action can aid this process. The enzyme-substrate complex
can lower the activation energy by contorting substrate molecules in such a way as to facilitate
bond-breaking, helping to reach the transition state. Finally, enzymes can also lower activation
energies by taking part in the chemical reaction itself. The amino acid residues can provide
certain ions or chemical groups that actually form covalent bonds with substrate molecules as a
necessary step of the reaction process. In these cases, it is important to remember that the
enzyme will always return to its original state at the completion of the reaction. One of the
hallmark properties of enzymes is that they remain ultimately unchanged by the reactions they
catalyze. After an enzyme is done catalyzing a reaction, it releases its product(s).
According to the induced-fit model, both enzyme and substrate undergo dynamic
conformational changes upon binding. The enzyme contorts the substrate into its
transition state, thereby increasing the rate of the reaction.


Self-Check
References
1. “6.5: Enzymes (https://cnx.org/contents/[email protected]:MnC6GuJi@7/Enzymes) ,”
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Week 6
Week 6
Let's Get Started

Now that we have covered the elements that come together to make life, it's time to take that
information and see how it comes together in living cells. Our understanding cells is a recent
phenomena in the history of the world and there is still much we don't know. What you will be
learning about cells is just a starter to a world with still much to explore.
The content from this week comes from Unit 3: The Cell (Objectives)

Outline
Lessons
Classification
Objective |
(1 part - 30 min.)
Unit 3
Cell Theory
Objective |
(3 parts - 37 min.)
Cell Organelles
Objective |
(3 parts - 40 min.)
101
Media
Cell Theory Interactive Video (7 min.)
Assignments
Classification (30 min.)
Cell Organelles Activity (5 min.)

Vo c a b u l a r y
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Week 6
Cell Theory, Part 1

Reading Section
Robert Hooke, 1605–1703.

Rita Greer, Portrait of Robert Hooke, 2004, Art, 503 x 600 pixels, wikimedia.org,
Wikimedia Commons (https://commons.wikimedia.org/wiki/
File:13_Portrait_of_Robert_Hooke. JPG)
In 1665 an English scientist named Robert Hooke looked at cork under a microscope. Hooke
saw thousands of chambers and called them cells. He gave the structures that name because
they reminded him of the cells, or small rooms, in a monastery. Around the same time, Antony
van Leeuwenhoek observed living cells and called them “animalcules.” We now know that all
cells are alive and that Hooke saw only the dead walls of the cork cells, but Hooke’s discovery
was important, and the term cells stuck. The discovery of cells began a long line of research. It
took another 174 years before the cell theory was formed.
German scientists Matthias Schleiden and Theodor Schwann first proposed the cell theory in
1839. Matthias Schleiden was the first person to state that plants were made of cells, due to his
discovery of plant cells using a microscope. Theodor Schwann was the first person to state that
animals were made of cells, also arriving at this conclusion with the use of a microscope. The
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cell theory became more formalized in 1855 when German researcher Rudolf Virchow extended
the principles of the theory. Virchow added the idea that new cells come from preexisting cells.
Combining all these ideas, the cell theory states the following:
1. All living things are made of cells.
2. Cells are the basic units of structure and function in living things.
3. All cells come from preexisting cells.
All Living Things Are Made of Cells

We know from unit 1 that one of the five characteristics of a living thing is that it is made from
cells. Now, as we review other characteristics of living things, ask yourself the following
question: would this characteristic be possible without cells? You might argue that these
characteristics could exist without cells, and there are certain situations where this is true.
However, we are about to learn that (in general) cells are fundamental to the characteristics of
living things.
Obtain and Use Energy
Because rocks are not made of cells, they cannot

collect or use energy like humans do when we eat
and exercise.
© BYU
Living things gain energy by eating or taking in energy from the sun (like plants when they
photosynthesize). To survive and function, living things must then use the energy they have
obtained. Obtaining and using energy is only possible with cells.
To see why this is true, let’s contrast this characteristic of living things against something that is
not living, and therefore has no cells, like a rock. I guess you could say that a rock obtains
energy when the sun makes the rock hot. But the rock has no system in place to capture that
heat energy and use it later for a different function: a rock isn’t going to use heat energy from the
sun to grow larger or to reproduce. Again, only living things are able to obtain and use energy.
This ability to store and change energy is possible because living things are made of cells.
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Respond to the Environment

Living things can respond to different situations because they are made of cells. Again, let’s
compare this characteristic with a rock. Obviously a rock does not have the ability to move away
from something that might cause it harm. If a rock “wanted” to be colder or hotter, it would not be
able to move to a location where its temperature would change, nor would the rock be able to
use its internal energy to heat or cool itself. In living things, however, cells create the ability to
initiate movement and respond to an environment.
Because rocks are not made of cells, they cannot respond to their environment like
living things can. Even trees can respond to their environment. For example, a tree
drops its leaves in the winter to conserve energy and then grows the leaves back
again each summer to take advantage of sunlight.
© BYU
Grow and Develop
Because rocks are not made of cells, they cannot grow and develop like this living plant.
© BYU
Because of cells, living things can grow and develop. Inside every cell there is a system that
controls the cell’s development. When a cell needs to grow, it sends out messages through this
system, which then causes cell growth to occur. A rock, on the other hand, can only change its
size when it is subject to environmental processes, like erosion. A rock cannot make these
changes by itself.
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Reproduce
Reproduction is controlled by a chemical message in cells. In some organisms, reproduction is
only possible when specific conditions are present.
Since a rock is not made of cells, it cannot reproduce. The only situation in which we might think
of a rock being able to reproduce would be if the earth shifted, causing the rock to break into
smaller pieces. But this isn’t really reproduction—you wouldn’t argue that by breaking a donut in
half you have created two donuts. You’ve simply broken a donut in half. I think we can agree
that only living things are able to reproduce, and that true reproduction is only possible with the
help of cells.
Because rocks are not made of cells, they cannot reproduce. Humans are made of
cells, and reproduction is an essential function of human life.
Photos in public domain.

Self-Check
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Week 6
Cell Theory, Part 2

Reading Section
A cell is the smallest structure that can still be considered living—it is a self-contained living unit.
Some organisms are called unicellular, which means that they are made up of only one cell.
Unicellular organisms include protists, bacteria, and some fungi.
In the future, we’ll learn about the different parts of a cell and the roles that each part plays. In
this lesson, though, you only need to understand where a cell fits in within the larger spectrum of
living and nonliving things. A cell is generally part of a larger living thing, and it is made of
nonliving things, called organelles. Let’s look at an example. Study the diagram below before
continuing on in your reading.
All living organisms are made of cells, and all cells are ultimately
made of atoms—however, atoms are not considered to be living.
© BYU
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One organ in your body that I am sure you are familiar with is your heart. The heart is found
between your lungs, behind your sternum, and slightly to the left in your chest cavity. The heart
is made up of many different kinds of tissue, including muscular tissue that allows it to contract,
or beat. The heart also contains nervous tissue, which allows it to receive and transmit electrical
impulses. These impulses are what cause it to contract. Tissues, like the muscle and nervous
tissues in your heart, are made of similar cells. This means that muscular tissue is made of
muscular cells, and nervous tissue is made of nervous cells.
Just as the different types of tissue allow your heart to perform its different functions, every cell
has different organelles that allow the cell to function. For the most part, all cells contain the
same basic set of organelles. Generally, cells have a cell membrane, nucleus, endoplasmic
reticulum, Golgi apparatus, and ribosomes. (Later in this unit, we will learn about each of these
organelles and how they function, so you don’t need to worry about the specific names of the
organelles at this point.)
Organelles are made of large molecules which are themselves composed of several atoms
hooked together. A molecule of water, for example, which is found in every part of a cell, is
made up of three atoms (two atoms of hydrogen and one atom of oxygen, H2O).
The human body is quite complex; it has many layers or levels of organization. In this hierarchy,
organ systems are one step above organs. This means that the heart is just one part of an
organ system, called the circulatory system. The function of the circulatory system is to transport
chemicals back and forth in the body. Besides the heart, the circulatory system also includes the
vessels (arteries, veins and capillaries) and blood. The circulatory system is just one of many
systems in the human body.
In contrast to the complexity of the human body, a unicellular organism is made up of only one
cell, which means that it contains only the four smallest levels in the hierarchy (a cell,
organelles, molecules, and atoms).
All Cells Come from Preexisting Cells

An idea that used to be accepted was known as spontaneous generation. An example of this
theory is that old, dirty clothing could lead to the development of mice. Today the idea of clothing
“giving birth” to mice sounds weird, but it made sense to the people who believed in the theory.
The problem with the theory of spontaneous generation is that according to the theory, a
nonliving thing (the clothing) had the ability to reproduce, and, not only could the clothing
reproduce, but it could create something that was very different structurally: a mouse made of
cells. As you know from the first unit, through the use of the scientific method, spontaneous
generation was eventually disproven. Today we know that a living cell can only come from
another living cell.
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Take a moment and think of all the cells that make up your body. Did you know that there are
over one million cells in just one drop of blood? So many cells make up your body that even
scientists have a hard time trying to estimate the total number of cells in the human body.
However, the general consensus for the number of cells in an average human body ranges from
10 trillion to 100 trillion. Regardless of these estimates, the important thing to know is that there
are a lot of cells in your body!
Where did all of these cells come from? From the cell theory we know that all cells come from
preexisting cells. Every human being, including you, started out as a fertilized egg, which is the
combination of an egg cell from a female and a sperm cell from a male. When these cells
combined, they made one new cell, so initially, you were only made of one cell. To get from
where you were then to where you are today, your cells have grown and divided over and over
again into many different cells. Each of your trillions of cells came from the division of another
cell. One cell split into two, and then those two cells split into four; eventually those four cells
became eight and so on.
As we continue to learn about cells, try to remember the three parts of the cell theory:
1. All living things are made from cells.
2. Cells are the basic units of structure of a living thing.
3. All cells come from preexisting cells.
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Self-Check
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Week 6
Cell Organelles

Reading Section
Cells are made up of a variety of different organelles that each have specific functions.
Sometimes organelles are simply called cell parts. You may remember from the previous lesson
that organelles are made up of molecules. In this part of the unit, we’ll look more closely at each
organelle, including its location, structure, and function. Keep in mind that not every cell is alike,
and therefore some cells do not have all of the following parts. We’ll discuss these differences in
cells later in the unit.
Animal cells (A) and plant cells (B) are similar. As you read through this lesson, you’ll be
able to identify some of the differences between animal cells and plant cells.
© BYU
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Cell Membrane
The cell membrane, or plasma membrane, is a layer of molecules that encapsulates and
encircles the cell. Every cell has a cell membrane. The function of the cell membrane is primarily
to regulate what enters and leaves the cell. If you were to compare a cell to a house, the cell
membrane would be the outer walls. The walls of a house are designed to separate what is in
the house from what is out of the house; however, a house does have doors, which allow certain
things to pass through the house. Similarly, the cell membrane also has entry points that allow
certain substances in and out of the cell.
Cell membrane.
© BYU
The cell membrane is actually composed of two identical layers that together are called a
bilayer. This bilayer is made of a lipid, or fat. The lipid bilayer is also embedded with proteins,
which allow different chemicals to pass in or out of the cell. You can think of the proteins as
doors. What kinds of things would need to get in or out of a cell? Cells need certain chemicals,
oxygen, food products, and messages from other cells in order to function correctly. Cells also
need to export waste products and messages. All these things enter and exit the cell through the
protein molecules. The doors, or membrane proteins, will not let just anything in or out of the
cell. In this process, I think of a cell as a secret clubhouse: you can knock on the door, but
unless you know the secret password, you will not be let in or out of the clubhouse.
Transportation in or out of a cell is accomplished with certain chemical markers that act like a
password to tell the membrane proteins in a cell, that a certain chemical or element is supposed
to pass through the cell membrane.
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Cell Wall
The cell wall is found mainly in plant cells. It is

hard, but porous, and gives the plant strength.
© BYU
In addition to the cell membrane, cell walls are found in plant, fungi, and protist cells but not in
animal cells. In fact, cell walls are one of the major differences between plant and animal cells.
The cell wall surrounds the cell membrane and is very porous. The pores allow chemicals to get
to the cell membrane where they can enter and leave the cell. The function of the cell wall is to
provide structural support. Cell walls are rigid and 100 times thicker than the plasma or cell
membrane. The cell wall helps to maintain the cell’s shape and protect the cell from damage.
Cell walls also help cells attach to one another. If you think of a tree, it doesn’t have a skeletal
system with bones that allow it to stand up against gravity. By providing rigid strength and
bonding, the collective rigidity of cell walls in a plant creates strong structures like those evident
in trees.
Nucleus
The nucleus is often considered the brain of the cell because it contains
DNA, which is the blueprint for how an organism looks and functions.
© BYU
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Week 6
The nucleus is frequently called the brain of the cell. As the name suggests, the nucleus is
typically found in the center of the cell and is round in shape. It is called the brain because it
contains deoxyribonucleic acid (DNA), which is the blueprint for the organism that the cell
belongs to. DNA is organized into string-like structures called chromosomes. Every cell of your
body has forty-six chromosomes in the nucleus of each cell. These chromosomes collectively
hold all of the information to run your body. A lot of times we refer to the information on the
chromosomes as genes. We will be discussing DNA and genetics in more detail in the next few
units. It is one of my favorite topics, so I can’t wait to get to it.
A nuclear membrane surrounds the nucleus, which acts in a similar way to the cell membrane.
The nuclear membrane has pores that allow chemicals to enter the nucleus. The pores also
allow information to be sent out from the DNA of the nucleus to control the cell. All messages
that leave the cell originate from the nucleus. Therefore, the overall function of the nucleus is to
control the cell and to interact with other cells. The nucleolus is the densest region of the
nucleus. Its function is to make ribosomes, which is another part of the cell you will learn about
briefly. Not all cells have a nucleus. All bacteria, which are unicellular, lack a nucleus, which
means the DNA in them is floating freely rather than being bound by a nuclear membrane.
Cytoplasm
Cytoplasm is the fluid that surrounds all the internal parts of the cell. This fluid is mostly water
and has many chemicals in it, including minerals, that are needed for the cell to survive. It is
through the cytoplasm that messages from the nucleus travel to other parts of the cell or even
outside of the cell.
Mitochondria
Fig. 2.11. A mitochondrion. ©

BYU
The mitochondria are considered the “powerhouses” of the cell. It is in the mitochondria that food
energy is converted to chemical energy. More specifically, a mitochondrion takes carbohydrates
and oxygen and uses them to produce carbon dioxide, water, and energy. The energy in a cell is
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called ATP, which stands for adenosine triphosphate. ATP is a chemical form of energy, and
every cell needs it to live. The mitochondria turn glucose (a carbohydrate) into ATP.
Different cells have different numbers of mitochondria in them. You might expect a muscle cell or
a cell that requires a lot of energy to need more mitochondria, and they do have more. All animal
cells have at least one mitochondrion, and plant cells have mitochondria as well.
Chloroplasts
Fig. 2.12. Chloroplast. ©

BYU
Chloroplasts are found in plants, some bacteria, and protists, three of the five kingdoms of living
things. (The other two kingdoms are fungi and animal.) The chloroplast, like the mitochondrion,
is involved in converting energy. Inside the chloroplast light energy is changed into glucose,
which is a form of energy. The glucose produced in the chloroplast then goes to the
mitochondria to be further changed into ATP. Chloroplasts also need carbon dioxide, water, and
light to function. The process chloroplasts use to change light energy into chemical energy in the
presence of water and carbon dioxide is called photosynthesis. Photosynthesis will be
discussed in more detail later in the course.
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Self-Check
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Week 6
Week 6
Cell Organelles, Part 2

