Biology Lab Report

DescriptionSCI123: BIOLOGY with BOTANY & ZOOLOGY
SYLLABUS
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Plagiarism Statement
I understand that I must use research conventions to cite and clearly mark other people’s ideas and words within my paper. I
understand that plagiarism is an act of intellectual dishonesty. I understand it is academically unethical and unacceptable to
do any of the following acts of which I will be immediately expelled without refund:
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To submit an essay written in whole or in part by another student as if it were my own.
To download an essay from the internet, then quote or paraphrase from it, in whole or in part, without acknowledging
the original source.
To restate a clever phrase verbatim from another writer without acknowledging the source.
To paraphrase part of another writer’s work without acknowledging the source.
To reproduce the substance of another writer’s argument without acknowledging the source.
To take work originally done for one instructor’s assignment and re-submit it to another teacher.
To cheat on tests or quizzes through the use of crib sheets, hidden notes, viewing another student’s paper, revealing
the answers on my own paper to another student through verbal or textual communication, sign language, or other
means of storing and communicating information–including electronic devices, recording devices, cellular telephones,
headsets, and portable computers.
To copy another student’s work and submit the work as if it were the product of my own labor.
IMPORTANT NOTE:
Use your book as a source for understanding, you don’t need to read it word
for word. This class is based on the Science of Life, how it is explored and
experimentation. You will be mostly required to share your thoughts on
ethical issues involving controversial topics in biology. Take notes! The
textbook for this class is at an IB level – which is a high honor’s level,
however, notes have been provided.
Overview of Biology
For this first week, use ONLY THE IOHS BIOLOGY NOTES PROVIDED
Read, study, and use for assignment application.
INTRODUCTION: THE NATURE OF SCIENCE AND BIOLOGY
LAB I: “Adaptive Traits”
READ TEXTBOOK NOTES
1.) What is meant by “theory”, “law”, and “hypothesis”?
2.) The purpose of a control in a scientific experiment is to ___. a) provide a basis of comparison between
experimental and non-experimental; b) indicate the dependent variable; c) indicate the independent
variable; d) provide a baseline from which to graph the data.
3.) Which of these theories is not a basis for modern biology? a) evolution; b) creationism; c) cell theory; d) gene
theory.
4.) Mushrooms belong to which of these taxonomic kingdoms? a) Plantae; b) Protista; c) Animalia; d) Fungi; e)
Monera
5.) Which of these is NOT a living organism? a) cactus; b) cat; c) algae; d) virus; e) yeast
6.) The scientist(s) credited with developing the theory of evolution by natural selection were ____. a) James
Watson and Francis Crick; b) Aristotle and Lucretius; c) Charles Darwin and Alfred Wallace; d) Robert Hooke
and Rudolph Virchow; e) James Watson and Charles Darwin
7.) When an organism consists of a single cell, the organism is referred to as ___. a) uninucleate; b) uniport; c)
unisexual; d) unicellular
8.) List the five kingdoms of life that are currently recognized by most scientists; tell generally what kinds of
organisms are classified in each kingdom.
ADD RESPONSE/S/ HERE
LAB I
A trait that assists an organism in survival and reproduction in a certain environment is said to be adaptive.
Observe two different animal species native to your own environment (squirrels, dogs, birds, etc…) What
sorts of adaptive traits do you observe? How do they aid in the animal’s survival? Write about it (no length
requirement).
ADD RESPONSE/S/ HERE
CELLS… The three cells you will be studying in this unit are prokaryote, animal and plant.
1.) What are the primary differences between animal and plant cells?
2.) What is the function of the organelles in these different cells?
ADD RESPONSE/S/ HERE
MITOSIS and MEIOSIS
3.) Summarize the phases of MITOSIS
4.) What is the function of Meiosis?
ADD RESPONSE/S/ HERE
CELLULAR TRANSPORT
5.) What is meant by Cellular Transport?
6.) Why is transport critical
ADD RESPONSE/S/ HERE
CELLS – ORIGINS
7.) Describe the types of microscopes and the types of information scientists can obtain using each one.
8.) Which of these is not a type of cell? a) bacterium; b) amoeba; c) sperm; d) virus
ADD RESPONSE/S/ HERE
CELLS II: CELLULAR ORGANIZATION
9.) Give the function and cellular location of the following basic eukaryotic organelles and structures: cell
membrane, nucleus, Golgi bodies, mitochondria, ribosomes, and cell walls.
ADD RESPONSE/S/ HERE
HEREDITY AND DNA
https://www.khanacademy.org/test-prep/mcat/biomolecules/mendelian-genetics/v/an-introduction-tomendelian-genetics
Use the link above for a video tour of “Genetics” to improve your understanding (watch all four)
HEREDITY
10.) What is meant by “heredity”?
11.) How do we inherit physical characteristics from our parents?
14.) For what is the Punnett square used?
15.) Summarize the Hardy-Wienberg Principle
ADD RESPONSE/S/ HERE
DNA REPLICATION ANIMATION
1.) Define DNA.
2.) What is the function of DNA?
3.) What is the purpose of replication?
4.) Explain the steps in DNA Replication.
ADD RESPONSE/S/ HERE
INTRODUCTION TO GENETICS
Human Genetics
1.) What happens when there’s an abnormality on a chromosome?
2.) For what is DNA testing used (may do additional research)?
3.) What is the difference between genotype and phenotype
ADD RESPONSE/S/ HERE
ANIMAL ORGAN SYSTEMS AND HOMEOSTASIS
READ TEXTBOOK NOTES
1.) List the principal organ systems in humans give its task.
2.) List one body system and the types of interactions it has with other body organ systems.
3.) Which of these is not a characteristic of living things? a) reproduction and heredity; b) metabolism; c)
response to stimulus d) all of the are characteristics of life
4.) Control of homeostasis in the body is accomplished by ____. a) Nervous system; b) Circulatory system; c)
Endocrine system; d) both a and c control homeostasis
5.) When we are cold we shiver. This releases heat from which organ system? a) Skeletal system; b) Muscular
system; c) Digestive system; d) Circulatory system
6.) Heat released when we shiver is transported from its source to the rest of the body by which of these organ
systems? a) Skeletal system; b) Muscular system; c) Digestive system; d) Circulatory system
7.) The digestive process consists of three sub-processes. Which of these is not part of the digestive process? a)
mechanical breakdown of food; b) circulation of food in the blood and lymph; c) absorption of food into the
blood or lymph; d) assimilation of the food into cells of the body
8.) Hormones are produced directly by organs and tissues of which of these body systems? a) Endocrine; b)
Circulatory; c) Reproductive; d) Nervous
9.) The removal of organic wastes from the body is accomplished by the ___ system? a) Digestive; b) Excretory;
c) Circulatory; d) Lymphatic
10.) Which of these is part of the central nervous system? a) brain; b) nerve ganglia; c) spinal cord; d) a and b; e) a
and c
11.) The spinal cord is located on which side of the body? a) dorsal; b) ventral; c) abdominal; d) cranial
12.) List the parts of the male reproductive system.
13.) Gametes are produced by which of these cell division processes? a) mitosis; b) binary fission; c)
photosynthesis; d) meiosis
14.) Blood leaves the heart through which of these types of blood vessels? a) capillaries; b) arteries; c) veins; d)
lymphatic vessels
15.) Storage of important ions such as phosphorous and calcium is done by which of these organ systems? a)
Skeletal; b) Muscular; c) Digestive; d) Excretory
ADD RESPONSE/S/ HERE
NOTE: Key Info – When doing your LABS
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The scientific method is a way to ask and answer scientific questions by making observations and
doing experiments.
The steps of the scientific method are to:
o Ask a Question
o Do Background Research
o Construct a Hypothesis
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Test Your Hypothesis by Doing an Experiment
Analyze Your Data and Draw a Conclusion
Communicate Your Results
It is important for your experiment to be a fair test. A “fair test” occurs when you change only one
factor (variable) and keep all other conditions the same.
Use your Biology Textbook – with your PDF Downloads
“BIOLOGY CAMBRIDGE” and ‘CELL BIOLOGY”
Read, study, and use for assignment application.
CELLS; CHEMISTRY OF LIFE
ASSIGNMENT: Chapters 2 & 3
QUESTIONS TO CONSIDER on page 14: Complete questions 3 and 4 based on your own
opinion.
Place your responses below.
CAN WE BELIEVE OUR EYES on page 27: Complete all and submit responses based on your
observation and reasonings.
Place your responses below.
LIPID QUESTIONS on page 46: Complete #s 1 and 2
Place your responses below.
ENZYMES QUESTIONS on page 57: Complete #9, 10
Place your responses below.
QUESTIONs on page 61: Complete #s 15 & 16
Place your responses below.
QUESTIONs on page 64: Complete #18
Place your responses below.
PLANTS
ASSIGNMENT: Read Chapter 9
Each section has Assessment Statements which are the key points you are expected to
learn as you explore your text. For each section, write down each assessment statement
and take notes. Use your notes to complete the assignment below.
END OF THE CHAPTER QUESTIONS: Complete questions 1, 6, 7, 8 and 10.
Place your responses below.
LAB PROJECT 1: Go to your class downloads and download your “Sample Projects
and Activities in Biology”. Complete the lab “Leaf Chromatography”. Include your
responses to all questions and include 2 photos of YOU doing your project.
https://learning-center.homesciencetools.com/article/leaf-chromatographyscience-project/ (Alternate Project Link can be used)
Place your responses and images below.
Use your Biology Textbook – with your PDF Downloads
“BIOLOGY CAMBRIDGE”
Read, study, and use for assignment application.
GENETICS
ASSIGNMENT: Chapters 4 & 10
QUESTIONS TO CONSIDER on page 76: Complete #s 3 and 4 based on your own morals and
reasoning.
Place your responses below.
QUESTIONS TO CONSIDER on page 88: Complete #s 3, 4 and 5 based on your own morals
and reasoning.
Place your responses below.
QUESTIONS TO CONSIDER on page 90: Complete #s 1 and 2 based on your own morals and
reasoning.
Place your responses below.
QUESTIONS TO CONSIDER on page 95: Complete #s 2 and 4 based on your own morals and
reasoning.
Place your responses below.
QUESTIONS TO CONSIDER on page 250: Complete #s 1, 2, 3
Place your responses below.