Reading Section
Ribosome
Ribosome.
© BYU
We can see ribosomes with an electron microscope, which is more powerful than a light
microscope. Ribosomes are very small, even smaller than viruses. They look like small dots.
Proteins—chemicals that control the cell and its functions—are made in ribosomes. DNA, found
inside the nucleus on the chromosomes, holds the information for how to make proteins. Here’s
how proteins are made: a copy of the DNA is taken to where a ribosome is located. At the
ribosome, the message is translated from the DNA language to the protein language. When the
ribosome is done creating the protein, the ribosome lets go of the protein, and then it can travel
to where it is supposed to go.
Ribosomes consist of two subunits that fit together. There is a large ribosomal subunit on the top
of the ribosome and a small ribosomal subunit on the bottom. The message from the DNA slides
between the two subunits to be “read,” and then the ribosome produces the protein from the
DNA’s instructions.
There are two different locations where we find ribosomes; the first place we find ribosomes is
floating in the cytoplasm. We call these ribosomes “free” because they are not attached to any
structures. Proteins made by free ribosomes are used to control the cell in which they were
made. These proteins will not leave the cell because they have been created for work inside the
cell.
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The other location we find ribosomes is attached to the endoplasmic reticulum, another
organelle in the cell that we will discuss next. These ribosomes are called “bound” ribosomes
because they are attached to another structure. Ribosomes attached to the endoplasmic
reticulum, or ER, produce proteins that will be exported out of the cell.
Endoplasmic Reticulum
The endoplasmic reticulum transports chemicals around the cell. You can think of it as a highway
where chemicals can get from one location to the next. The words endoplasmic reticulum mean
“intercellular network.” Instead of saying the full words endoplasmic reticulum, scientists use the
abbreviation ER. The ER has multiple layers of channels, which provide a path for chemicals to
travel.
There are two types of ER, smooth and rough. These names correspond to their appearance:
the rough ER is dotted and rough looking, whereas the smooth is not. The dots attached to the
rough ER are the ribosomes, which, as you know, make proteins that are exported out of the
cell. The pancreas produces many proteins that are used in digestion, so pancreatic cells have a
lot of rough ER in them.
Smooth ER produces and stores lipids. The main lipids it produces are cholesterol and
phospholipids. The Smooth ER also detoxifies a cell. To detoxify means to take a harmful
chemical and break it down into nonharmful chemicals. One of the many functions of the liver is
to detoxify chemicals in the body so it contains a lot of smooth ER. Some people have abused
their livers to the point that they can no longer function properly. Taking in excessive amounts of
alcohol and other harmful substances can tax your liver to the point that it will either need to be
replaced via a transplant or it will fail, resulting in death. It is important not to take medications or
chemicals into your body that are not good for you because they will cause your liver to work
harder than necessary to detoxify those chemicals.
Endoplasmic reticulum transports chemicals around the cell. © BYU
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Golgi Apparatus
The Golgi apparatus is like a post office. It packages and ships molecules made at one location
in the cell that will be used at another location, whether in or out of the cell. For example, a
protein, made by a ribosome, that needed to be transported out of the cell, would first have to go
through the Golgi apparatus. When the protein has been packaged properly by the Golgi
apparatus and it reaches the cell membrane, the cell membrane will then let it out.
The Golgi apparatus acts like a post office, packaging and delivering
molecules to different places within and outside of the cell.
© BYU
The structure of the Golgi apparatus consists of flattened membranous sacs. It almost looks like
pita bread, and it is unique in that it has a definite specific orientation. Molecules can only enter
the Golgi on one side. This “receiving” side of the Golgi is called the cis face. The trans face is
the “shipping” side of the Golgi, where the packaged molecules leave the Golgi. The Golgi is
used to process many chemicals besides proteins; for example, when waste products are
produced in the cell, the products will go into the Golgi, to be packaged and shipped to the part
of the cell that breaks them down, or, depending on the “address” given to the package, the
package may be sent to the cell membrane where it can leave the cell. The scientific name for
one of these packages is a vesicle. At any given moment, there may be many vesicles moving
around in a cell to the places they are supposed to be going, whether to or from the Golgi. The
Golgi apparatus or Golgi bodies, as they are sometimes called, have no specific location inside
the cell.
Lysosome
The lysosome processes material in the cell so that other

organelles in the cell can use the material. © BYU
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Lysosomes are sacs in the cell that contain enzymes, which break down products into smaller
pieces. A lysosome breaks down three different kinds of products in a cell. The first type of
product that a lysosome processes is food from outside of the cell. This food product enters the
cell as a food vacuole, which is a sac with food. This sac of food needs to be processed so the
cell can use the vacuole’s contents. The process includes taking the contents of the vacuole,
breaking down any particles, and releasing them to their destination. One common element in a
food vacuole is glucose. After glucose is processed by the lysosome, it is released to eventually
make its way to the mitochondria where ATP can be created. Some other products that are
needed for cellular function and are transported in vacuoles are amino acids and other simple
molecules. The second type of product that is processed by a lysosome is an organelle that is
no longer functioning properly. A lysosome will break down the organelle and return any usable
parts to the cytoplasm, where they can be accessed again (or in other words, recycled). The
third product is any cellular debris. When this debris is no longer helpful for the cell, it is digested
by a lysosome. You can think of lysosomes as the cleaners, or the garbage disposals of the cell.
The ER and the Golgi are helpful in the production of lysosomes.
Vacuoles
Vacuoles are spherical storage spaces; in plant cells, they are typically large.
© BYU
A vacuole is any sac in the cell that is used for storage. Vacuoles store chemicals ranging from
water and salts to pigments, gasses, and energy molecules. Vacuoles are shaped like round
sacs. Some organisms have larger vacuoles than others. The vacuoles in animal cells are
primarily used for storage. Animal cells range from having a few small vacuoles to having none
at all. In plant cells, however, the vacuole can be very large, taking up a great deal of space
(50–80 percent of the space in the plant cell). When a plant cell has not received enough
nutrients, the vacuole decreases in size because the products stored in the vacuole are used.
This is why a flower that has been cut will wilt over time. When the plant has been cut and no
longer receives nutrition from the ground, it has to rely on the nutrition and water in its vacuoles.
Over time, as it uses up those stored nutrients, the vacuoles within it decrease in size; this is
when the flower wilts, or bends.
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Week 6
In plant cells, the nucleus and other organelles are actually found around the periphery of the
cell because the vacuole is so large. The vacuole has an additional function, which is to provide
structural support. As discussed in the previous paragraph, the fullness of the vacuole gives a
flower stem its strength. As the vacuoles in plant cells decrease in size, the plant becomes more
bendable and less rigid.
Some plants contain poisons that are used as a defense mechanism against predators. These
poisons are stored in the vacuoles of the plants’ cells. We know that the color green in plants
comes from the chloroplasts of the cell, but it is the vacuole that gives the plant other colors like
red, yellow, and blue. Next time you see a flower, remember that it is the vacuole of the cell that
makes it so colorful.
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Self-Check
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Week 7
Week 7
Let's Get Started

Though cell types have many similar processes, cells vary greatly. This week you will be
introduced to the major types of cells, how they are alike, and how they are different.

Outline
Lessons
Types of Cells
Objective |
(5 parts - 120 min.)
Media
Types of Cells Interactive Video (8 min.)
Assignments
Types of Cells Activity (5 min.)
Self-Check (10 min.)
Human Cell Types Deep Dive GoReact Video (30 min.)
Stem Cells Deep Dive Paper (60 min.)

Vo c a b u l a r y
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Week 7
Types of Cells

Reading Section
All parts of the cell work together to perform the overall function assigned to the cell. Cells within
the same tissue can have the same function and, as a result, look and act similarly. Cells from
different tissues or organs might have different functions, so they will look different. For
example, a pancreatic cell from one part of the pancreas may look identical to another
pancreatic cell, while a pancreatic cell will look different from a muscle cell because they have
different functions. Depending on the function of a cell, they will naturally have different numbers
or sizes of certain organelles. The human body consists of trillions of cells that are similar but
not exactly the same. Human cells can vary in function, shape, and size. Let’s look at some
more examples of these variations.
One of the many functions of the liver is to help detoxify chemicals in the body. What organelle
in the cell helps with this function? You are right if you said the endoplasmic reticulum. The
smooth ER functions to detoxify chemicals; therefore, you might expect liver cells to have more
smooth ER in them than other cells.
The pancreas is an organ that produces a lot of enzymes. Many pancreatic enzymes are used
for digestion in other parts of the digestive system. This means that the enzymes that are
produced in the pancreas leave the pancreas and go to the part of the digestive system where
they are needed. What part of the cell makes enzymes that leave the cell? You are right if you
said bound ribosomes or the rough ER. The bound ribosomes make enzymes that leave the
cell; therefore, you might expect pancreatic cells to have more bound ribosomes than other cells
have.
The kidneys are organs that filter the blood. The kidneys take out any waste products and form
urine. Because the kidneys are constantly working, they need a lot of energy, or ATP. Which part
of the cell produces ATP? You are correct if you thought of mitochondria. The mitochondria take
food energy in the form of glucose and change it to ATP, which is cellular energy. What
assumption can you make about the structure of a kidney cell? You would be correct if you
guessed that kidney cells have more mitochondria than other cells.
So far we have discussed how certain types of organelles are important in different cells and
what functions they perform. The examples I have provided have been from human cells, but,
as you already have learned, there are differences between plant and animal cells. The next two
sections will look at major differences between categories of cells.
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Week 7
Animals Cells Versus Plant Cells
This figure shows some of the structural differences between

animal cells (top) and plant cells (bottom). © BYU
Although both plant and animal cells have nuclei, they are different from each other in many
ways. Let’s look at some differences between plants and animals.
We already know that plants can create energy using sunlight in a process called
photosynthesis. We also know that animals cannot photosynthesize. Cells that can create their
own energy source (through sunlight) are called autotrophic, while cells that can’t create their
own energy source (like animal cells) are heterotrophic. Which part of the cell is responsible for
photosynthesis? You are correct if you said the chloroplast. This is why plant cells have
chloroplasts and animal cells don’t. Animal cells also lack cell walls. The cell wall is found
outside of the plasma membrane and gives plant cells structure and protection.
Another difference between plant and animal cells is that the vacuole, the part of the cell that is
used for storage, is much larger in plant cells than animal cells. As mentioned previously, about
50 to 80 percent of a mature plant cell’s area is made of the central vacuole. Animal cells also
have vacuoles, but they are much, much smaller than those in plant cells.
Prokaryotic Cells Versus Eukaryotic Cells

The first way a scientist can distinguish among all living organisms is by the presence or
absence of a nucleus. This breaks up living things into two distinct groups. If a nucleus is
present, a cell is called eukaryotic. If the cell does not have a nucleus, the cell is categorized as
prokaryotic. Eu- means “true,” pro- means “before,” and -karyon means “nucleus.” Eukaryotes
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include plants, animals, fungi, and protists. Prokaryotes are unicellular organisms and consist
entirely of bacteria.

Self-Check
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Week 8
Week 8
Let's Get Started

When you learned about cell organelles, you learned about the structures within cells that carry
out its various functions. You also learned somewhat about how those structures influence each
other. But individual cells, alone, are very limited. It is in the way cells interact with each other
and with the world around them that allows for complex organisms to live and thrive. In this
lesson, you'll look at cell transport, the key to cell interaction.

Outline
Lessons
Cell Transport
Objective |
(5 parts - 50 min.)
Media
Cell Transport Interactive video (10 min.)
Assignments
Osmosis Lab (15 min.)
Osmosis Lab quiz (5 min.)
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q ( )
Everyday Homeostasis Check (5 min.)
Experiences 2: Create Your Own Petri Dish (20 min.)

Vo c a b u l a r y
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Week 8
Week 8
Cell Transport

Reading Section
Homeostasis
Homeostasis is a term we learned previously. We understand that homeostasis is the ability to
keep internal conditions suitable for living. This ability occurs on many levels, from the entire
organism all the way down to each individual cell. One example of homeostasis at a cellular
level is how cells deal with sodium levels. If there were too much sodium in a cell, then water
would automatically rush into the cell to try to dilute the sodium, and ultimately the cell would
explode. Homeostasis, in most cases, is a very fine, controlled process that makes life possible.
We’ve established that living things are made of cells, and so we certainly can’t have cells
exploding all over the place and still be in a healthy, thriving situation. Being off by even the
smallest degree can mean death to the cell, and if enough of an organism’s cells die, it will
eventually mean death to the organism as well.
A person with type I diabetes is no longer able to produce insulin, a chemical used in the
regulation of blood sugar. The inability of their body to create homeostasis with regard to blood
sugar affects every major organ of the body. Without medical intervention, the person would
eventually lose their eyesight; have increased odds of dying of heart failure; be at a greater risk
for bone fractures; be prone to bacterial infections of the skin, particularly on their feet; and
ultimately suffer from kidney and nervous system problems. All these conditions occur simply
because the sugar level of the blood is not kept at the right amount. This is just one example of
how critical it is for cells to be able to maintain homeostasis.
It is extremely important for our bodies to keep conditions at a suitable level so that all our parts
can function properly. One way our body reaches homeostasis is by the movement of fluids and
chemicals into or out of the cell.
When a membrane allows any substance to pass through it, the membrane is called permeable.
When a membrane blocks all substances, it is called impermeable. When a membrane blocks
some substances and not others it is called semipermeable. You can see this illustrated below.
The next section will define three ways our bodies transfer substances in and out of the cell;
these transfers occur through diffusion, osmosis, and active transport.
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The object on the left is permeable because it allows all substances to go through;
the middle object is semipermeable because it allows some objects to go through
but not others; the object on the right is impermeable because it allows nothing to
slip through.
© BYU
Diffusion
Diffusion is simply a name for the fact that, in a liquid or gaseous state, molecules move from an
area of higher concentration to an area of lower concentration. You can think of molecules as
claustrophobic (afraid of confined spaces). Molecules would rather be in an area where there
are fewer molecules than in an area where there are more molecules.
The process of diffusion is the tendency for molecules in a gaseous or liquid state to
move from an area of high concentration (a) to an area of lower concentration (b).
© BYU
Using what you have learned from the previous sentence, make a hypothesis about what will
happen when you put a drop of food coloring into a glass of water. Did you come up with
something like, “Over time, the molecules of food coloring will spread out evenly in the glass”? If
you did, you are right. In the laboratory assignment for this unit, we will be testing this
hypothesis.
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Week 8
Since chemicals must get into and out of cells, the chemicals are usually forced in and out by
following the principle of diffusion. Whether a chemical molecule will move across a membrane
(or diffuse) is dependent upon two factors. The first factor is the size of the molecule trying to
pass through—is the molecule too large to pass through the opening? The second factor is the
concentration of that molecule on both sides of the membrane. As stated above, the
concentration needs to be higher on the outside and lower on the inside for the molecule to
diffuse to inside the cell.
When a molecule is small enough to get through a permeable membrane and the concentration
of that molecule is less on one side of the membrane, molecules on the more concentrated side
will pass through the membrane to the less-concentrated side.
Sometimes when a molecule such as glucose needs to get into the cell, the membrane stops it.
The only way the molecule can enter the cell is through the process of facilitated diffusion. In
this process, the molecule enters one of the specialized channel proteins, which will help it
across the barrier. No energy is required for this process to occur. The important difference
between facilitated diffusion and diffusion is that the gradient, or difference in the concentration
levels, doesn’t affect the movement of the molecule in facilitated diffusion: the protein enables
the molecule to pass through the membrane, regardless of the concentration of the molecules
surrounding the membrane. Without this protein, the molecule would not be able to pass.
In facilitated diffusion, proteins help molecules pass through

membranes.
© BYU
Osmosis
Osmosis is like diffusion; the only difference is that water is moving through the membrane
instead of particles (or solute, as they are called). The same conditions apply to osmosis as in
diffusion; water will move to equal out the concentration of a chemical on two sides of a
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membrane. Water passes through the membrane from high-water concentration (lower solute
concentration) to the side with low-water concentration (higher solute concentration).
Active Transport
Sometimes a cell needs more help getting through the membrane than it receives from diffusion.
In that case, the cell uses a process called active transport. Special channel markers in the
membrane grab the needed molecule and force it into the cell. (The reverse also happens when
the membrane pumps items out of the cell.) The most important example of the active transport
system is the sodium-potassium pump. In this system, sodium ions are pumped out of the cell,
and potassium ions are pumped into the cell against their concentration gradients. The
important thing to remember about active transport is that, in order for the process to occur, it
requires energy, or ATP. The cell needs the chemicals to enter or leave the cell so desperately
that it must use energy to transfer the chemicals. The sodium-potassium pump is made of four
proteins that act as an enzyme to pump sodium out of the cell and potassium into the cell with
the fuel provided by ATP.

Self-Check
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Week 8
Week 8
Experiences 2: Create Your Own Petri Dish

Instructions
A petri dish is a container that has gelatin with nutrients in it that encourage bacterial and fungal
growth. You are going to create a petri dish so you can determine which microorganisms caused
your sourdough starter to grow. To create a petri dish, you will need the following:
Materials
Gelatin1, water2, bouillon cubes3, mixing bowl4, spoon5, shallow glass

dish6, sugar7, cotton swabs8, plastic wrap9
two packets of gelatin (about 5 teaspoons)

1 cup water
low-sodium beef bouillon cube (getting a low-sodium bouillon is important because sodium
kills bacteria)
2 teaspoons of sugar
mixing bowl
two shallow dishes
lids for the dishes or plastic wrap
Q-tips or other cotton swabs
spoon to stir everything
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Procedure
1. Boil the water.
2. Mix the boiled water, bouillon cube, gelatin, and sugar in a mixing bowl. Make sure there
are no clumps.
3. Pour the mixture into your dishes.
4. Cover the dishes with lids or plastic wrap and place in the fridge overnight so it hardens.
5. Dip the cotton swab in your sourdough starter and rub the swab back and forth over the
entire gelatin.
6. Repeat step five with a clean cotton swab on the second petri dish.
Experiment
In this activity, in addition to seeing what type of organisms are inside the sourdough starter, you
will also be testing two different areas to see which one will promote better cell growth. Choose
one factor that you feel will have an impact on cell growth. Some ideas you can test are
temperature, amount of light, or amount of moisture in the air. These are just ideas, and you are
welcome to choose one of the listed variables or choose one of your own.
To show your work, do the following:
1. In your notebook, write a hypothesis about what factor you think will cause the most
growth of microorganisms on your petri dish. (I think that ________ will cause the
most growth because ________.)
2. Make sure the two dishes are covered. Place each of the two petri dishes in a
different area so that you can test your hypothesis. For example, if your hypothesis
had to do with the amount of light, you would place one dish where it would get a lot
of light and one dish where it would not get very much light.
3. Observe the growth each day and record your observations for each day for one
week in your notebook. Be sure to note things such as the size of the colonies each
day, the amount of different colonies, the colors of the colonies, etc. Make a table to
record your observations. Here is an idea of a table you could create:
Area 1 Area 2
Observations for day 1
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Week 8
Now that you have made the petri dishes and grown the organisms from the sourdough starter
on it, answer the reflection questions below. After unit 4, you will submit a reflection assignment
that will be a collection of all the reflection questions, so I recommend that you type your
answers in a document on your computer so you can easily put them all together and submit
them later.
Here’s a video that can help you understand the process of creating your own petri dish:
Please watch this video in the online course.
Reflection Questions
Here are your reflection questions for this activity. Remember to keep the answers in your
experience journal for submission after Activity 3.
1. What was your hypothesis regarding which factor would cause the most amount of
growth on the petri dishes?
2. What were the observations you made about the two petri dishes in the different areas
for each day? (Use the table that you created for number 8 of the procedure; be sure
to have observations for each area each day.) Arrange the observations into a table.
3. What conclusion(s) can be drawn from your observations? Be sure to use your
data/observations to explain your conclusions.
Question mark ©
BYU
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References
1. Photo (https://www.flickr.com/photos/stevendepolo/3787431046) by Steven
Depolo (https://www.flickr.com/photos/stevendepolo/) via Flickr. CC BY 2.0
2. Photo (https://www.pexels.com/photo/water-drop-40784/) by Pixabay via
Pexels.
3. Photo (https://commons.wikimedia.org/wiki/File:Br%C3%BChw%C3%BCrfel-
1.jpg) by Rainer Z (https://de.wikipedia.org/wiki/Benutzer:Rainer_Zenz) via
Wikimedia Commons.CC BY-SA 3.0
(https://creativecommons.org/licenses/by-sa/3.0/deed.en) .
4. Photo (https://pxhere.com/en/photo/931289) by PXhere.
5. Photo (https://commons.wikimedia.org/wiki/File:Soup_Spoon.jpg) by Donovan
Govan via Wikimedia Commons. CC BY-SA 3.0
(https://creativecommons.org/licenses/by-sa/3.0/) .
6. Photo (https://pixabay.com/fr/photos/plaque-bleu-finlandais-blanc-2262331/)
by Pixabay.
7. Photo (https://www.flickr.com/photos/30478819@N08/46148146934) by Marco
Verch (https://www.flickr.com/photos/30478819@N08/) via Flickr. CC BY 2.0
8. Photo (https://pixabay.com/fr/photos/%C3%A9couvillons-coton-
%C3%A9couvillon-166409/) by Pixabay.
9. Photo (https://pixabay.com/fr/photos/diapositive-emball%C3%A9s-transparent-
967256/) by Pixabay.
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Week 9
Let's Get Started

Since cells do all the work in our bodies, we need to know how cells get their energy. Because
the sun is the origin for all energy on this planet, we need to understand how the energy from
the sun becomes useful to our cells. And for that we need to understand plant cell energy.
Welcome to this week's topic!
The content from this week comes from Unit 4: Cellular Energy (Objectives)

Outline
Lessons
Unit 4
Plant Pigments
Objective |
(3 parts - 45 min.)
Light Dependent and Independent Reactions

Objective |
(6 parts - 65 min.)
Media
Photosynthesis Interactive Video (10 min.)
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Assignments
Plant Pigment Lab (15 min.)
Plant Pigment Lab Quiz (5 min.)
Light Dependent and Independent Reactions Activity (5 min.)
Photosynthesis Virtual Lab (15 min.)
Photosynthesis Virtual Lab Quiz (5 min.)

Vo c a b u l a r y
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Light and Pigments1

Reading Section
W h a t Is L i g h t E n e r g y ?
The sun emits an enormous amount of electromagnetic radiation (solar energy). Humans can
see only a fraction of this energy, which portion is therefore referred to as “visible light.” The
manner in which solar energy travels is described as waves. Scientists can determine the
amount of energy of a wave by measuring its wavelength, the distance between consecutive
points of a wave. A single wave is measured from two consecutive points, such as from crest to
crest or from trough to trough.
Wavelength, Crest, Trough

The wavelength of a single wave is the distance between two consecutive points of similar
position (two crests or two troughs) along the wave.
Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun
and other stars. Scientists differentiate the various types of radiant energy from the sun within
the electromagnetic spectrum. The electromagnetic spectrum is the range of all possible
frequencies of radiation. The difference between wavelengths relates to the amount of energy
carried by them.
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Wavelength Spectrum
The sun emits energy in the form of electromagnetic radiation. This radiation exists at different
wavelengths, each of which has its own characteristic energy. All electromagnetic radiation,
including visible light, is characterized by its wavelength.
Each type of electromagnetic radiation travels at a particular wavelength. The longer the
wavelength (or the more stretched out it appears in the diagram), the less energy is carried.
Short, tight waves carry the most energy. This may seem illogical, but think of it in terms of
moving a a piece of heavy rope. It takes little effort by a person to move a rope in long, wide
waves. To make a rope move in short, tight waves, a person would need to apply significantly
more energy.
The electromagnetic spectrum shows several types of electromagnetic radiation originating from
the sun, including X-rays and ultraviolet (UV) rays. The higher-energy waves can penetrate
tissues and damage cells and DNA, which explains why both X-rays and UV rays can be
harmful to living organisms.
Absorption of Light
Light energy initiates the process of photosynthesis when pigments absorb the light. Organic
pigments, whether in the human retina or the chloroplast thylakoid, have a narrow range of
energy levels that they can absorb. Energy levels lower than those represented by red light are
insufficient to raise an orbital electron to a populatable, excited (quantum) state. Energy levels
higher than those in blue light will physically tear the molecules apart (called bleaching). So
retinal pigments can only “see” (absorb) 700 nm to 400 nm light, which is therefore called visible
light. For the same reasons, plants pigment molecules absorb only light in the wavelength range
of 700 nm to 400 nm; plant physiologists refer to this range for plants as photosynthetically
active radiation.
The visible light seen by humans as white light actually exists in a rainbow of colors. Certain
objects, such as a prism or a drop of water, disperse white light to reveal the colors to the
human eye. The visible light portion of the electromagnetic spectrum shows the rainbow of
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colors, with violet and blue having shorter wavelengths, and therefore higher energy. At the
other end of the spectrum toward red, the wavelengths are longer and have lower energy.
Colors of Visible Light Spectrum

The colors of visible light do not carry the same amount of energy. Violet has the shortest
wavelength and therefore carries the most energy, whereas red has the longest wavelength and
carries the least amount of energy. (credit: modification of work by NASA)
Understanding Pigments
Different kinds of pigments exist, and each has evolved to absorb only certain wavelengths
(colors) of visible light. Pigments reflect or transmit the wavelengths they cannot absorb, making
them appear in the corresponding color.
Chlorophylls and carotenoids are the two major classes of photosynthetic pigments found in
plants and algae; each class has multiple types of pigment molecules. There are five major
chlorophylls: a, b, c and d and a related molecule found in prokaryotes called
bacteriochlorophyll. Chlorophyll a and chlorophyll b are found in higher plant chloroplasts and
will be the focus of the following discussion.
With dozens of different forms, carotenoids are a much larger group of pigments. The
carotenoids found in fruit—such as the red of tomato (lycopene), the yellow of corn seeds
(zeaxanthin), or the orange of an orange peel (β-carotene)—are used as advertisements to
attract seed dispersers. In photosynthesis, carotenoids function as photosynthetic pigments
that are very efficient molecules for the disposal of excess energy. When a leaf is exposed to full
sun, the light-dependent reactions are required to process an enormous amount of energy; if
that energy is not handled properly, it can do significant damage. Therefore, many carotenoids
reside in the thylakoid membrane, absorb excess energy, and safely dissipate that energy as
heat.
Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from
visible light, which is the absorption spectrum. The graph in shows the absorption spectra for
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chlorophyll a, chlorophyll b, and a type of carotenoid pigment called β-carotene (which absorbs
blue and green light). Notice how each pigment has a distinct set of peaks and troughs,
revealing a highly specific pattern of absorption. Chlorophyll a absorbs wavelengths from either
end of the visible spectrum (blue and red), but not green. Because green is reflected or
transmitted, chlorophyll appears green. Carotenoids absorb in the short-wavelength blue region,
and reflect the longer yellow, red, and orange wavelengths.
Chlorophyll a and Chlorophyll b Pigments

(a) Chlorophyll a, (b) chlorophyll b, and (c) β-carotene are hydrophobic organic pigments found
in the thylakoid membrane. Chlorophyll a and b, which are identical except for the part indicated
in the red box, are responsible for the green color of leaves. β-carotene is responsible for the
orange color in carrots. Each pigment has (d) a unique absorbance spectrum.
Many photosynthetic organisms have a mixture of pigments; using them, the organism can
absorb energy from a wider range of wavelengths. Not all photosynthetic organisms have full
access to sunlight. Some organisms grow underwater where light intensity and quality decrease
and change with depth. Other organisms grow in competition for light. Plants on the rainforest
floor must be able to absorb any bit of light that comes through, because the taller trees absorb
most of the sunlight and scatter the remaining solar radiation.
Forest. Credit: Jason Hollinger.

OpenStax (https://openstax.org/books/biology/pages/8-2-the-light-
dependent-reactions-of-photosynthesis) Biology, CC BY 4.0
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Plants that commonly grow in the shade have adapted to low levels of light by changing the
relative concentrations of their chlorophyll pigments. (credit: Jason Hollinger)
When studying a photosynthetic organism, scientists can determine the types of pigments
present by generating absorption spectra. An instrument called a spectrophotometer can
differentiate which wavelengths of light a substance can absorb. Spectrophotometers measure
transmitted light and compute from it the absorption. By extracting pigments from leaves and
placing these samples into a spectrophotometer, scientists can identify which wavelengths of
light an organism can absorb. Additional methods for the identification of plant pigments include
various types of chromatography that separate the pigments by their relative affinities to solid
and mobile phases.

Self-Check
References
1. “8.2: The Light-Dependent Reactions of Photosynthesis
(https://cnx.org/contents/[email protected]:-CmzvUct@13/The-Light-Dependent-
Reactions-of-Photosynthesis) ,” OpenStax CNX, CC BY 4.0
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Products and Processes of Photosynthesis, Part 1

Reading Section
First of all, what types of organisms employ photosynthesis? You should be able to guess
plants, which are the most popularly talked about group that uses photosynthesis; however,
other organisms also use it. Some protists, bacteria, and blue-green algae also have the ability
to use sunlight for food. However, for the sake of simplicity, throughout this lesson I’ll be
referring to plants. Keep in mind that the process is the same whether it takes place in plants,
bacteria, blue-green algae, or protists.
We can explain photosynthesis with an equation. The graphic image below contains a word
equation for photosynthesis. If you have not taken chemistry, you may not understand how an
equation works. On the left, you will see molecules that the plant takes in. An arrow sign
separates the left side of the equation from the right side of the equation. The right side shows
the products, or in other words, what is produced and given off by the plant.
Photosynthesis equation. This equation reads, “water and carbon dioxide, in the
presence of light, produce carbohydrates and oxygen.” © BYU
Let’s see where all the components in the equation come from and go. The plant takes in water
from the soil. This process occurs naturally except in plants that are introduced into their
environment. Your houseplants or the plants in your yard are examples of introduced plants. You
may have to water these plants because certain types of introduced plants require more water
than they would naturally get in the area where you live. So, the water comes from the
environment and is usually taken in by the roots of the plant. The plant takes in carbon dioxide
from the air. On the other hand, humans breathe out carbon dioxide, which makes me wonder
about people who say their plants like it when they talk to them. Maybe the plants are getting
more carbon dioxide from the people breathing out on them than they would otherwise.
The products of photosynthesis are carbohydrates and oxygen. The plant uses carbohydrates
for energy. (Remember, we discussed how this works in lesson 1.) This is the goal of the plant—
to take in light and produce carbohydrates, which it needs to survive. The oxygen is then given
off to the environment. This is a very good thing because we breathe the oxygen that plants give
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off. If it were not for plants, humans would not be able to survive on earth. Humans are
dependent on plants, both for the oxygen they produce and as a food source.
In photosynthesis, water and carbon dioxide are absorbed by the plant, with
light, to produce carbohydrates and oxygen.
© BYU
Another type of equation for photosynthesis is the chemical equation for the chemicals involved.
Do you know the chemical formula for water? If you said H2O, you’re right. Carbon dioxide is
one carbon molecule and two (di-) oxygen molecules, thus making CO2. A simple chemical
formula for carbohydrates is C6H12O6, and the formula for oxygen is O2. You may ask why there
are two oxygen atoms in one molecule of oxygen. Oxygen will not be found by itself in nature. A
chemical equation for photosynthesis looks like this:
Chemical equation for photosynthesis © BYU
Where does photosynthesis occur? The actual chemical reactions take place in the plant leaves,
as shown in the illustration below. As you learned previously, chloroplast is an organelle found in
plants and is the site of photosynthesis. Chloroplast is a green pigment found in the cells in the
leaves of plants and other photosynthetic organisms. Another important structure in the function
of photosynthesis is the stomata. The stomata are tiny pores in the leaves of the plant that allow
oxygen to be released and carbon dioxide to be obtained. I think of stomata as the respiratory
system of the plant; in other words, plants breathe through the stomata. Last, water is obtained
usually by the roots of the plant. The vascular tissue in the plant transports water from the roots
to the leaves, where it is needed for photosynthesis. I think of vascular plant tissue as being like
blood vessels because it helps transport chemicals from one place to another. The vascular
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tissue will also come into play at the very end of the process of photosynthesis. When the plant
has transformed the light into energy, the vascular tissue transports this energy to every cell of
the organism in order for it to function properly.
Photosynthesis happens in two main areas of a plant, in the chloroplast

organelle and in the stomata in the leaf.
© BYU
How does photosynthesis work? The process of photosynthesis is broken down into two steps.
The two steps are called the light-dependent reactions (or light reactions) and the light-
independent reactions (or Calvin cycle). Light reactions can only occur in the presence of light,
hence the name. The Calvin cycle can occur in the light or dark, but it usually occurs during the
day. Both of these reactions are represented by the chemical equation for photosynthesis
discussed earlier. By the end of both reactions, we should have used all the chemicals on the
left side and should have produced the products on the right side of the equation. Let’s see if
that is the case.
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Light Reactions
The plant takes in light during light reactions, as you might guess from the name. If light is not
available, the reactions will not occur and carbohydrates will not be produced; thus the plant will
die from lack of energy (carbohydrates) if enough time passes without any light. Below, you will
find the steps that occur in the light reactions.
The light energy makes water (H2O) split apart. The result of water being split apart is two
hydrogen ions (H*) and one atom of oxygen.
The atom of oxygen combines with another atom of oxygen to make O2. As you learned
earlier, it is not found alone in a stable state. The oxygen leaves the plant as a waste
product. The plant does not need the oxygen, but humans need oxygen to survive, so they
benefit from the waste products of the plant.
Light also makes electrons in the plant become excited. These excited electrons are used for
two purposes. One function is to provide energy to make ATP, which, as you already know, is
an energy molecule called adenosine triphosphate. The other function of the electrons
excited by sunlight is to make the energy molecule NADPH, with help from the hydrogen
ions (H*) produced by the splitting of water. The ATP and NADPH created in this step are
used in the Calvin cycle.
To summarize what has occurred here, look at the table below to see what has been used and
what has been produced:
Used Produced
light—received from the sun oxygen—given off to the environment
water (H2O)—received from the ATP and NADPH—used in the Calvin
soil cycle