LAB
LAB: Complete “Genetic” Activity – Download. Complete and copy/paste
below
ADD RESPONSE/S/ HERE
Use your Biology Textbook – with your PDF Downloads
“BIOLOGY CAMBRIDGE”
Read, study, and use for assignment application.
NUCLEIC ACIDS; CELL RESPIRATION
ASSIGNMENT: Chapters 7 & 8
QUESTIONS TO CONSIDER on page 172: Complete #s 1, 2, 3, 4
Place your answers below.
FOR CHAPTER 7: Draw and label a diagram showing the structure of a peptide bond
between two amino acids. Place a photo of your drawing below.
Place your responses below.
FOR CHAPTER 7: List three differences between fibrous and globular proteins.
Place your responses below.
QUESTIONS TO CONSIDER beginning on page 206: Complete #18, 19, 23, 24 and 30
Place your responses below.
CHAPTER 8 : What is meant by the term ‘limiting factor’?
List three limiting factors for photosynthesis.
Place your responses below.
Use your Biology Textbook – with your PDF Downloads
“BIOLOGY CAMBRIDGE”
Read, study, and use for assignment application.
THE HUMAN BODY
ASSIGNMENT: Chapters 6 & 11
QUESTIONS TO CONSIDER on page 139: Complete #s 1 & 2
ALSO page 140: Complete #s 6, 7, 8 and 9
Place your responses below.
Additional QUESTIONS:
• Define ‘pathogen’.
• Explain why antibiotics are effective against bacteria but not against viruses.
• Distinguish between ‘antigens’ and ‘antibodies’.
• Explain antibody production.
• Outline the effects of HIV on the immune system.
ESSAY: Research and discuss the cause, transmission and social implications of AIDS. (no minimum page
count)
Place your responses below.
QUESTIONS TO CONSIDER on page 142: Complete #s 1, 2, 3, 4
Place your answers Below.
QUESTIONS TO CONSIDER on page 162: Complete #s 1, 2, 3, 4
Place your answers Below.
QUESTIONS TO CONSIDER on page 164: Complete #s 1, 2, 3
Place your answers Below.
End of the Chapter QUESTIONS on page 164: Complete # 1, 2, 3, 8 and 11
Use your Biology Textbook – with your PDF Downloads
“BIOLOGY CAMBRIDGE”
Read, study, and use for assignment application.
ECOLOGY & EVOLUTION
ASSIGNMENT: Chapters 5
QUESTIONS TO CONSIDER on page 109: Complete #s 1, 2
Place your answers Below.
LAB PROJECT 1: Go to your class downloads and download your “Sample Projects
and Activities in Biology”. Complete the lab “Design Challenge: Building a filtration
Apparatus”. Include your responses to all questions and include 2 photos of YOU
doing your project.
Copy/Paste all LAB Components Below
LAB PROJECT 2: Go to your class downloads and download your “Sample Projects
and Activities in Biology”. Complete the lab “Oil Spill Clean-Up Challenge”. Include
your responses to all questions and include 2 photos of YOU doing your project.
Copy/Paste all LAB Components Below
PAPER LAB 2: You are a respected zoologist that has spent the last ten years studying the
animals in the world’s rain forests. In all those years, you have not seen one new species of
animal – until today. Miles from your base camp this morning you have observed a spectacular
animal never before described. You must describe its appearance, determine some of its daily
habits, fit it in today’s classification system, give it a scientific name, and present your
information in a written report.
ADD RESPONSE/S/ HERE
RESEARCHED PERSUASIVE ESSAY:
Research the question: Should beef from a cloned cow be approved for sale by the
FDA? Share a persuasive essay explaining why it should or should not. Provide at
least 2 reliable sources and include the citation information. 2 page minimum.
ADD ESSAY HERE
IOHS BIOLOGY Notes Use for Week One
INTRODUCTION: THE NATURE OF SCIENCE AND BIOLOGY
Biology: The Science of Our Lives
Biology literally means “the study of life”. Biology is such a broad field, covering the minute workings of
chemical machines inside our cells, to broad scale concepts of ecosystems and global climate change.
Biologists study intimate details of the human brain, the composition of our genes, and even the
functioning of our reproductive system. Biologists recently all but completed the deciphering of the
human genome, the sequence of deoxyribonucleic acid (DNA) bases that may determine much of our
innate capabilities and predispositions to certain forms of behavior and illnesses. DNA sequences have
played major roles in criminal cases (O.J. Simpson, as well as the reversal of death penalties for many
wrongfully convicted individuals), as well as the impeachment of President Clinton (the stain at least did
not lie). We are bombarded with headlines about possible health risks from favorite foods (Chinese,
Mexican, hamburgers, etc.) as well as the potential benefits of eating other foods such as cooked
tomatoes. Infomercials tout the benefits of metabolism-adjusting drugs for weight loss. Many Americans
are turning to herbal remedies to ease arthritis pain, improve memory, as well as improve our moods.
Can a biology book give you the answers to these questions? No, but it will enable you learn how to sift
through the biases of investigators, the press, and others in a quest to critically evaluate the question. To
be honest, five years after you are through with this class it is doubtful you would remember all the details
of metabolism. However, you will know where to look and maybe a little about the process of science that
will allow you to make an informed decision. Will you be a scientist? Yes, in a way. You may not be
formally trained as a science major, but you can think critically, solve problems, and have some idea
about what science can and cannot do. I hope you will be able to tell the shoe from the shinola.