Self-Check
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The Calvin Cycle

Reading Section
The Calvin Cycle works like a cycle where ATP, CO2, and
NADPH are put in and carbohydrates (C6 H12 O6 ) are produced.
© BYU
The purpose of the Calvin cycle is to use carbon dioxide to produce sugar. The plant uses the
sugar for plant growth and functions, or the sugar can be stored for use during the winter. As the
name implies, the Calvin cycle works like a cycle. Materials are added into the cycle, and the
end products are pumped out. The materials that are added into the cycle are ATP and NADPH,
which the plant produced in the light reactions, and CO2, which the plant gets from the air. When
these materials are present in the chloroplast of the plant, the cycle will put together a molecule
of glucose (C6H12O6), which the plant will use for energy to survive. If you look carefully at the
molecule of glucose, you might be able to guess where each of the atoms comes from. The
carbon comes from carbon dioxide. The hydrogen comes from NADPH—the H at the end of
NADPH is broken off and helps make glucose. The oxygen in the molecule comes from carbon
dioxide.
Table 3.3
Used Produced
CO2—plants receive from air Carbohydrates
water ATP and NADPH—made in the light reactions
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Once the ATP and NADPH have given off energy by breaking a bond during the Calvin cycle,
the resulting molecules, ADP (adenosine diphosphate) and NADP, go back to the light reactions
to be re-energized. As you already know, the function of these chemicals is for energy. So, you
can imagine that all day long these molecules go from the light reactions where they get energy
to the Calvin cycle where they drop off the energy so sugar can be made. Sugar is the ideal
form of energy for plants. It takes a lot of ATP and NADPH as well as six molecules of carbon
dioxide to form one molecule of sugar in the Calvin cycle.
Photosynthesis Review
It is important to know what happens in each stage of photosynthesis, such as where the plant
got the materials and where the products were made. The table below may help you as you
think through what you have just learned. If you read through the table and something doesn’t
make sense, take a minute to review the material in this lesson.
water (H2O) split by light during light reactions

carbon dioxide
taken in by plant, used in the Calvin cycle
(CO2)
light plant absorbs light from the sun, used in light reactions
ATP and NADPH produced in light reactions, used in the Calvin cycle
carbohydrates
final product of the Calvin cycle—the goal of the process
(C6H12O6)
produced as water is split in light reactions—given off to environment as
oxygen (O2)
waste product

Self-Check
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Week 10
Week 10
Let's Get Started

Human cells don't have the ability to perform photosynthesis. Instead, human cells take the
processed energy byproducts from plants and convert them into useful forms. This week's
lesson takes you into that process.

Outline
Lessons
Cellular Respiration Basics

Objective |
(7 parts - 62 min.)
Media
Glycolysis Interactive Video (7 min.)
Electron Transport Chain (8 min.)
Fermentation (9 min.)
Assignments
Cellular Respiration Activity (5 min.)
149
Photosynthesis vs Cellular Respiration Activity (5 min.)
Energy Cycle Model Deep Dive (45 min.)

Vo c a b u l a r y
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Week 10
Cellular Respiration Basics

Reading Section
Cellular respiration is the process by which energy is harvested from glucose. In this process,
cells “burn” or break down the glucose to get ATP, an energy source for cellular functions. The
process of cellular respiration is broken down into three steps: glycolysis, the Krebs cycle, and
electron transport chain. Before getting into what happens specifically in each of these steps,
let’s look at the overall goal of cellular respiration. The following is a chemical equation for
cellular respiration.
Chemical equation for cellular respiration © BYU
Again, cellular respiration is the process of creating usable energy from glucose. Looking at the
equation, you should be familiar with each of the chemicals. Look more closely at the equation
and notice which chemicals are on each side of the arrow symbol. If you noticed that this
reaction is the opposite of photosynthesis (except for light), you are correct. The food energy
used to make chemical energy is carbohydrates. Your body gets this energy from the food you
eat. Your body gets oxygen from the environment simply by breathing it in—remember that
plants create oxygen as a byproduct of photosynthesis. Carbon dioxide is given off as a waste
product (as shown by being on the right side of the arrow). Water is also given off as a waste
product of this reaction, but it is reused in other processes of the cell. Do not let this confuse
you. Because we use so much water in cellular functions and by breathing and sweating, we
should be drinking lots of water. Water is given off as a waste product in this specific reaction
even though overall, our bodies must take it in.
Glycolysis
The word glycolysis means “glucose breaking.” Lysis means “to break” and glyco refers to the
carbohydrate glucose. In glucose breaking, we are doing just that—glucose is being broken
apart. Remember that glucose is a simple sugar (monosaccharide) made up of six carbon
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atoms. Glycolysis is the only step of cellular respiration that does not occur in the mitochondria
of the cell. Glycolysis occurs in the cytoplasm while the Krebs cycle and the electron transport
chain occur in the mitochondria.
Have you ever heard the expression “it takes money to make money”? This is a phrase you can
apply to the process of glycolysis. Glycolysis requires two ATP in order to function. It seems a
little strange to use ATP when the real goal is to make ATP. It seems like it is not a good plan to
“burn” something you are trying to make. But the reality is that the process requires energy to go,
and the energy (ATP) that needs to be added (which is only two molecules) is immediately
recovered. By this I mean the process of glycolysis produces four molecules of ATP. This energy
is now free to be used for cellular functions in the cell. By using two ATP, the cell is able to make
four ATP, therefore coming out with two ATP (two were used and four were made, for a net gain
of two).
As you already know, in glycolysis, glucose is broken down. This results in the production of two
molecules of pyruvate (also called pyruvic acid). Pyruvate is an energy molecule made of three
carbon atoms. Glucose is made of six carbons, and so, if you spit it apart and get two pyruvate
molecules, it makes sense that they are composed of three carbons each. Other products
produced in glycolysis include four molecules of ATP (energy), water (which is a waste product
of the reaction), and two molecules of NADP (energy molecule), which will be used in the last
step. So of the four products created in glycolysis, two of them are “free to go” and two of them
will be used to continue the process of cellular respiration. Can you guess which products go
where? ATP and water can leave, but NADH and pyruvate will be used in other processes.
NADH is used in the third step of the electron transport chain, and pyruvate is used in the
second step of the Krebs cycle.
The table below summarizes what happens in glycolysis.
Summary of Glycosis
Used Produced
4 ATP
2 NADH
Glucose (broken down) 2 ATP
2 Pyruvate
H2O

Self-Check
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The Krebs Cycle

Reading Section
The Krebs cycle, also called the citric acid cycle, is the second step in the process of cellular
respiration. You may remember that the mitochondrion is the powerhouse of the cell. It is termed
the powerhouse because it is where the production of energy takes place. Glycolysis occurs in
the cytoplasm. NADH and pyruvate, which the cell created during glycolysis, will be “shipped”
into the mitochondria, where the next two steps occur.
In the Krebs cycle, the two pyruvate molecules created by the breakdown of glucose will be
used along with oxygen. This step is called a cycle because as long as the molecules are
present to “feed” into the system, it will continue to run. During the process of the Krebs cycle,
the mitochondria take the energy from the pyruvate to create other energy molecules. For every
one glucose molecule (which means for every two molecules of pyruvate), the Krebs cycle
yields the following: 8 NADH, 2 FADH2, 2 ATP and 6 CO2. Let’s see what happens to these
molecules. The NADH and FADH2 molecules will go to the electron transport chain to create
more energy. The ATP created in this step is available energy for any part of the cell to use. The
carbon dioxide molecules are considered a waste product by the body, which means that having
the CO2 around is not of benefit, so you get rid of the CO2 produced during the Krebs cycle
when you exhale.
Below is an image showing the Krebs cycle. As you can see from the diagram below, the two
pyruvates produced in glycolysis are used. As these pyruvates are cycled around in the
mitochondria, it produces 6 molecules of CO2, 2 molecules of ATP, 2 molecules of FADH2, and 8
molecules of NADH. The NADH and FADH2 will be used in the next step of cellular respiration
known as the electron transport chain.
Krebs Cycle © BYU
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The Krebs Cycle

Used Produced Purpose
8 NADH to electron transport chain
2 FADH2 to electron transport chain
2 pyruvates
2 ATP available for use
6 CO2 waste product
E l e c t r o n Tr a n s p o r t C h a i n
Have you ever heard of the game “hot potato”? It is a game where you sit in a circle and one
person has the “hot potato.” Because it is “hot,” you don’t want it because it will “burn” your
hands. When the music starts, the potato (which can be any object) gets passed around in the
circle. When the music stops, the person holding the hot potato is “out.” The electron transport
chain is a little like the hot potato game: the energy molecules get passed through a number of
proteins where they give off an excited electron, and, in the process, energy is captured in the
form of ATP.
The electron transport chain uses the molecules of NADH and FADH2 that were produced
during glycolysis and the Krebs cycle. In the electron transport chain, the hydrogens from NADH
and FADH2 are broken and make a gradient where there is more hydrogen the other side of the
mitochondria membrane. As you learned earlier with diffusion, the hydrogens will flow from high
concentration to low concentration, but they are only able to move through a special protein in
the membrane of the mitochondria called ATP synthase. As they move through the ATP
synthase, 32 molecules of ATP are produced.
The image below shows the electron transport chain. As you can see from the image, the
electron transport chain is very involved. You do not need to know all the different parts. Use the
image to see that NADH and FADH2 are donating hydrogen and then the hydrogen ions move
through ATP synthase to produce ATP.
Electron transport chain © BYU
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Watch this animation of the electron transport chain:
The table below summarizes the chemical reactions of this step of cellular respiration.
Used Produced Notes

NADH ATP NADH and FADH2 created from earlier processes
FADH2 H2O water is a waste product
For every one molecule of glucose, 36 molecules of ATP are created. Can you figure out how
many molecules of ATP are created in the electron transport chain? Take a minute to review the
numbers for the first two steps.
Glycolysis—2 ATP
Krebs cycle—2 ATP
Electron transport chain—32 ATP

Self-Check
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Anaerobic Respiration

Reading Section
Have you ever done a physical activity where you had to start breathing really hard, such as
biking, hiking, or swimming? If you continued to push through this, breathing hard, you most
likely woke up very sore the next day. As you learned earlier, your body uses oxygen to produce
energy in the form of ATP. However, sometimes our bodies are not able to get enough oxygen
for the activity we are doing. If there is not enough oxygen available to convert the glucose to
ATP, then your body will go through a process called anaerobic respiration. The term anaerobic
means “without oxygen.” In addition to energy, a byproduct of anaerobic respiration is a
chemical called lactic acid. That burning feeling you get during intense exercise is lactic acid
building up in your muscles. The acid will be reabsorbed by the body in a matter of hours, but
while it’s there it damages the muscle tissue. That is why intense exercise typically causes us to
be sore the next day.
The process of cellular respiration, as you already know, yields thirty-six molecules of ATP per
molecule of glucose. Because oxygen is not used in anaerobic processes, glycolysis is done so
only two molecules of ATP are produced for each glucose molecule. You can see that you get
much more energy per glucose when there is oxygen present. When lactic acid is produced,
your body must be saying, “I am so desperate for ATP that I am willing to take only two
molecules per glucose instead of thirty-six.” When the body is resting, the lactic acid that was
produced during anaerobic respiration mixes with oxygen and produces pyruvic acid. The
pyruvic acid goes through the Krebs cycle as normal.
There are other organisms that also go through anaerobic respiration, but instead of producing
lactic acid, they produce ethanol and carbon dioxide. One of the most common organisms that
does this is yeast. This process is known as alcohol fermentation, and yeast is used in multiple
ways because it goes through this process. Bakers will use yeast to make bread rise, because
the CO2 produced by the yeast gets captured in the dough and causes it to puff out so the bread
is more fluffy. Brewers use yeast to create wine and beer from the ethanol it produces.
If you would like more help with understanding anaerobic respiration, this video is a great
resource:

Self-Check
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Week 11
Let's Get Started

This week you will have the opportunity to take what you have learned so far and apply it in a
variety of ways. You are going to play with yeast (a simple cellular organism) as well as do some
work collecting and analyzing data. This week also marks the end of the first three experience
activities, so you will be submitting your work for all three activities (including this week's
activity).

Outline
Lessons
Experiences 3
Objective
(1 part - 60 min.)
Examples and Non-examples, Data, and References

Objective
(2 parts - 35 min.)
Media
Assignments
157
Assignments
Experiences 3: Metabolism of Yeast Experiment (60 min.)
Examples and Non-Examples Activity (15 min.)
Data Activity (20 min.)
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Week 11
Week 11
Experiences 3: Metabolism of Yeast Experiment

Instructions
In this experiment, you will be testing how well yeast is able to metabolize different types of
sugar. In the previous unit, you learned about cellular respiration with the first step being
glycolysis. Yeast is able to break down glucose into carbon dioxide. In this experiment, we will
measure how well yeast is able to metabolize different sugars, based on the amount of carbon
dioxide produced.
For this experiment, you will be seeing which type of carbohydrate (honey, table sugar, flour)
that yeast is able to metabolize best. We will be measuring this by capturing the amount of
carbon dioxide produced in a balloon. Yeast, water, and a different carbohydrate will be placed
in each bottle, and then a balloon will be placed over it to capture the carbon dioxide produced.
The carbohydrate in the balloon that grows the largest will be the one that yeast can metabolize
best. To perform this experiment, you will need the following:
Materials
Liter bottle1, water2, yeast3, sugar4, honey5, flour6, ruler7, string8,

uninflated balloons9
159
four 1-liter bottles with caps (plastic water bottles work well)
four balloons that are the same size and able to fit over the opening of the bottles
4 tablespoons yeast (1 tablespoon for each bottle)
1 tablespoon table sugar
1 tablespoon honey
1 tablespoon flour
4 cups very warm water (1 cup for each water bottle)
marker to label each water bottle
string
ruler
Create a Hypothesis
In your notebook, create a hypothesis about which carbohydrate (flour, table sugar, or honey)
you believe the yeast will be able to metabolize easiest. Be sure to explain why you chose that
carbohydrate.
Procedure
1. Place one cup of very warm water (around 100 degrees Fahrenheit) in each of the four
plastic water bottles.
2. Label 1 water bottle “no carbohydrates,” another bottle “table sugar,” another bottle
“honey,” and the fourth bottle “flour.”
3. Place 1 tablespoon of table sugar in the bottle labeled “table sugar.”
4. Place 1 tablespoon of honey in the bottle labeled “honey.”
5. Place 1 tablespoon of flour in the bottle labeled “flour.”
6. Add 1 tablespoon of yeast to each of the four bottles.
7. Cap each bottle and shake so everything mixes.
8. Stretch a balloon over the mouth of each water bottle. If the balloon seems like it will not
stay on, wrap some tape around it.
9. Wait for about 20 minutes.
10. Measure the diameter of each balloon by wrapping a string around the middle of each
balloon and marking the point on the string that touches the beginning point of the string.
Then measure that section of the string using a ruler. An example of using this method to
measure a cup is below:
String around a glass © BYU
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String being measured on a ruler ©

BYU
11. Record the size of each balloon in your notebook.
Now that you have tested various nutritive elements with your yeast, answer the reflection
questions below. After unit 4, you will submit a reflection assignment that will be a collection
of all the reflection questions. I recommend that you type your answers in a document on
your computer so you can easily put them together and submit them later.
Question mark ©
BYU
1. Record the data for the size of each balloon.

2. What conclusions can you draw based off the data you listed above?
3. Since this was an anaerobic process, what step of cellular respiration did the yeast use to
break down the carbohydrates placed in the bottles, and what was produced that caused
the balloons to inflate?
4. The bottle that had only yeast and water was used as a control. What conclusions can you
draw by comparing the control to the other bottles that had different types of carbohydrates
in them?
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References
1. Photo (https://www.klipartz.com/en/sticker-png-thedy) by Klipartz.
2. Photo (https://www.pexels.com/photo/water-drop-40784/) by Pexels.
3. Photo (https://en.wikipedia.org/wiki/File:Dry_yeast.jpg) in public domain.
(https://www.flickr.com/photos/30478819@N08/) via Flickr. CC BY 2.0
5. Photo (https://pixabay.com/fr/photos/miel-jaune-apiculteur-nature-1958464/) by
Pixabay.
7. Photo (https://pixabay.com/fr/photos/millim%C3%A8tres-m%C3%A9trique-mesure-
953423/) by Pixabay.
8. Photo (https://en.wikipedia.org/wiki/File:Spool_of_string.jpg) by Fcb981 via Wikimedia
Commons. CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0/) .
9. Photo (https://pixabay.com/fr/photos/patron-ballon-ballons-anniversaire-22080/) by
Pixabay.
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Week 12
Week 12
Let's Get Started

You won't find a crime show made in the last 20 years that isn't influenced by our understanding
of DNA. However, there is much that is portrayed incorrectly about DNA in our popular media.
The basics, including the fact that each person's DNA is unique, are well known. However, you
may not be aware of the finer details about DNA. We will change that this week.
Before that happens, you're going to look at how scientific knowledge is shared. The references
activity will allow you to see how scientific understanding builds from scientific study to scientific
study. You will make a video about what you have learned, so pick a topic you can get excited
about.
The content from this week comes from Unit 5: DNA (Objectives)

Outline
Lessons
Examples and Non-examples, Data, and References

Objective |
(1 parts - 60 min.)
Introduction to DNA
Objective |
(3 parts - 55 min.)
163
DNA Replication
Objective |
(3 parts - 85 min.)
Media
DNA Replication Video (4 min.)
Assignments
DNA Timeline Deep Dive (30 min.)
Match the Bases Activity (5 min.)
DNA Replication Deep Dive (30 min.)
Crime Lab Deep Dive (30 min.)

Vo c a b u l a r y
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Week 12
Week 12
Introduction to DNA

Reading Section
DNA takes the shape of a double helix, or a twisted ladder. janjf93, DNA RNA
strand, retrieved February 7, 2020, Pixabay, pixabay.com (https://
pixabay.com/vectors/dna-rna-strand-biology-
school-3500555/) , Pixabay License
Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in
the development and function of all known living organisms. Because DNA is made of nucleic
acids, we will be spending this entire unit talking about them.
The function of DNA molecules is to store information. DNA is like a set of blueprints or a book
of instructions. DNA has all the “recipes” for making chemicals or proteins. The proteins don't
actually do the work; they are like a boss: they tell everything what to do. The segments of
DNA that carry genetic information are called genes. You have probably heard the term genes
many times before, especially when talking about inheritance. For example, “He got his red-
hair genes from his grandmother” or “It's in her genes to be a good dancer.”
Structure of DNA
A chromosome is made of DNA. DNA is a long chain of nucleic acids (nucleotides) hooked
together. A nucleotide is composed of sugar and phosphate chemicals connected to a
nitrogenous base, as shown in the image below.
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DNA is a long chain of nucleotides, which is just molecules of

sugar and phosphate connected by a base.
© BYU
You may have heard of DNA being described as a double helix or a twisted ladder. The sugars
and phosphates make up the sides of this ladder, and the bases make up the rungs in the
middle, as shown in this image:
DNA is made up of nucleotides whose bases are hooked

together. In real life they are twisted, but are shown here
straight like a ladder. © BYU
In prokaryotic cells such as bacteria, the chromosomes are found in the cell’s cytoplasm. In
eukaryotic organisms such as animals, plants, and fungi, the DNA is found in the nucleus of the
cell.
Remember, if the above image were a real molecule of DNA, the ladder would be twisting, but it
is easier to study when we flatten it out. The alternating phosphate-sugar structures make up
the sides of the ladder. The sugar-phosphate alternation is the same whether the DNA belongs
to a bacteria, virus, mold, flower, or human. All DNA has the exact same sugar-phosphate
backbone. The differences among organisms are caused from the arrangement of bases on the
rungs of this ladder. If you were to use DNA as a ladder, you would step on the bases and hold
on to the sugar-phosphate backbone as you climbed.
In the image above, the bases are rectangles. This is not their true shape. I like to picture them
flat because I can picture the ladder shape better. They are actually three-dimensional groups of
atoms.
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There are four different types of bases: adenine, thymine, cytosine, and guanine. The
arrangement of these four bases is what makes us similar to and different from each other.
When working with DNA, it is not necessary to write out the full names of the bases. We can
indicate a base by using the first letter of the base’s name. From here on out, we will refer to the
bases as A, T, C, and G. Inspect the following pictures of the four bases. Remember, it is the
arrangement of these bases in our DNA that makes us different. For example, let’s consider the
eye color gene. The length of the gene would be the same for both of us. Let’s say that it is only
ten bases long. Your bases may read ATTAGACTAG. That would code for your eye color. My
gene may read ATGACTAGTA. Eye color is actually controlled by a combination of many genes.
Most genes are hundreds of bases in length.
Most of the time, when a segment of DNA is diagrammed, it is not necessary to draw out the
complete structure of the bases. Usually, it is good enough to indicate where the specific bases
are because the structure is well known. The four bases are put into two categories: purines and
pyrimidines. Adenine and guanine are purines; thymine and cytosine are pyrimidines.
Purines include adenine and guanine; pyrimidines include thymine and cytosine.
© BYU
Examine the pictures of the bases in the image above. Can you identify a difference between
purines and pyrimidines? As you look at the general structure of the bases, notice that the
purines have two ring structures and that the pyrimidines have only one ring structure. To
remember this, I remember that the shorter word (purine) represents the bigger bases, and the
longer word (pyrimidine) represents the smaller bases.
Look back at the structure of the double helix at the beginning of this lesson, especially noting
the lines drawn between the bases. These lines are bonds that keep the molecule together. Is
there always the same number of bonds? You are correct if you said no. Some bases have two
bonds drawn between them, and other bases have three bonds drawn between them. This was
drawn intentionally because the guanine and cytosine make three bonds, while adenine and
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thymine make two bonds. Because the bases will make different numbers of bonds, only certain
bases will bond with other bases, which is explained by Chargaff's rules for base pairing.
There are two parts to Chargaff’s rules. First, a purine (adenines and guanines) always bonds
with a pyrimidine (thymines and cytosines). Let's think again about the structure of a ladder.
Each rung of the ladder needs to be the same length. If a rung is too short, it will not attach to
both sides, and thus would make it less sturdy. If the rung is too long, there will be extra material
sticking out of the side of the ladder. The majority of the time, DNA is coiled tightly over and over
again. If there were extra pieces of material when the DNA was unwinding, it would probably get
caught up and break. A purine always bonds with a pyrimidine, and a bond between these two
makes each rung the exact same size and the DNA molecule stable and structurally strong.
The second part of Chargaff’s rules is that adenine (A) and thymine (T) will always bond
together, and cytosine (C) and guanine (G) will always bond together. These restrictions make it
less likely that a mistake will happen when the DNA duplicates—which we’ll talk about later.
Chargaff’s rules are important, so remember: Ts will only bond with As, and Cs will only bond
with Gs.
Many times DNA is diagramed as a simple graphic. While the DNA backbone is made up of the
repeating sugar and phosphate molecules, they are not always shown. The bases in the middle
are sometimes shown to interlock by using special shapes. These special shapes represent the
number of bonds a base will make and how it will only bond with its corresponding base. The
following image is an example of the DNA base pairing I’ve been discussing—examine it now to
help you visualize and remember the structure of DNA.
This arrangement of DNA bases illustrates Chargaff’s rules clearly: Ts will

only bond with As, and Cs will only bond with Gs. © BYU

Self-Check
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Week 12
Week 12
DNA Replication

Reading Section
We’ve already learned that all cells come from preexisting cells. This means that a cell must
divide into two cells in order for cells to be produced. For example, you once started out as a
single cell (a fertilized egg). This one cell then divided into two, and the two divided again,
making a total of four cells. You can probably guess what the four cells did next. Yep, they
divided and made eight cells. The eight then made sixteen, and the sixteen made thirty-two,
then the thirty-two made sixty-four, then the sixty-four made one hundred and twenty-eight, etc.
Within a short period of time, millions of cells were created through the process of cell division.
The last lesson in this unit will focus on this process.
Pizza: photo (https://pixabay.com/fr/photos/pizza-alimentaire-italien-

cuit-3007395/) from Pixabay; cell: photo
(https://pixabay.com/fr/illustrations/cellules-humaine-m%C3%A9dicaux-
1872666/) from Pixabay.
Let’s pretend you have a whole supreme pizza with many different types of toppings. You take a
knife and cut your pizza into two pieces. You then cut each piece in half. As a result, you have
four pieces of pizza. Imagine doing this same process (cutting each piece in half) five more
times. Can you try to figure out how many pieces of pizza you would have? Here is a hint: the
correct number is in the paragraph above. The answer is 128 pieces of pizza. Do you think all
128 pieces would have each type of topping found on the original pizza? If you gave a person
one slice of a 128-piece pizza, do you think they would be able to name all the toppings that
were on the original pizza? I don’t think so. This is where you think to yourself, “What does this
have to do with biology?” In order for each cell to function like the cell it came from, the original
cell must have made an entire copy of the DNA before it divided—so unlike the pizza, no matter
how often the cells divide, the cells would always have the complete number of “toppings” found
in its makeup.
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As you may already know, each of your cells has a full copy of DNA in it. In order for the divided
cells to all have the same DNA in them, the DNA must be copied before a cell divides. If this did
not occur, the cells would only have a portion of the complete copy of DNA. Without a full copy
of DNA, the cell would be limited to certain functions. For example, let’s think of DNA as like a
cookbook. The cookbook has all types of recipes in it, from breakfast to dessert. Let’s say that
over time, random pages of the book were ripped out. One day you create a menu for dinner. It
includes an appetizer, a salad, a main dish, and a dessert. You go to the cookbook and discover
that you only have the recipes for the appetizer and salad. You cannot cook everything you
wanted to cook because you are missing the instructions for them. DNA replication needs to
occur before cell division because if it didn’t, the new cell wouldn’t have all the information in its
instructions to produce everything the new cell would need. In this section, we will look at the
process of making two copies of DNA from one original copy.
So, the goal here with DNA replication is to take one molecule of DNA and make two of them.
Remember that DNA is a double-stranded, twisted molecule. Also remember that DNA is
located in the nucleus of a cell, so the process of DNA replication will occur in the nucleus. The
first step is to untwist the DNA helix and begin to unzip the parent strand. In this step, the bonds
that connect the bases (A to T, and C to G) and keep the two strands together are broken.
The image below, A, shows a parent strand in its usual double helix shape and a parent strand
in the untwisted shape, which means it’s ready for separation and replication. As the original
parent strand separates (B), the new complementary bases will come in to match up with the
original DNA strands, forming daughter strands (C and D). It is important that the new bases are
complementary to, or match up with, the parent strands, because the daughter strands need to
have the exact information that the parent strand has. We know that this will happen correctly,
because the bases have specific base pairing. In other words, Ts will only bind with As, and Cs
will only bind with Gs. Remember that!
If you look at C, you’ll notice that the daughter strands form in different directions. They form in
different directions because the two strands in a DNA helix are oriented differently. The head of
one strand is attached to the tail of the second strand, and vice versa (this is called antiparallel
orientation). In replication, you can only create complementary strands from the head to the tail.
In the leading strand, a continuous row of bases forms from the head to the tail. On the lagging
strand, the replication is happening in the opposite direction, creating segments called Okazaki
fragments. Since the head of this strand isn’t exposed yet, the strands form in segments—from
as close as they can get to the head, down to where the last segment left off. As the original
parent strand continues to separate, more bases can attach, starting as close to the head as
possible and then continuing toward the tail.
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DNA replication: (A) original double helix, (B) double

helix unwinds, (C) backbone and complementary
bases assemble, (D) strands wind up to make helix,
(E) two double helixes. © BYU
After the new complementary bases are in place, the sugar-phosphate backbone bonds
together. After this step, there are two identical DNA molecules (D in the image at right). The
two separate molecules of DNA will twist around each other to create the helix structure. Now
there are two separate molecules of DNA where there was only one before (E), which means
that the DNA has been successfully replicated.
What controls the process of replication? Enzymes, which are made of protein, control it. There
are specific and separate enzymes that control the separation of the double helix, the insertion
of the correct base, and the construction of the backbone. The final step in DNA replication
occurs when an enzyme proofreads the new order of the bases to make sure they were
correctly put into place.
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To summarize, enzymes control every step of DNA replication. The steps of DNA replication are
as follows:
1. The original DNA molecule is separated.
2. New and complementary bases pair up with the original bases.
3. The sugar-phosphate backbone is constructed.
4. The backbone bonds to bases, and bases bond to each other.
5. The bases are proofread to make sure everything is correct, and the new strands twist
together, forming two identical double helixes.
The following video shows DNA replication in 3D animation.

Self-Check
172
Week 13
Week 13
Let's Get Started

Translation and transcription are terms that sound like they come out of a foreign language
course. (And you may think sometimes that studying biology is like taking a foreign language!)
In terms of DNA, translation and transcription have to do with copying of the information found in
DNA. When would DNA information need copying? Whenever a new cell is created. This week
you will learn how and where DNA information is replicated.

Outline
Lessons
Transcription
Objective |
(3 parts - 30 min.)
Translation
Objective |
(3 parts - 40 min.)
Media
From DNA to Protein Interactive Video (5 min.)
Translation Video (3.5 min.)

Protein Synthesis Interactive Video (15 min.)
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Assignments
Transcription Activity (5 min.)
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Week 13
Week 13
Transcription

Reading Section
First of all, what is protein synthesis? We know from previous instruction that ribosomes are
where protein synthesis occurs. We also learned that the nucleus is called the “brain” of the cell
because the DNA is inside the nucleus. DNA is the important record that dictates what will
happen inside your body. It has the blueprints for making every cell, and it tells the cells what
they should do. The way that DNA tells the cells what to do is by making proteins. Proteins are
made according to the blueprints on the DNA. Enzymes, or proteins, are the actual doers of the
cell. They are the ones that cause things to happen. If a cell divides, it is because a protein told
it to. If water or salts are brought into the cell, it is because a protein told the cell membrane to
allow them to come in.
Proteins are made in protein synthesis. In this section, we will discover how DNA dictates which
proteins are made and how the proteins are made. Protein synthesis is broken down into two
steps: transcription and translation. When these two steps are completed, a complete protein
will be made based on DNA.
Let's pretend you have been offered your dream job far from where you currently live. In order
for the company to put you in the position, they must have your birth certificate, your driver’s
license, and your social security card.
Would you mail them your original records? Take a minute to think of what you would do.
Some of you might just mail them your records because of how great the job is. Others of you
would make copies of the records and mail the copies. The reason it would be wise to make
copies of these types of records is that they are hard or impossible to replace. What if you sent
your originals, and they got lost in the mail? What if the company lost your originals, or just
never gave them back?
This same situation is happening inside every cell of your body. The original copy is just like
DNA. It has the necessary information on it to produce the protein. Remember, proteins are
produced at the ribosome. DNA is inside the nucleus and the ribosomes are outside the
nucleus. If the DNA left the nucleus, it could get lost or damaged. This would be very bad
because the cell would not be able to function properly without the DNA, or with damaged DNA.
Transcription is the process of making a copy of DNA so the copy can leave the nucleus and go
where it needs to, while the DNA can stay inside the nucleus, where it is protected. Typically,
when a copy is made for protein synthesis, only the important information is copied. Imagine it
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this way: if you only need the recipe for one meal, you are not going to copy the entire
cookbook. This is the same situation in transcription. Every chromosome has hundreds of genes
on it. A chromosome is made of tightly coiled strands of DNA and is found in the nucleus. A
gene is a segment of a chromosome that codes (provides the plan or template) for a protein. If a
certain protein needs to be made, then only that part of the DNA (the gene) is copied. Genes
are of all different lengths. Some genes are made up of only a few hundred bases, and some
have up to 600,000.
The copied DNA is called “messenger RNA.” Messenger RNA, or mRNA, is able to leave the
nucleus and venture out into the cell, because it is not exactly the same as the DNA it came
from — it has some special molecules called “caps” and “markers” that allow it to live outside of
the nucleus. Once it meets up with a ribosome, it can start to make proteins. If the messenger
RNA gets lost or injured, another copy of the DNA can be made, and thus the cell can continue
to live and function correctly.
A gene is a segment of DNA that will be translated into a protein molecule.