Science and the Scientific Method
Science is an objective, logical, and repeatable attempt to understand the principles and forces operating
in the natural universe. Science is from the Latin word, scientia, to know. Good science is not dogmatic,
but should be viewed as an ongoing process of testing and evaluation. One of the hoped-for benefits of
students taking a biology course is that they will become more familiar with the process of science.
Humans seem innately interested in the world we live in. Young children drive their parents batty with
constant “why” questions. Science is a means to get some of those whys answered. When we shop for
groceries, we are conducting a kind of scientific experiment. If you like Brand X of soup, and Brand Y is
on sale, perhaps you try Brand Y. If you like it you may buy it again, even when it is not on sale. If you
did not like Brand Y, then no sale will get you to try it again.
In order to conduct science, one must know the rules of the game (imagine playing Monopoly and having
to discover the rules as you play! Which is precisely what one does with some computer or videogames
(before buying the cheatbook). The scientific method is to be used as a guide that can be modified. In
some sciences, such as taxonomy and certain types of geology, laboratory experiments are not necessarily
performed. Instead, after formulating a hypothesis, additional observations and/or collections are made
from different localities.
Steps in the scientific method commonly include:
Observation: defining the problem you wish to explain.
Hypothesis: one or more falsifiable explanations for the observation.
Experimentation: Controlled attempts to test one or more hypotheses.
Conclusion: was the hypothesis supported or not? After this step the hypothesis is either modified or
rejected, which causes a repeat of the steps above.
After a hypothesis has been repeatedly tested, a hierarchy of scientific thought develops. Hypothesis is the
most common, with the lowest level of certainty. A theory is a hypothesis that has been repeatedly tested
with little modification, e.g. The Theory of Evolution. A Law is one of the fundamental underlying
principles of how the Universe is organized, e.g. The Laws of Thermodynamics, Newton’s Law of
Gravity. Science uses the word theory differently than it is used in the general population. Theory to most
people, in general nonscientific use, is an untested idea. Scientists call this a hypothesis.
Scientific experiments are also concerned with isolating the variables. A good science experiment does
not simultaneously test several variables, but rather a single variable that can be measured against a
control. Scientific controlled experiments are situations where all factors are the same between two test
subjects, except for the single experimental variable.
Consider a commonly conducted science fair experiment. Sandy wants to test the effect of gangsta rap
music on pea plant growth. She plays loud rap music 24 hours a day to a series of pea plants grown under
light, and watered every day. At the end of her experiment she concludes gangsta rap is conducive to
plant growth. Her teacher grades her project very low, citing the lack of a control group for the
experiment. Sandy returns to her experiment, but this time she has a separate group of plants under the
same conditions as the rapping plants, but with soothing Led Zeppelin songs playing. She comes to the
same conclusion as before, but now has a basis for comparison. Her teacher gives her project a better
grade.
Theories Contributing to Modern Biology
Modern biology is based on several great ideas, or theories:
The Cell Theory
The Theory of Evolution by Natural Selection
Gene Theory
Homeostasis
Robert Hooke (1635-1703), one of the first scientists to use a microscope to examine pond water, cork
and other things, referred to the cavities he saw in cork as “cells”, Latin for chambers. Mattias Schleiden
(in 1838) concluded all plant tissues consisted of cells. In 1839, Theodore Schwann came to a similar
conclusion for animal tissues. Rudolf Virchow, in 1858, combined the two ideas and added that all cells
come from pre-existing cells, formulating the Cell Theory. Thus there is a chain-of-existence extending
from your cells back to the earliest cells, over 3.5 billion years ago. The cell theory states that all
organisms are composed of one or more cells, and that those cells have arisen from pre-existing cells.
Figure 1. James Watson (L) and
Francis Crick (R), and the model they
built of the structure of
deoxyribonucleic acid, DNA. While a
model may seem a small thing, their
development of the DNA model
fostered increased understanding of
how genes work. Image from the
Internet.
In 1953, American scientist James Watson and British scientist Francis Crick developed the model for
deoxyribonucleic acid (DNA), a chemical that had (then) recently been deduced to be the physical carrier
of inheritance. Crick hypothesized the mechanism for DNA replication and further linked DNA to
proteins, an idea since referred to as the central dogma. Information from DNA “language” is converted
into RNA (ribonucleic acid) “language” and then to the “language” of proteins. The central dogma
explains the influence of heredity (DNA) on the organism (proteins).
Homeostasis is the maintenance of a dynamic range of conditions within which the organism can
function. Temperature, pH, and energy are major components of this concept. Thermodynamics is a field
of study that covers the laws governing energy transfers, and thus the basis for life on earth. Two major
laws are known: the conservation of matter and energy, and entropy. These will be discussed in more
detail in a later chapter. The universe is composed of two things: matter (atoms, etc.) and energy.
These first three theories are very accepted by scientists and the general public. The theory of evolution is
well accepted by scientists and most of the general public. However, it remains a lightning rod for school
boards, politicians, and television preachers. Much of this confusion results from what the theory says and
what it does not say.
Development of the Theory of Evolution
Modern biology is based on several unifying themes, such as the cell theory, genetics and inheritance,
Francis Crick’s central dogma of information flow, and Darwin and Wallace’s theory of evolution by
natural selection. In this first unit we will examine these themes and the nature of science.
The Ancient Greek philosopher Anaxiamander (611-547 B.C.) and the Roman philosopher Lucretius (9955 B.C.) coined the concept that all living things were related and that they had changed over time. The
classical science of their time was observational rather than experimental. Another ancient Greek
philosopher, Aristotle developed his Scala Naturae, or Ladder of Life, to explain his concept of the
advancement of living things from inanimate matter to plants, then animals and finally man. This concept
of man as the “crown of creation” still plagues modern evolutionary biologists (See Gould, 1989, for a
more detailed discussion).
Post-Aristotlean “scientists” were constrained by the prevailing thought patterns of the Middle Ages — the
inerrancy of the biblical book of Genesis and the special creation of the world in a literal six days of the
24-hour variety. Archbishop James Ussher of Ireland, in the late 1600’s calculated the age of the earth
based on the genealogies from Adam and Eve listed in the biblical book of Genesis. According to
Ussher’s calculations, the earth was formed on October 22, 4004 B.C. These calculations were part of
Ussher’s book, History of the World. The chronology he developed was taken as factual, and was even
printed in the front pages of bibles. Ussher’s ideas were readily accepted, in part because they posed no
threat to the social order of the times; comfortable ideas that would not upset the linked applecarts of
church and state.
Figure 2. Archbishop James Ussher. Image from the
Internet.
Often new ideas must “come out of left field”, appearing as wild notions, but in many cases prompting
investigation which may later reveal the “truth”. Ussher’s ideas were comfortable, the Bible was viewed
as correct, and therefore the earth must be only 5000 years old.
Geologists had for some time doubted the “truth” of a 5,000 year old earth. Leonardo da Vinci (painter of
the Last Supper, and the Mona Lisa, architect and engineer) calculated the sedimentation rates in the Po
River of Italy. Da Vinci concluded it took 200,000 years to form some nearby rock deposits. Galileo,
convicted heretic for his contention that the Earth was not the center of the Universe, studied fossils
(evidence of past life) and concluded that they were real and not inanimate artifacts. James Hutton,
regarded as the Father of modern geology, developed the Theory of Uniformitarianism, the basis of
modern geology and paleontology. According to Hutton’s work, certain geological processes operated in
the past in much the same fashion as they do today, with minor exceptions of rates, etc. Thus many
geological structures and processes cannot be explained if the earth was only a mere 5000 years old.
The Modern View of the Age of the Earth
Radiometric age assignments based on the rates of decay of radioactive isotopes, not discovered until the
late 19th century, suggest the earth is over 4.5 billion years old. The Earth is thought older than 4.5 billion
years, with the oldest known rocks being 3.96 billion years old. Geologic time divides into eons, eroas,
and smaller units. An overview of geologic time may be obtained at
http://www.ucmp.berkeley.edu/help/timeform.html.
Figure 3. The geologic time scale, highlighting some of the firsts in the evolution of life. One way to
represent geological time. Note the break during the Precambrian. If the vertical scale was truly to scale
the Precambrian would account for 7/8 of the graphic. This image is from
http://www.clearlight.com/~mhieb/WVFossils/GeolTimeScale.html.
Development of the modern view of Evolution
Erasmus Darwin (1731-1802; grandfather of Charles Darwin) a British physician and poet in the late
1700’s, proposed that life had changed over time, although he did not present a mechanism. GeorgesLouis Leclerc, Comte de Buffon (pronounced Bu-fone; 1707-1788) in the middle to late 1700’s proposed
that species could change. This was a major break from earlier concepts that species were created by a
perfect creator and therefore could not change because they were perfect, etc.
Swedish botanist Carl Linne (more popularly known as Linneus, after the common practice of the day
which was to latinize names of learned men), attempted to pigeon-hole all known species of his time
(1753) into immutable categories. Many of these categories are still used in biology, although the
underlying thought concept is now evolution and not immutability of species. Linnean hierarchical
classification was based on the premise that the species was the smallest unit, and that each species (or
taxon) belonged to a higher category.
Kingdom Animalia
Phylum (Division is used for plants) Chordata
This image is from
http://linnaeus.nrm.se/botany/fbo/welcome.html.en.
Class Mammalia
Order Primates
Family Hominidae
Genus Homo
species sapiens
Linneus also developed the concept of binomial nomenclature, whereby scientists speaking and writing
different languages could communicate clearly. For example Man in English is Hombre in Spanish,
Mensch in German, and Homo in Latin. Linneus settled on Latin, which was the language of learned men
at that time. If a scientist refers to Homo, all scientists know what he or she means.
William “Strata” Smith (1769-1839), employed by the English coal mining industry, developed the first
accurate geologic map of England. He also, from his extensive travels, developed the Principle of
Biological Succession. This idea states that each period of Earth history has its own unique assemblages
of fossils. In essence Smith fathered the science of stratigraphy, the correlation of rock layers based on
(among other things) their fossil contents. He also developed an idea that life had changed over time, but
did not overtly state that.