© BYU
How does DNA get copied into mRNA? The first step in copying a segment of DNA is to
separate the double helix, but not the entire thing. Remember, we just need a particular
segment, or gene. There is a protein that will identify where the correct gene is, and then the
two strands of DNA open up to allow the copy to be made.
We will be focusing on the top section of the DNA in the illustrations. The bottom strand of DNA
is complementary (Ts are with As and Cs are with Gs) to the top strand. The new mRNA strand
will be formed by using the top strand as a template.
Before we go on, we must know some more information concerning RNA. There are a few
differences between DNA and RNA. Some of the differences are that RNA is single-stranded,
while DNA is double-stranded. RNA stands for ribonucleic acid, while DNA stands for
deoxyribonucleic acid. This means that the DNA has one less oxygen than RNA (de- means
“without” and oxy- means “oxygen”). And lastly, RNA has uracil instead of thymine. Because
RNA does not have any Ts, where a T would be found (across from an A), there will be a U
instead. So earlier, when I said that As always bind with Ts, it was actually not true. In the case
of mRNA being created, a U is the complementary base that binds with the A.
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mRNA is a copy of a gene found on the DNA. © BYU
To see how this works, let’s look at the unzipped double helix in the image at the right. An
mRNA molecule will form opposite the DNA molecule. The bases that correctly pair up come in,
and the sugar-phosphate backbone binds as well.
The mRNA strand that has been produced here is complementary to the DNA. Notice that there
are Us in place of Ts on the mRNA strand. The mRNA strand can now leave the chromosomes
(in the nucleus) and go out to the ribosomes (in the cell), where a protein can be made from the
copy.
To summarize, transcription is when a gene, which is a portion of DNA, is copied into a

complementary strand of RNA (mRNA). This is done because the DNA does not leave the
nucleus, so it can remain safe for future use. Also, mRNA has markers on it that tell the nucleus
that it can be let out.

Self-Check
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Week 13
Translation

Reading Section
Translation is the second and last step in protein synthesis. In this step, a protein is assembled
by hooking amino acids together. The order in which the amino acids are assembled determines
the type of protein that is built. This ordering is controlled by the information found on the mRNA
strand, which was created during transcription in the nucleus of the cell. In this way, the mRNA
gives instructions, or we can say it “codes,” for a specific protein to be built.
mRNA will leave the nucleus and go to a ribosome that is free (in the cytoplasm) or
bound (attached to endoplasmic reticulum).
© BYU
As you may remember, the ribosomes are the site of protein synthesis. Ribosomes are found
either attached to the endoplasmic reticulum of the cell or free-floating in the cytoplasm.
Ribosomes that are associated with the endoplasmic reticulum are called bound ribosomes,
and those that are in the cytoplasm are called free ribosomes. If the protein that the mRNA
codes for will be used by the cell, the mRNA will go to a free ribosome. If the protein to be
created will be sent out of the cell, then the mRNA will travel to a bound ribosome (see the
image at right).
It’s important to understand how the bases on the mRNA strand give instructions for amino
acids to be assembled into a complete protein. A group of three mRNA bases is called a codon.
Each codon is an instruction, or “code,” for a specific amino acid. For example, the codon UGC
codes for the amino acid cysteine. You can use the table below to find what amino acids the
different codons will code for.
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Week 13
Let’s look for the codon AUG. First, start by finding A (the first base) along the left side of the
table. Put your finger on A so you don’t lose your place. Next, find the second base U along the
bottom of the graph. Put another finger on the U, and then move your two fingers together until
you end up in one box. You should be in the top row, in the third box from the left (the first word
in the box is “asparagine”). Lastly, find the third base on the right-hand side of the row your box
is in. The third base is G. Track the G over into your box. What is the amino acid that AUG
codes for? If you said methionine, you are correct.
Find the amino acids that GAU, UUU, CAC, GCC and UAU code for.
First Base in lysine lysine asparagine asparagine A

Codon lysine arginine methionine threonine G
A
asparagine serine isoleucine threonine U
asparagine serine isoleucine threonine C
glutamic
glycine valine alanine A
acid
glutamic
G glycine valine alanine G
acid
aspartic acid glycine valine alanine U
aspartic acid glycine valine alanine C Third Base in
stop Codon
stop codon leucine serine A
codon
U stop codon tryptophan leucine serine G
tyrosine cysteine phenylalanine serine U
tyrosine cysteine phenylalanine serine C
glutamine arginine leucine proline A
glutamine arginine leucine proline G
C
histidine arginine leucine proline U
histidine arginine leucine proline C
A G U C
Second Base in Codon
The answers are aspartic acid for GAU, phenylalanine for UUU, histidine for CAC, alanine for
GCC, and tyrosine for UAU. It may take some practice. You will be given the information from
this table on both the unit quiz and the final exam to help you find the amino acid when given a
specific codon. So, if you didn’t get all of the above answers correct, make sure you understand
why, reread the section, and practice finding codons on your own.
Now that you know how to read the chart, let’s see how amino acids are actually brought
together in the correct order, as determined by the codons on the mRNA.
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After transcription, newly created mRNA leaves the nucleus and makes its way to a
ribosome, which is made of a large and a small subunit. I sometimes picture this
arrangement like a stapler and paper. The paper (or mRNA, in this case) slips between the
two parts of the stapler (ribosome). Just like a stapler, a ribosome’s bigger part is on top.
Amino acids are brought to the ribosome to be assembled into a protein by transfer RNA
(tRNA).The tRNA matches up with the mRNA at docking stations (shown in light blue).
Notice that each docking station lines up with a codon on the mRNA. There are two docking
stations on the ribosome.
Three nucleotide bases on the bottom of the tRNA form an anticodon. It is complementary
to the codon on the mRNA. Because they match up, the correct amino acid will be added to
the protein. In this example, the codon AUG matches up with the anticodon of the tRNA that
reads UAC. Look at the table above. What is the name of the amino acid that tRNA will
bring in? Did you pick methionine (abbreviated as “Met” in the illustration)? If so, you are
correct. If not, were you looking for the anticodon? The table with amino acids will only work
with the codon. The docking station on the right will fill up first. Then the ribosome will move
toward the right.
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This illustration shows you that the ribosome will move one codon length down the mRNA
strand once the correct tRNA has filled the docking station on the right. The tRNA that was
in the docking station on the right is now in station on the left, and another tRNA fills the
right-hand docking station. The codon on the right reads GAA, and the correct anticodon is
CUU. The tRNA on the right brought with it the amino acid named glutamic acid (labeled
“Glu” in the illustration). Now both docking stations are full.
There are three things that happen once both docking stations are occupied by tRNA. First,
the two amino acids that are next to each other will bond together. Next, the tRNA that is on
the left will let go of its amino acid. Lastly, the tRNA on the left will leave the ribosome. This
last part will happen in conjunction with the ribosome moving down the strand toward the
right. From this point, the process will repeat until the mRNA is finished translating.
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With the ribosome moving toward the right, the tRNA that was holding the two amino acids
moved from the right docking station into the left docking station. In this step, the
corresponding tRNA anticodon to the codon GUA has filled the right docking station. The
tRNA brought with it the amino acid valine. Now, once again, both docking stations are full
and you may be able to guess what will happen next.
First, the amino acids will bond together. Second, the tRNA on the left will let go of its amino
acid. And third, the tRNA will be bumped out of the ribosome as the ribosome shifts down
the mRNA strand. This step leaves us with three amino acids hooked together.
When the ribosome shifts to the right, it opens up the right docking station, which in this
illustration has been filled with the tRNA carrying the amino acid labeled “Try” for
tryptophan. The tRNA holding the three amino acids is now in the left spot.
Valine and tryptophan hook together. Then the left tRNA lets go of the amino acid. Finally,
the left tRNA moves out of the docking station as the ribosome moves to the right.
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By doing this process four times, we have created a protein four amino acids in length. In
actuality, most proteins are made up of hundreds of amino acids hooked together. This
process of bringing in the amino acids continues until the mRNA reads UAA, UAG, or UGA.
Go back up to the table and find out which amino acid these codons stand for. You are
correct if you found STOP. When the ribosome comes to the stop codon, it lets go of the
mRNA, and the finished protein is released.
The illustration below shows two important things. First, it shows that many ribosomes can travel
down the same strand of mRNA, each creating identical proteins. And second, when the protein
gets to the end of the mRNA, the ribosome and the completed protein will be released into the
cytoplasm. The protein will go to perform its function, and the ribosome can be used again to
make more proteins. When the cell does not need to continue to make more of the protein, the
mRNA strand will be broken down into its components (sugar, phosphate, and base).
© BYU
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Take a look at this animation of the process.
Summary
The goal of protein synthesis is to make specific proteins according to the genetic code found on
the DNA. The process occurs in two stages. Transcription is the first step. This is where a
portion of DNA is copied to a molecule of mRNA. The mRNA then leaves the nucleus, where the
DNA must stay. The mRNA then travels to a ribosome. Translation is the second step of protein
synthesis. This is where the proteins are actually assembled. The ribosome attaches to the
mRNA, and tRNA molecules bring amino acids. The tRNA that has the corresponding anticodon
to the mRNA codon brings in the correct amino acid. The amino acids hook together, and a
protein is formed. This is how genetic information encoded in DNA provides instructions for
assembling protein molecules.

Self-Check
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Week 14
Week 14
Let's Get Started

The goal with copying something is to create an exact duplicate. The problem is that doing so is
virtually impossible. Even photocopying machines introduce noise into the duplication. When
cell information is copied incorrectly, bad things (and sometimes good things) can happen in the
body. This week you will look at what happens when translation and transcription don't work as
they are intended to do.

Outline
Lessons
Mutations
Objective |
(3 parts - 16 min.)
Media
Mutations Interactive Video (4 min.)
Sickle Cell Anemia (2 min.)
Assignments
Gene Therapy Deep Dive (90 min.)
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Experiences 4: DNA Extraction (30 min.)

Vo c a b u l a r y
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Week 14
Experiences 4: DNA Extraction

Instructions
Now that you have learned about DNA, we are going to extract DNA from strawberry cells and
another food of your choice. Remember to keep notes and photos from your observations in
your notebook. To perform this experiment, you will need the following:
Materials
Water1, dish soap2, rubbing alcohol3, salt4, strawberry5, Ziploc bag6,

rubber bands7, paper towels8, clear cup9
2 teaspoons water
¼ teaspoon dish soap
a pinch of salt
1 cup rubbing alcohol
a strawberry (fresh or frozen, but let it thaw if frozen)
Ziploc bag (sandwich size)
paper towel
a rubber band
a clear cup
another food of your choice that would be easy to smash (for example, peaches, blueberries,
or raspberries)
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Create a Hypothesis
In this experiment, you are going to extract DNA from a strawberry and another food item of
your choice. Based on what you have learned about DNA from the previous unit, create a
hypothesis that answers the following question: Do both foods contain DNA, and if so, which
one will have more DNA? Be sure to explain why you formed the hypothesis you did.
Procedure
1. Put the rubbing alcohol in the freezer for at least 30 minutes. Rubbing alcohol will not
freeze, so you can leave it in there longer if necessary.
2. Put the strawberry in the Ziploc bag, making sure the bag is sealed.
3. Mash up the strawberry.
4. Add 2 teaspoons of water to your clear cup.
5. Add ¼ teaspoon of dish soap to the cup. The dish soap will help to rupture the cell
membrane so the DNA is released more easily.
6. Add a pinch of salt to the cup. The salt will cause the DNA to clump together so it will be
easier to see.
7. Stir the mixture.
8. Add the water-soap-salt mixture to the bag with the mashed-up strawberry.
9. Make sure the bag is sealed, then mix the contents of the bag by squishing them together.
10. Place a paper towel over the cup, and then put a rubber band over the paper towel to hold
it onto the cup.
11. Gently push down the middle of the paper towel so it makes a well to hold the strawberry
mixture.
12. Slowly pour the strawberry mixture onto the paper towel. Make sure to not let it overflow
(that would be messy). The paper towel will filter out all the pulp and allow some of the
liquid to get into the cup.
13. It might take some time to filter the liquid out; give it about 5 minutes. You do not need a lot
of liquid; even just a few drops will work.
14. Remove the paper towel with all the strawberry pulp, and throw it away.
15. Now get the rubbing alcohol from the freezer. Add 1 cup of rubbing alcohol to the cup with
the filtered strawberry liquid.
16. Watch the liquid in the cup, looking for white strands to rise up toward the top. These white
strands are the DNA from the strawberry.
17. Repeat steps 1-16 using another food of your choice, and compare the amount of DNA
between the strawberry and your food item of choice.
Now that you have extracted DNA from strawberries, answer the reflection questions below.
After unit 6, you will submit a reflection assignment that will be a collection of all the
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reflection questions, so I recommend typing your answers in a document on your computer

so you can easily put them together and submit them later.
Question mark
© BYU
What was the hypothesis you created? Be sure to explain your reasoning for the hypothesis.
1. Use evidence from your experiment of extracting DNA from strawberries and the other
food of your choice to respond to the following statement: All food contains DNA.
2. DNA is so small that you have to use special microscopes to see it. If DNA is so tiny, why
were you able to see it with your naked eye?
3. You used soap in this experiment to break apart the cell membranes in the food you used.
Why would this be necessary to extract the DNA?
4. Explain one difference between the DNA extracted from the strawberry and the DNA
extracted from the other food item of your choice.
5. Explain why it is necessary for all living organisms to have DNA.
References
1. Photo (https://www.pexels.com/photo/water-drop-40784/) by Pexels.
2. Photo (https://www.flickr.com/photos/yourbestdigs/36740424785/in/album-
72157685398529050/) by Flickr.
3. Photo (https://commons.wikimedia.org/wiki/File:Rubbing_alcohol.JPG) by Craig Spurrier
(https://commons.wikimedia.org/wiki/User:Cspurrier) via Wikimedia Commons. CC BY 2.5
189
187
4. Photo (https://commons.wikimedia.org/wiki/File:Korean_sea_salt.jpg) by National Institute

of Korean Language via Wikimedia Commons. CC BY-SA 2.0 KR
(https://creativecommons.org/licenses/by-sa/2.0/kr/deed.en) .
5. Photo (https://pixabay.com/fr/photos/fraise-d%C3%A9couper-fruits-alimentaire-3394422/) by
Pixabay.
6. Photo (https://commons.wikimedia.org/wiki/File:Ziplock.jpg) in public domain.
7. Photo (https://commons.wikimedia.org/wiki/File:Rubber_bands.jpg) by FML
(https://commons.wikimedia.org/wiki/User:FML) via Wikimedia Commons. CC BY-SA 2.5
(https://creativecommons.org/licenses/by-sa/2.5/deed.en) .
8. Photo (https://commons.wikimedia.org/wiki/File:Paper_towels_1_2018-03-01.jpg) by Fastily
(https://commons.wikimedia.org/wiki/User_talk:Fastily) via Wikimedia Commons. CC BY-
SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0/deed.en) .
9. Photo (https://pixabay.com/fr/photos/verre-boire-verre-%C3%A0-eau-claire-3132832/) by
Pixabay.
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Week 15
Let's Get Started

We have talked about cell copying. There is another type of cellular creation that we must talk
about: reproduction. Reproduction isn't merely copying cells, it's creating the template for a new
life. This week we begin by talking about the two cellular reproductive processes: mitosis and
meiosis.
The content from this week comes from Unit 6: Cellular Reproduction (Objectives)

Outline
Lessons
Mitosis
Objective |
(4 parts - 51 min.)
Meiosis
Objective |
(4 parts - 41 min.)
Media
Mitosis Interactive Video (16 min.)
Meiosis Interactive Video (2 min.)

Phases of Meiosis Interactive Video (2 min.)
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Assignments
Cell Development Activity (5 min.)

Vo c a b u l a r y
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Week 15
Cell Growth Reading

Reading Section
All living things grow and develop. You have definitely grown. You have grown from the size you
were as a baby to many times that size by now. The way most organisms grow is by producing
more cells. In this section, we will look at how cells replicate, or divide, in order to make more
cells.
Cell Division
Cell growth is essential to survival. Cell division allows organisms to grow, as well as heal. The
way we grow is by making more cells. The way we heal is by making more cells to replace those
that were lost. For example, if I were to scrape my arm, my arm heals by having the skin cells
around it copy themselves until the scrape is covered up. There are two types of cell division:
mitosis and meiosis. Mitosis occurs in most living cells. This is a typical type of cell division.
Meiosis allows sexual reproduction to happen and occurs only in gamete cells. Gametes are
cells that are used for reproduction (i.e., egg and sperm cells). We will discuss meiosis later.
Diagram of the cell cycle broken down into mitosis and

interphase. Notice how mitosis takes up a relatively short amount
of time in the cycle. © BYU
When a cell divides, it goes through two processes: interphase and mitosis. Interphase is the
preparatory phase in cell division. Mitosis is the process a cell goes through during active cell
division. It is at the end of mitosis that you will have two identical cells. So the goal with cell
division is to begin with one cell and to completely separate it into two functioning cells. In the
illustration at right, you can see that mitosis is only part of a larger process. The illustration
shows the cell cycle, which is broken down into interphase and mitosis.
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When a cell divides, it goes through two processes: interphase and mitosis. Interphase is the
preparatory phase in cell division. Mitosis is the process a cell goes through during active cell
division. It is at the end of mitosis that you will have two identical cells. So the goal with cell
division is to begin with one cell and to completely separate it into two functioning cells. In the
illustration at right, you can see that mitosis is only part of a larger process. The illustration
shows the cell cycle, which is broken down into interphase and mitosis.
Interphase
Before cells actually split apart, there must be some preparation. The preparatory steps of the
cell cycle are called interphase. Interphase is composed of three steps: G1, S, and G2. Specific
events occur in each step.
G1—During Gap 1 (G1), the cell will experience rapid growth. The cell will take in more nutrients
and water for it to use for the following steps. The centriole, which is used to pull the replicated
chromosomes apart in mitosis, is copied.
S—The S phase stands for synthesis. In the S phase, the DNA is replicated. In order for cells to
divide, there must be the replication of the DNA from the nucleus. This is because every cell
needs a complete copy of the DNA. If cells divided and did not replicate the DNA, then not every
cell would have a complete code for survival. In G1, there is only one copy of each
chromosome. During S phase, each chromosome becomes a replicated chromosome, thus
doubling the amount of DNA in the cell. Most cells will have only forty-six chromosomes, but
during this step, the chromosomes duplicate, giving the cell twice as much DNA as a normal
cell.
So, if a cell that has just undergone S phase has twice the amount of DNA, how many
chromosomes does it have? If we simply added forty-six and forty-six, there would be ninety-
two, but in S phase, the chromosome will be replicated and will consist of two double helices
that are attached to each other. Even though there is twice the amount of DNA, it is still called a
single chromosome. Therefore, the cell still has forty-six replicated chromosomes at the end of
S phase.
Look at the illustration of this concept (below). The object on the left is an unreplicated
chromosome. It is a double helix; however, it is hard to see because it is so tightly wound. The
replicated chromosome is composed of two sister chromatids. When a sister chromatid is not
attached to another sister chromatid, then we call it a chromosome (unreplicated). When the
sister chromatid is attached to another sister chromatid, then we call it a chromosome
(replicated). The sister chromatids will join at the centromere, which is usually in the middle of
the chromosome (centro- referring to center).
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Unreplicated and replicated chromosomes. © BYU
G2—In Gap 2 (G2), final preparations for cell division must be made. Everything must be ready
before mitosis can begin. To help understand this phase, I think of how I prepare for going out to
a special event. Let’s pretend I have a fancy event I will be going to. I have already put on nice
clothes and made sure that I look presentable. It is here, at G2, that I do a double check. I will
look in a full-length mirror to make sure everything is correct. If there is something missing, it is
noticed here. This is just like G2. The major preparation has already happened; we are just
doing a double check that everything is ready to go. It is difficult to see the steps of interphase
because the DNA is not in its condensed form. However, to help us visualize the steps, examine
the diagrams below.
Interphase includes the G1, S, and G2 phases where the

chromosomes prepare for mitosis. © BYU
Once all the preparations have taken place in interphase, the cell will undergo the actively
dividing portion of the cell cycle: mitosis.

Self-Check
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Week 15
Mitosis Reading

Reading Section
Mitosis is the process of active cell division. Because everything should be ready to go at the
completion of interphase, the cell can physically divide into two parts. Mitotic division can be
broken down into five steps, which are listed and discussed below. Even though there are
distinct events that happen in each step, the process is fluid—it happens gradually.
Prophase
Step 1. During prophase, chromosomes condense, the nucleus

disappears, and the centrioles move to opposite sides of the cell.
© BYU
During prophase, the chromosomes become more visible. This is because they condense into a
compacted form. When I think of uncoiled chromosomes, I picture spaghetti. In interphase
(specifically S phase), when the DNA is replicating, the chromosome needs to be spread out in
order to unzip and make a new copy. But how easy is it to pick out a piece of spaghetti from a
bowl without breaking it? It would be much easier to pick out a piece of, say, macaroni. This is
because macaroni is smaller and more compact. Now is the time to try to move the
chromosomes around. We are not looking at any of the information found on them, so it
becomes easier to shift them around if they are smaller. The chromosomes are replicated, which
happened in S phase of interphase. This means that each chromosome is composed of two
sister chromatids that are attached to each other at their centromere.
Also during prophase, the nucleus disappears so the chromosomes can be moved around the
cell, and the centrioles move to opposite sides of the cell. The centrioles are part of the
cytoskeleton (or support) structures that are useful in pulling the chromosome into two parts in a
later step.
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Metaphase
Step 2. During metaphase, chromosomes line up in the center of

the cell and spindle fibers from the centrioles attach to their
centromeres.
© BYU
During metaphase, the chromosomes line up along an imaginary plane in the center of the cell.
For a normal human somatic (body) cell, there are forty-six replicated chromosomes in one line.
While the chromosomes are lined up in the middle, spindle fibers come out of the centrioles and
attach to the centromeres of the chromosome, as shown in the illustration at the right. I picture
the centrioles as Spider-Man. There are two spidermen on either side of the cell. Between the
two Spider-Men is the line of chromosomes. Each Spider-Man wants half of each replicated
chromosome (sister chromatid). Because they are too far away to just grab with their hands,
they use their wrist webs that shoot out to attach at the centromere of each chromosome.
Anaphase
Step 3. During anaphase, the sister chromatids get pulled

apart towards opposite ends of the cell by the attached spindle
fibers. © BYU
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During anaphase, the replicated chromosomes split apart and travel to opposite sides of the
cell. The strands of material originating from the centriole (spindle fibers) pull the chromosomes
apart at their centromere, as shown in the illustration. How many chromosomes are in the
illustration? There are six chromosomes. Once the replicated chromosome is split in half, the
two sister chromatids are no longer joined at the centromere, which actually means that we
cannot call them sister chromatids anymore. The former sister chromatids are now individual
molecules of DNA called chromosomes or unreplicated chromosome, each one made of a
double helix.
Cell division has not fully taken place. Even though the DNA has separated, there is still only
one cell. How many chromosomes are in a human cell during anaphase? Hint—there were
forty-six replicated chromosomes in metaphase, and now there are only unreplicated
chromosomes (they split apart). You are correct if you doubled forty-six to get ninety-two
chromosomes, which is twice the number of chromosomes of any cell during normal,
nondividing existence.
At the end of anaphase, the chromosomes have been pulled completely over to one of the sides
of the cell. You can identify this phase by looking for two masses of chromosomes that have
been separated.
Te l o p h a s e
Step 4. During telophase, chromosomes begin to uncoil and

a nucleus reforms around each group of DNA.
© BYU
During telophase, the cell membrane begins to pinch off between the two groups of
chromosomes. A nucleus forms around each group of chromosomes, and the chromosomes
begin to uncoil. Why would the chromosomes uncoil at this point of cell division? Why do the
chromosomes coil up and condense during prophase? Take a minute to try to answer these
questions before moving on.
If the purpose of the chromosomes condensing in prophase is to be able to move them around
easier, and we just finished getting the chromosomes to where they needed to go (to the
opposite sides of the cell), then the purpose of condensing has been completed. Looking at the
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Step 4 illustration above, you can see the lengthening of the chromosomes as well as the
nuclear membrane. How many chromosomes are there in telophase? You can still say ninety-
two even though there are forty-six on each side because there is still only one cell. The cell has
not completely divided yet. Which brings us to the next phase—cytokinesis.
Cytokinesis
Step 5. During cytokinesis, the cytoplasm, organelles, and

chromosomes divide and form two separate cells. © BYU
Cytokinesis is the final step of the process, and it involves complete division of the two cells (see
the Step 5 illustration). It is during this step of mitosis that all of the cytoplasm, cell organelles,
nucleus, and chromosomes are completely separated from each other. In a human cell, you will
now have two cells, each with forty-six chromosomes. That concludes the entire process of
mitosis as well as cellular division. The mission of going from one cell to two cells, with identical
DNA, has been accomplished. Well done.
Because the process of mitosis is fairly detailed, it is important for you to visualize the process a
number of times. I usually like to go through the information at least two or three times so I can
be sure to remember what happens in each step. Do not get discouraged if you do not
understand it the first time. It usually takes a while for the information to sink in.

Self-Check
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Meiosis, Part 11

Reading Section
Sexual reproduction requires fertilization, the union of two cells from two individual organisms.
If those two cells each contain one set of chromosomes, then the resulting cell contains two sets
of chromosomes. Haploid cells contain one set of chromosomes. Cells containing two sets of
chromosomes are called diploid. The number of sets of chromosomes in a cell is called its
ploidy level. If the reproductive cycle is to continue, then the diploid cell must somehow reduce
its number of chromosome sets before fertilization can occur again, or there will be a continual
doubling in the number of chromosome sets in every generation. So, in addition to fertilization,
sexual reproduction includes a nuclear division that reduces the number of chromosome sets.
Most animals and plants are diploid, containing two sets of chromosomes. In each somatic
cell of the organism (all cells of a multicellular organism except the gametes or reproductive
cells), the nucleus contains two copies of each chromosome, called homologous chromosomes.
Somatic cells are sometimes referred to as “body” cells. Homologous chromosomes are
matched pairs containing the same genes in identical locations along their length. Diploid
organisms inherit one copy of each homologous chromosome from each parent; all together,
they are considered a full set of chromosomes. Haploid cells, containing a single copy of each
homologous chromosome, are found only within structures that give rise to either gametes or
spores. Spores are haploid cells that can produce a haploid organism or can fuse with another
spore to form a diploid cell. All animals and most plants produce eggs and sperm, or gametes.
Some plants and all fungi produce spores.
The nuclear division that forms haploid cells, which is called meiosis, is related to mitosis. As
you have learned, mitosis is the part of a cell reproduction cycle that results in identical daughter
nuclei that are also genetically identical to the original parent nucleus. In mitosis, both the parent
and the daughter nuclei are at the same ploidy level—diploid for most plants and animals.
Meiosis employs many of the same mechanisms as mitosis. However, the starting nucleus is
always diploid and the nuclei that result at the end of a meiotic cell division are haploid. To
achieve this reduction in chromosome number, meiosis consists of one round of chromosome
duplication and two rounds of nuclear division. Because the events that occur during each of the
division stages are analogous to the events of mitosis, the same stage names are assigned.
However, because there are two rounds of division, the major process and the stages are
designated with a “I” or a “II.” Thus, meiosis I is the first round of meiotic division and consists
of prophase I, prometaphase I, and so on. Meiosis II, in which the second round of meiotic
division takes place, includes prophase II, prometaphase II, and so on.
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Meiosis I
Meiosis is preceded by an interphase consisting of the G1, S, and G2 phases, which are nearly
identical to the phases preceding mitosis. The G1 phase, which is also called the first gap
phase, is the first phase of the interphase and is focused on cell growth. The S phase is the
second phase of interphase, during which the DNA of the chromosomes is replicated. Finally,
the G2 phase, also called the second gap phase, is the third and final phase of interphase; in
this phase, the cell undergoes the final preparations for meiosis.
During DNA duplication in the S phase, each chromosome is replicated to produce two identical
copies, called sister chromatids, that are held together at the centromere by cohesin proteins.
Cohesin holds the chromatids together until anaphase II. The centrosomes, which are the
structures that organize the microtubules of the meiotic spindle, also replicate. This prepares the
cell to enter prophase I, the first meiotic phase.
Prophase I
Early in prophase I, before the chromosomes can be seen clearly microscopically, the
homologous chromosomes are attached at their tips to the nuclear envelope by proteins. As the
nuclear envelope begins to break down, the proteins associated with homologous chromosomes
bring the pair close to each other. Recall that, in mitosis, homologous chromosomes do not pair
together. In mitosis, homologous chromosomes line up end-to-end so that when they divide,
each daughter cell receives a sister chromatid from both members of the homologous pair.
The synaptonemal complex, a lattice of proteins between the homologous chromosomes, first
forms at specific locations and then spreads to cover the entire length of the chromosomes. The
tight pairing of the homologous chromosomes is called synapsis. In synapsis, the genes on the
chromatids of the homologous chromosomes are aligned precisely with each other. The
synaptonemal complex supports the exchange of chromosomal segments between non-sister
homologous chromatids, a process called crossing over. Crossing over can be observed visually
after the exchange as chiasmata (singular = chiasma) (Figure).
In species such as humans, even though the X and Y sex chromosomes are not homologous
(most of their genes differ), they have a small region of homology that allows the X and Y
chromosomes to pair up during prophase I. A partial synaptonemal complex develops only
between the regions of homology.
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Early in prophase I, homologous chromosomes come together to form a synapse.

The chromosomes are bound tightly together and in perfect alignment by a protein
lattice called a synaptonemal complex and by cohesin proteins at the centromere.
Located at intervals along the synaptonemal complex are large protein assemblies
called recombination nodules. These assemblies mark the points of later chiasmata and
mediate the multistep process of crossover—or genetic recombination—between the non-sister
chromatids. Near the recombination nodule on each chromatid, the double-stranded DNA is
cleaved, the cut ends are modified, and a new connection is made between the non-sister
chromatids. As prophase I progresses, the synaptonemal complex begins to break down and
the chromosomes begin to condense. When the synaptonemal complex is gone, the
homologous chromosomes remain attached to each other at the centromere and at chiasmata.
The chiasmata remain until anaphase I. The number of chiasmata varies according to the
species and the length of the chromosome. There must be at least one chiasma per
chromosome for proper separation of homologous chromosomes during meiosis I, but there
may be as many as 25. Following crossover, the synaptonemal complex breaks down and the
cohesin connection between homologous pairs is also removed. At the end of prophase I, the
pairs are held together only at the chiasmata (Figure
(https://cnx.org/contents/[email protected]:GYZS3DDP@9/The-Process-of-Meiosis#fig-ch11-01-02) )
and are called tetrads because the four sister chromatids of each pair of homologous
chromosomes are now visible.
The crossover events are the first source of genetic variation in the nuclei produced by meiosis.
A single crossover event between homologous non-sister chromatids leads to a reciprocal
exchange of equivalent DNA between a maternal chromosome and a paternal chromosome.
Now, when that sister chromatid is moved into a gamete cell it will carry some DNA from one
parent of the individual and some DNA from the other parent. The sister recombinant chromatid
has a combination of maternal and paternal genes that did not exist before the crossover.
Multiple crossovers in an arm of the chromosome have the same effect, exchanging segments
of DNA to create recombinant chromosomes.
202
Week 15
Crossover occurs between non-sister chromatids of homologous chromosomes.