Abraham Gottlob Werner and Baron Georges Cuvier (1769-1832) were among the foremost proponents
of catastrophism, the theory that the earth and geological events had formed suddenly, as a result of some
great catastrophe (such as Noah’s flood). This view was a comfortable one for the times and thus was
widely accepted. Cuvier eventually proposed that there had been several creations that occurred after
catastrophies. Louis Agassiz (1807-1873) proposed 50-80 catastrophies and creations.
Jean Baptiste de Lamarck (1744-1829) developed one of the first theories on how species changed. He
proposed the inheritance of acquired characteristics to explain, among other things, the length of the
giraffe neck. The Lamarckian view is that modern giraffe’s have long necks because their ancestors
progressively gained longer necks due to stretching to reach food higher and higher in trees. According to
the 19th century concept of use and disuse the stretching of necks resulted in their development, which
was somehow passed on to their progeny. Today we realize that only bacteria are able to incorporate nongenetic (no heritable) traits. Lamarck’s work was a theory that plainly stated that life had changed over
time and provided (albeit an erroneous) mechanism of change.
Additional information about the biological thoughts of Lamarck is available by clicking here.
Darwinian evolution
Charles Darwin, former divinity student and former medical student, secured (through the intercession of
his geology professor) an unpaid position as ship’s naturalist on the British exploratory vessel H.M.S.
Beagle. The voyage would provide Darwin a unique opportunity to study adaptation and gather a great
deal of proof he would later incorporate into his theory of evolution. On his return to England in 1836,
Darwin began (with the assistance of numerous specialists) to catalog his collections and ponder the
seeming “fit” of organisms to their mode of existence. He eventually settled on four main points of a
radical new hypothesis:
Adaptation: all organisms adapt to their environments.
Variation: all organisms are variable in their traits.
Over-reproduction: all organisms tend to reproduce beyond their environment’s capacity to support them
(this is based on the work of Thomas Malthus, who studied how populations of organisms tended to grow
geometrically until they encountered a limit on their population size).
Since not all organisms are equally well adapted to their environment, some will survive and reproduce
better than others — this is known as natural selection. Sometimes this is also referred to as “survival of
the fittest”. In reality this merely deals with the reproductive success of the organisms, not solely their
relative strength or speed.
Figure 4. Charles Darwin (right) and Alfred Wallace (left), the co-developers of
the theory of evolution by means of natural selection. Image of Charles Darwin
from http://zebu.uoregon.edu/~js/glossary/darwinism.html.Image of A.R. Wallace
(right) is modified from
http://www.prs.k12.nj.us/schools/phs/science_Dept/APBio/Natural_Selection.html.
Unlike the upper-class Darwin, Alfred Russel Wallace (1823-1913) came from a different social class.
Wallace spent many years in South America, publishing salvaged notes in Travels on the Amazon and
Rio Negro in 1853. In 1854, Wallace left England to study the natural history of Indonesia, where he
contracted malaria. During a fever Wallace managed to write down his ideas on natural selection.
In 1858, Darwin received a letter from Wallace, in which Darwin’s as-yet-unpublished theory of evolution
and adaptation was precisely detailed. Darwin arranged for Wallace’s letter to be read at a scientific
meeting, along with a synopsis of his own ideas. To be correct, we need to mention that both Darwin and
Wallace developed the theory, although Darwin’s major work was not published until 1859 (the book On
the Origin of Species by Means of Natural Selection, considered by many as one of the most influential
books written [follow the hyperlink to view an online version]). While there have been some changes to
the theory since 1859, most notably the incorporation of genetics and DNA into what is termed the
“Modern Synthesis” during the 1940’s, most scientists today acknowledge evolution as the guiding theory
for modern biology.
Recent revisions of biology curricula stressed the need for underlying themes. Evolution serves as such a
universal theme. An excellent site devoted to Darwin’s thoughts and work is available by clicking here. At
that same site is a timeline showing many of the events mentioned above in their historical contexts.
The Diversity of Life
Evolutionary theory and the cell theory provide us with a basis for the interrelation of all living things.
We also utilize Linneus’ hierarchical classification system, adopting (generally) five kingdoms of living
organisms. Viruses, as discussed later, are not considered living. Click here for a table summarizing the
five kingdoms. Recent studies suggest that there might be a sixth Kingdom, the Archaea.
Figure 5. A simple phylogenetic representation of three domains of life” Archaea,
Bacteria (Eubacteria), and Eukaryota (all eukaryotic groups: Protista, Plantae,
Fungi, and Animalia). Image from Purves et al., Life: The Science of Biology, 4th
Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com), used with permission.
Table 1. The Five Kingdoms.
Kingdom
Monera
(in the
broadest
sense,
including
organisms
usually
placed in the
Domain
Archaea).
Protista
Methods of
Nutrition
Organization Environmental Significance
Photosynthesis, Single-celled,
chemosynthesis, filament, or
decomposer,
colony of
parasitic.
cells; all
prokaryotic.
Monerans play various roles in
almost all food chains, including
producer,consumer, and
decomposer.
Examples
Bacteria (E. coli),
cyanobacteria
(Oscillatoria),
methanogens, and
thermacidophiles.
Cyanobacteria are important
oxygen producers.
Many Monerans also produce
nitrogen, vitamins, antibiotics, and
are important compoents in human
and animal intestines.
Photosynthesis, Single-celled, Important producers in ocean/pond Plankton (both
absorb food
filamentous,
food chain.
phytoplankton and
from
colonial, and
zooplankton), algae
environment, or multicelled; all Source of food in some human
(kelp, diatoms,
cultures.
trap/engulf
eukaryotic.
dinoflagellates),and
smaller
Phytoplankton component that is Protozoa (Amoeba,
organisms.
Paramecium).
one of the major producers of
oxygen
Absorb food
from a host or
from their
environment.
Fungi
Plantae
All
heterotrophic.
Almost all
photosynthetic,
although a few
parasitic plants
are known.
Single-celled, Decomposer, parasite, and
filamentous, to consumer.
multicelled; all
Produce antibiotics,help make
eukaryotic.
bread and alcohol.
Mushrooms
(Agaricus
campestris, the
commercial
mushroom), molds,
mildews, rusts and
Crop parasites (Dutch Elm
smuts (plant
Disease, Karnal Bunt, Corn Smut,
parasites), yeasts
etc.).
(Saccharomyces
cerevisae, the
brewer’s yeast).
All
Food source, medicines and drugs, Angiosperms (oaks,
multicelled,
dyes, building material, fuel.
tulips,
photosynthetic,
cacti),gymnosperms
Producer
in
most
food
chains.
autotrophs..
(pines, spuce, fir),
mosses,
ferns,liverworts,
horsetails
(Equisetum, the
scouring rush)
All
heterotrophic.
Animalia
Multicelled
heterotrophs
capable of
movement at
some stage
during their
life history
(even couch
potatoes).
Consumer level in most food
Sponges,
chains
worms,molluscs,
(herbivores,carnivores,omnivores). insects,
starfish,mammals,
Food source, beasts of burden and amphibians,fish,
transportation, recreation, and
birds, reptiles, and
companionship.
dinosaurs, and
people.
Monera, the most primitive kingdom, contain living organisms remarkably similar to ancient fossils.
Organisms in this group lack membrane-bound organelles associated with higher forms of life. Such
organisms are known as prokaryotes. Bacteria (technically the Eubacteria) and blue-green bacteria
(sometimes called blue-green algae, or cyanobacteria) are the major forms of life in this kingdom. The
most primitive group, the archaebacteria, are today restricted to marginal habitats such as hot springs or
areas of low oxygen concentration.
Figure 6. Representative photosynthetic cyanobacteria: Oscillatoria (left) and Nostoc
(right). The left image is cropped from
gopher://wiscinfo.wisc.edu:2070/I9/.image/.bot/.130/Cyanobacteria/Oscillatoria_130.
The right image is cropped from
gopher://wiscinfo.wisc.edu:2070/I9/.image/.bot/.130/Cyanobacteria/Nostoc_130.
Protista were the first of the eukaryotic kingdoms, these organisms and all others have membrane-bound
organelles, which allow for compartmentalization and dedication of specific areas for specific functions.
The chief importance of Protista is their role as a stem group for the remaining Kingdoms: Plants,
Animals, and Fungi. Major groups within the Protista include the algae, euglenoids, ciliates, protozoa,
and flagellates.
Figure 7. Scanning electron micrographs of diatoms (Protista).There are
two basic types of diatoms: bilaterally symmetrical (left) and radially
symmetrical (right). Images are from
http://WWW.bgsu.edu/departments/biology/algae/index.html.
Figure 8. Light micrographs of some protistans. The images are
Copyright 1994 by Charles J. O’Kelly and Tim Littlejohn, used by
permission from:
http://megasun.bch.umontreal.ca/protists/gallery.html.
Fungi are almost entirely multicellular (with yeast, Saccharomyces cerviseae, being a prominent
unicellular fungus), heterotrophic (deriving their energy from another organism, whether alive or dead),
and usually having some cells with two nuclei (multinucleate, as opposed to the more common one, or
uninucleate) per cell. Ecologically this kingdom is important (along with certain bacteria) as decomposers
and recyclers of nutrients. Economically, the Fungi provide us with food (mushrooms; Bleu
cheese/Roquefort cheese; baking and brewing), antibiotics (the first of the wonder drugs, penicillin, was
isolated from a fungus Penicillium), and crop parasites (doing several billion dollars per year of damage).
Figure 9. Examples of fungi. The images are from
http://www.cinenet.net/users/velosa/thumbnails.html.
Plantae include multicelled organisms that are all autotrophic (capable of making their own food by the
process of photosynthesis, the conversion of sunlight energy into chemical energy). Ecologically, this
kingdom is generally (along with photosynthetic organisms in Monera and Protista) termed the producers,
and rest at the base of all food webs. A food web is an ecological concept to trace energy flow through an
ecosystem. Economically, this kingdom is unparalleled, with agriculture providing billions of dollars to
the economy (as well as the foundation of “civilization”). Food, building materials, paper, drugs (both
legal and illegal), and roses, are plants or plant-derived products.