The result is an exchange of genetic material between
homologous chromosomes.
Prometaphase I
The key event in prometaphase I is the attachment of the spindle fiber microtubules to the
kinetochore proteins at the centromeres. Kinetochore proteins are multiprotein complexes that
bind the centromeres of a chromosome to the microtubules of the mitotic spindle. Microtubules
grow from centrosomes placed at opposite poles of the cell. The microtubules move toward the
middle of the cell and attach to one of the two fused homologous chromosomes. The
microtubules attach at each chromosomes’ kinetochores. With each member of the homologous
pair attached to opposite poles of the cell, in the next phase, the microtubules can pull the
homologous pair apart. A spindle fiber that has attached to a kinetochore is called a kinetochore
microtubule. At the end of prometaphase I, each tetrad is attached to microtubules from both
poles, with one homologous chromosome facing each pole. The homologous chromosomes are
still held together at chiasmata. In addition, the nuclear membrane has broken down entirely.
203

Self-Check
References
1 “11.1: The Process of Meiosis
(https://cnx.org/contents/[email protected]:GYZS3DDP@9/The-Process-of-Meiosis) ,” OpenStax
204
Week 15
Week 15
Meiosis, Part 21

Reading Section
Metaphase I
During metaphase I, the homologous chromosomes are arranged in the center of the cell with
the kinetochores facing opposite poles. The homologous pairs orient themselves randomly at
the equator. For example, if the two homologous members of chromosome 1 are labeled a and
b, then the chromosomes could line up a-b, or b-a. This is important in determining the genes
carried by a gamete, as each will only receive one of the two homologous chromosomes. Recall
that homologous chromosomes are not identical. They contain slight differences in their genetic
information, causing each gamete to have a unique genetic makeup.
This randomness is the physical basis for the creation of the second form of genetic variation in
offspring. Consider that the homologous chromosomes of a sexually reproducing organism are
originally inherited as two separate sets, one from each parent. Using humans as an example,
one set of 23 chromosomes is present in the egg donated by the mother. The father provides
the other set of 23 chromosomes in the sperm that fertilizes the egg. Every cell of the
multicellular offspring has copies of the original two sets of homologous chromosomes. In
prophase I of meiosis, the homologous chromosomes form the tetrads. In metaphase I, these
pairs line up at the midway point between the two poles of the cell to form the metaphase plate.
Because there is an equal chance that a microtubule fiber will encounter a maternally or
paternally inherited chromosome, the arrangement of the tetrads at the metaphase plate is
random. Any maternally inherited chromosome may face either pole. Any paternally inherited
chromosome may also face either pole. The orientation of each tetrad is independent of the
orientation of the other 22 tetrads.
This event—the random (or independent) assortment of homologous chromosomes at the

metaphase plate—is the second mechanism that introduces variation into the gametes or
spores. In each cell that undergoes meiosis, the arrangement of the tetrads is different. The
number of variations is dependent on the number of chromosomes making up a set. There are
two possibilities for orientation at the metaphase plate; the possible number of alignments
therefore equals 2n, where n is the number of chromosomes per set. Humans have 23
chromosome pairs, which results in over eight million (223) possible genetically distinct
gametes. This number does not include the variability that was previously created in the sister
205
chromatids by crossover. Given these two mechanisms, it is highly unlikely that any two haploid
cells resulting from meiosis will have the same genetic composition.
To summarize the genetic consequences of meiosis I, the maternal and paternal genes are
recombined by crossover events that occur between each homologous pair during prophase I.
In addition, the random assortment of tetrads on the metaphase plate produces a unique
combination of maternal and paternal chromosomes that will make their way into the gametes.
Random, independent assortment during metaphase I can be demonstrated by considering a cell with a set of two
chromosomes (n= 2). In this case, there are two possible arrangements at the equatorial plane in metaphase I.
The total possible number of different gametes is 2n, where n equals the number of chromosomes in a set. In this
example, there are four possible genetic combinations for the gametes. With n = 23 in human cells, there are over
8 million possible combinations of paternal and maternal chromosomes.
Anaphase I
In anaphase I, the microtubules pull the linked chromosomes apart. The sister chromatids
remain tightly bound together at the centromere. The chiasmata are broken in anaphase I as the
microtubules attached to the fused kinetochores pull the homologous chromosomes apart.
206
Week 15
Te l o p h a s e I a n d C y t o k i n e s i s
In telophase, the separated chromosomes arrive at opposite poles. The remainder of the typical
telophase events may or may not occur, depending on the species. In some organisms, the
chromosomes decondense and nuclear envelopes form around the chromatids in telophase I. In
other organisms, cytokinesis—the physical separation of the cytoplasmic components into two
daughter cells—occurs without reformation of the nuclei. In nearly all species of animals and
some fungi, cytokinesis separates the cell contents via a cleavage furrow (constriction of the
actin ring that leads to cytoplasmic division). In plants, a cell plate is formed during cell
cytokinesis by Golgi vesicles fusing at the metaphase plate. This cell plate will ultimately lead to
the formation of cell walls that separate the two daughter cells.
Two haploid cells are the end result of the first meiotic division. The cells are haploid because at
each pole, there is just one of each pair of the homologous chromosomes. Therefore, only one
full set of the chromosomes is present. This is why the cells are considered haploid—there is
only one chromosome set, even though each homolog still consists of two sister chromatids.
Recall that sister chromatids are merely duplicates of one of the two homologous chromosomes
(except for changes that occurred during crossing over). In meiosis II, these two sister
chromatids will separate, creating four haploid daughter cells.
Meiosis II
In some species, cells enter a brief interphase, or interkinesis, before entering meiosis II.
Interkinesis lacks an S phase, so chromosomes are not duplicated. The two cells produced in
meiosis I go through the events of meiosis II in synchrony. During meiosis II, the sister
chromatids within the two daughter cells separate, forming four new haploid gametes. The
mechanics of meiosis II is similar to mitosis, except that each dividing cell has only one set of
homologous chromosomes. Therefore, each cell has half the number of sister chromatids to
separate out as a diploid cell undergoing mitosis.
Prophase II
If the chromosomes decondensed in telophase I, they condense again. If nuclear envelopes
were formed, they fragment into vesicles. The centrosomes that were duplicated during
interkinesis move away from each other toward opposite poles, and new spindles are formed.
Prometaphase II
The nuclear envelopes are completely broken down, and the spindle is fully formed. Each sister
chromatid forms an individual kinetochore that attaches to microtubules from opposite poles.
Metaphase II
The sister chromatids are maximally condensed and aligned at the equator of the cell.
207
Anaphase II
The sister chromatids are pulled apart by the kinetochore microtubules and move toward
opposite poles. Non-kinetochore microtubules elongate the cell.
The process of chromosome alignment differs between meiosis I and meiosis II. In prometaphase I, microtubules
attach to the fused kinetochores of homologous chromosomes, and the homologous chromosomes are arranged
at the midpoint of the cell in metaphase I. In anaphase I, the homologous chromosomes are separated. In
prometaphase II, microtubules attach to the kinetochores of sister chromatids, and the sister chromatids are
arranged at the midpoint of the cells in metaphase II. In anaphase II, the sister chromatids are separated.
Te l o p h a s e I I a n d C y t o k i n e s i s
The chromosomes arrive at opposite poles and begin to decondense. Nuclear envelopes form
around the chromosomes. Cytokinesis separates the two cells into four unique haploid cells. At
this point, the newly formed nuclei are both haploid. The cells produced are genetically unique
because of the random assortment of paternal and maternal homologs and because of the
recombining of maternal and paternal segments of chromosomes (with their sets of genes) that
occurs during crossover. The entire process of meiosis is outlined below.
208
Week 15
An animal cell with a diploid number of four (2n = 4) proceeds through the stages of meiosis to form four haploid
daughter cells.
209

Self-Check
References
1. “11.1: The Process of Meiosis
(https://cnx.org/contents/[email protected]:GYZS3DDP@9/The-Process-of-Meiosis) ,”
210
Week 16
Week 16
Let's Get Started

It is now time to make some comparisons between mitosis and meiosis. Since the two
processes are related, but not the same, it is good to review the differences between them.
The content from this week comes from Unit 6: Cellular Reproduction (Objectives)

Outline
Lessons
Mitosis vs Meiosis
Objective |
(5 parts - 94 min.)
Media
Mitosis vs Meiosis Interactive Video (3 min.)
Mitosis vs Meiosis Interactive Video 2 (8 min.)
Comparison activity (5 min.)
Assignments
Mitosis Meiosis Presentation Deep Dive (60 min.)
211

Vo c a b u l a r y
212
Week 16
Week 16
Comparing Mitosis and Meiosis1

Reading Section
Mitosis and meiosis are both forms of division of the nucleus in eukaryotic cells. They share
some similarities, but also exhibit distinct differences that lead to very different outcomes (see
figure below). Mitosis is a single nuclear division that results in two nuclei that are usually
partitioned into two new cells. The nuclei resulting from a mitotic division are genetically identical
to the original nucleus. They have the same number of sets of chromosomes, one set in the
case of haploid cells and two sets in the case of diploid cells. In most plants and all animal
species, it is typically diploid cells that undergo mitosis to form new diploid cells. In contrast,
meiosis consists of two nuclear divisions resulting in four nuclei that are usually partitioned into
four new cells. The nuclei resulting from meiosis are not genetically identical and they contain
one chromosome set only. This is half the number of chromosome sets in the original cell, which
is diploid.
The main differences between mitosis and meiosis occur in meiosis I, which is a very different
nuclear division than mitosis. In meiosis I, the homologous chromosome pairs become
associated with each other, are bound together with the synaptonemal complex, develop
chiasmata and undergo crossover between sister chromatids, and line up along the metaphase
plate in tetrads with kinetochore fibers from opposite spindle poles attached to each kinetochore
of a homolog in a tetrad. All of these events occur only in meiosis I.
When the chiasmata resolve and the tetrad is broken up with the homologs moving to one pole
or another, the ploidy level—the number of sets of chromosomes in each future nucleus—has
been reduced from two to one. For this reason, meiosis I is referred to as a reduction division.
There is no such reduction in ploidy level during mitosis.
Meiosis II is much more analogous to a mitotic division. In this case, the duplicated
chromosomes (only one set of them) line up on the metaphase plate with divided kinetochores
attached to kinetochore fibers from opposite poles. During anaphase II, as in mitotic anaphase,
the kinetochores divide and one sister chromatid—now referred to as a chromosome—is pulled
to one pole while the other sister chromatid is pulled to the other pole. If it were not for the fact
that there had been crossover, the two products of each individual meiosis II division would be
identical (like in mitosis). Instead, they are different because there has always been at least one
crossover per chromosome. Meiosis II is not a reduction division because although there are
fewer copies of the genome in the resulting cells, there is still one set of chromosomes, as there
was at the end of meiosis I.
213
Meiosis and mitosis are both preceded by one round of DNA replication; however, meiosis includes two nuclear
divisions. The four daughter cells resulting from meiosis are haploid and genetically distinct. The daughter cells
resulting from mitosis are diploid and identical to the parent cell.
Self-Check
References
1. “11.1 The Process of Meiosis
(https://cnx.org/contents/[email protected]:GYZS3DDP@9/The-Process-of-Meiosis) ,”
Openstax CNX Biology, CC BY 4.0
214
Week 17
Week 17
Let's Get Started

The content from this week is a summary activity (making yogurt) and the submission of the
summary of your second set of experiences. You should also be preparing for your final exam.

Outline
Lessons
Experiences 5: Making Yogurt

Objective
(1 part - 70 min.)
Media
Easy Homemade Greek Yogurt Tutorial (10 min.)
Assignments
Experiences 5: Making Yogurt Activity (60 min.)
215
Week 17
Experiences 5: Making Yogurt

Instructions
You have learned in previous activities how useful microorganisms can be in producing certain
types of food. In this experiment, you will be creating yogurt using milk and bacteria. Yogurt is
produced when bacteria eat the sugars in milk and produce lactic acid. The lactic acid lowers
the pH of the yogurt, giving yogurt its tart taste. The acidity of the yogurt also makes it difficult for
other organisms to survive in it, which is why yogurt typically lasts longer than regular milk.
In this experiment, you will observe fermentation by using different starter cultures of yogurt to
break down the sugars of milk into lactic acid. You will also be testing different types of yogurt to
see which are best to use as starter cultures when making yogurt. To perform this experiment,
you will need the following:

Materials
Milk1, yogurt2, tablespoon3, cup4, spoons5, pot6, thermometer7, crock

pot8, plastic containers9
216
Week 17
1 quart milk
4 different brands of single-serving yogurts to use as starter cultures. Here are the different
types of yogurt to use:
1. plain regular yogurt with live and/or active cultures
2. regular yogurt with flavoring added
3. plain Greek yogurt with live and/or active cultures
4. Greek yogurt with flavoring added
spoon
pot
stove
4 containers, all the same size and shape with lids, and each able to hold at least 1 cup of
liquid
tablespoon to measure the yogurt
one-cup measuring cup to measure the milk
thermometer for liquids
a cooler or a slow cooker for creating a water bath (see instructions directly below to help
you decide which method will work best for you)

Create a Hypothesis
In this lab, you will be creating yogurt using four different types of yogurt. Create a hypothesis on
which type of the four yogurts will work best.

Procedure
1. Heat the milk over medium heat until the milk reaches 180°F. Be sure to stir the milk
regularly so that it does not scald at the bottom of the pot.
2. Remove the milk from the heat and let it cool to around 110°F.
3. Pour 1 cup of the milk into each of the four containers.
4. Add 1 tablespoon of the regular plain yogurt into one container and label the container.
5. Add 1 tablespoon of the flavored regular yogurt into another container and label the
container.
6. Add 1 tablespoon of the plain Greek yogurt into another container and label.
7. Add 1 tablespoon of the flavored Greek yogurt into the last container and label.
8. Create a hot water bath using one of the following methods:
Fill a cooler with water at 130°F just to the height of the liquid in the containers. The
cooler needs to be large enough that all four containers can fit; fill it with water just up
to the level of the liquid in the jars. Make sure to close the lid on the cooler while
incubating the yogurt.
217
Use a slow cooker, but only if the slow cooker is able to run low enough to keep the
temperature of the water at 110°F. The slow cooker needs to be large enough that all
four containers can fit; fill it with water just up to the level of liquid in the jars. Put the lid
on the slow cooker.
9. Let the yogurt incubate for 8–12 hours.
10. Refrigerate the yogurt for at least 2 hours.
11. Observe each yogurt and write your observations, making note of the texture, thickness,
color, and (if you are brave enough) the taste of each of the four yogurts.
Here is a video that can help you with the process:

Now that you have created yogurt, answer the reflection questions below. After unit 6, you will
submit a reflection assignment that will be a collection of all the reflection questions, so I
recommend typing your answers in a document on your computer so you can easily put them
together and submit them later.
Question mark
© BYU
1. What was the hypothesis you created? Be sure to explain your reasoning for you
hypothesis.
2. What observations did you make about the four different yogurts you created?
3. What yogurt did you conclude was the best yogurt starter? Be sure to include observations
from your experiment to support your conclusion.
4. In the unit before this experiment, you learned about mitosis. What is mitosis, and how
does it relate to the yogurt-making experiment?
218
Week 17
References
1. Photo (https://pixabay.com/fr/photos/bouteille-de-lait-lait-bouteille-2740848/) by
Pixabay.
2. Photo (https://commons.wikimedia.org/wiki/File:Turkish_strained_yogurt.jpg) by
Takeaway (https://commons.wikimedia.org/wiki/User:Takeaway) via Wikimedia
Commons. CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0/deed.en) .
4. Photo
(https://commons.wikimedia.org/wiki/File:Measuring_Cup_isolated_on_White_Backgroun
d.jpg) by Jonatan Svensson Glad (https://www.wikidata.org/wiki/Q28709959) via
Wikimedia Commons. CC BY-SA 4.0 (https://creativecommons.org/licenses/by-
sa/4.0/deed.en) .
5. Photo (https://www.pexels.com/photo/baking-cooking-kitchen-utensils-natural-
2355717/) by Pexels.
6. Photo (https://www.pexels.com/photo/black-and-gray-cooking-pot-and-frying-pan-with-
tomatoes-877226/) by Pexels.
7. Photo (https://www.flickr.com/photos/79892177@N00/3773209534) by Steven Jackson
(https://www.flickr.com/photos/jackson3/) via Flickr. CC BY 2.0
8. Photo (https://commons.wikimedia.org/wiki/File:6_quart_Crock_Pot_slow_cooker.jpg)
by Your Best Digs via Wikimedia Commons. CC BY 2.0
9. Photo (https://www.pxfuel.com/en/free-photo-jmwps) by PXFuel.
219

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Biology 041

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Biology 041—Biology, Part 1

Copyright © 2021 Brigham Young University. All rights reserved.

• this introductory letter

Let's Get Started

The Scientific Method

The Characteristics of Life

Sunflower video (1.5 min.)

Scientific Method Activity (5 min.)

Scientific Method Lab (10 min.)

Scientific Method Set-up Assignment (20 min.)

The Characteristics of Life Activity (5 min.)

Levels of Organization of Living Things activity (5 min.)

Self-Checks (15 min.)

Please view this vocabulary deck in your online course.

The Scientiﬁc Method1

Sir Francis Bacon (1561–1626) is

The scientific method consists of a series of well-defined

Please complete this self-check exercise in your online course.

The Characteristics of Life1

A toad represents a highly organized structure consisting of cells,

Sensitivity or Response to Stimuli

Watch this video to see how sunflowers respond to light.

Please return to the online course to view this video.

Growth and Development

Polar bears (Ursus maritimus) and other mammals living in ice-

The California condor (Gymnogyps californianus) uses chemical

Levels of Organization of Living Things1

All molecules, including this DNA molecule, are composed of atoms.

consists of a nucleus surrounded by electrons. Atoms form molecules. A molecule is a chemical

Some cells contain aggregates of macromolecules surrounded by membranes; these are

Please return to the online course to explore this interaction.

Please complete this self-check exercise in your online course.

Let's Get Started

Biotic and Abiotic Factors

Water and the Building Blocks of Life

Water and Life video (11 min.)

Experiences 1: Sourdough Starter (60 min.)

Properties of Water Lab: Tension (10 min.)

Properties of Water Deep Dive Assignment (30 min.)

Properties of Water Activity (5 min.)

Self-Checks (15 min.)

Please view this vocabulary deck in your online course.

Biotic and Abiotic Factors

Please view this video in your online course.

About Your Five Biology Experiences Assignments

Introduction to Your Biology Experiences

Experiences Timeline © BYU

Experiences 1: Sourdough Starter

Please watch this video in your online course.

Follow the steps below to create your starter:

Water1, wheat flour2, flour3, and plastic wrap4

Here's a video that goes through the sourdough creation process:

Please watch this video in your online course.

Questions and Notes

(https://www.flickr.com/photos/30478819@N08/) via Flicker. CC BY 2.0.

The Building Blocks of Life1

Define matter and elements

Table 2.1. Approximate Percentage of Elements in Living Organisms (Humans)