Figure 10. Examples of plants. The left image of species of Equisetum is cropped and reduced from
gopher://wiscinfo.wisc.edu:2070/I9/.image/.bot/.130/Fern_Allies/Sphenophyta/Equisetum/E._arvense_an
d_E._laevigatum_KS. The center image of Iris, is reduced and cropped from
gopher://wiscinfo.wisc.edu:2070/I9/.image/.bot/.401/Flowering_Plants/Monocots/Iridaceae/Iris/Iris_pum
ula_habit. The right image of Pereskia (Cactaceae) is reduced from
gopher://wiscinfo.wisc.edu:2070/I9/.image/.bot/.401/Flowering_Plants/Dicots/Cactaceae/Pereskia/Pereski
a_leafy_stem_RK.
Animalia consists entirely of multicelluar heterotrophs that are all capable (at some point during their life
history) of mobility. Ecologically, this kingdom occupies the level of consumers, which can be
subdivided into herbivore (eaters of plants) and carnivores (eaters of other animals). Humans, along with
some other organisms, are omnivores (capable of functioning as herbivores or carnivores). Economically,
animals provide meat, hides, beasts of burden, pleasure (pets), transportation, and scents (as used in some
perfumes).
Figure 11. Examples of animals. The left image of a jellyfish is from
http://www.smoky.org/~mtyler/bio/coelenterata.html. The center image of a tree frog is from
http://frog.simplenet.com/froggy/images/wild28.gif. The right image of the chimpanzee is
from http://www.selu.com/~bio/PrimateGallery/art/Copyright_Free02.html.
Characteristics of living things
Living things have a variety of common characteristics.
Organization. Living things exhibit a high level of organization, with multicellular organisms being
subdivided into cells, and cells into organelles, and organelles into molecules, etc.
Homeostasis. Homeostasis is the maintenance of a constant (yet also dynamic) internal environment in
terms of temperature, pH, water concentrations, etc. Much of our own metabolic energy goes toward
keeping within our own homeostatic limits. If you run a high fever for long enough, the increased
temperature will damage certain organs and impair your proper functioning. Swallowing of common
household chemicals, many of which are outside the pH (acid/base) levels we can tolerate, will likewise
negatively impact the human body’s homeostatic regime. Muscular activity generates heat as a waste
product. This heat is removed from our bodies by sweating. Some of this heat is used by warm-blooded
animals, mammals and birds, to maintain their internal temperatures.
Adaptation. Living things are suited to their mode of existence. Charles Darwin began the recognition of
the marvelous adaptations all life has that allow those organisms to exist in their environment.
Reproduction and heredity. Since all cells come from existing cells, they must have some way of
reproducing, whether that involves asexual (no recombination of genetic material) or sexual
(recombination of genetic material). Most living things use the chemical DNA (deoxyribonucleic acid) as
the physical carrier of inheritance and the genetic information. Some organisms, such as retroviruses (of
which HIV is a member), use RNA (ribonucleic acid) as the carrier. The variation that Darwin and
Wallace recognized as the wellspring of evolution and adaptation, is greatly increased by sexual
reproduction.
Growth and development. Even single-celled organisms grow. When first formed by cell division, they
are small, and must grow and develop into mature cells. Multicellular organisms pass through a more
complicated process of differentiation and organogenesis (because they have so many more cells to
develop).
Energy acquisition and release. One view of life is that it is a struggle to acquire energy (from sunlight,
inorganic chemicals, or another organism), and release it in the process of forming ATP (adenosine
triphosphate).
Detection and response to stimuli (both internal and external).
Interactions. Living things interact with their environment as well as each other. Organisms obtain raw
materials and energy from the environment or another organism. The various types of symbioses
(organismal interactions with each other) are examples of this.
Levels of Organization
Biosphere: The sum of all living things taken in conjunction with their environment. In essence, where
life occurs, from the upper reaches of the atmosphere to the top few meters of soil, to the bottoms of the
oceans. We divide the earth into atmosphere (air), lithosphere (earth), hydrosphere (water), and biosphere
(life).
Ecosystem: The relationships of a smaller groups of organisms with each other and their environment.
Scientists often speak of the interrelatedness of living things. Since, according to Darwin’s theory,
organisms adapt to their environment, they must also adapt to other organisms in that environment. We
can discuss the flow of energy through an ecosystem from photosynthetic autotrophs to herbivores to
carnivores.
Community: The relationships between groups of different species. For example, the desert communities
consist of rabbits, coyotes, snakes, birds, mice and such plants as sahuaro cactus (Carnegia gigantea),
Ocotillo, creosote bush, etc. Community structure can be disturbed by such things as fire, human activity,
and over-population.
Species: Groups of similar individuals who tend to mate and produce viable, fertile offspring. We often
find species described not by their reproduction (a biological species) but rather by their form (anatomical
or form species).
Populations: Groups of similar individuals who tend to mate with each other in a limited geographic area.
This can be as simple as a field of flowers, which is separated from another field by a hill or other area
where none of these flowers occur.
Individuals: One or more cells characterized by a unique arrangement of DNA “information”. These can
be unicellular or multicellular. The multicellular individual exhibits specialization of cell types and
division of labor into tissues, organs, and organ systems.
Organ System: (in multicellular organisms). A group of cells, tissues, and organs that perform a specific
major function. For example: the cardiovascular system functions in circulation of blood.
Organ: (in multicellular organisms). A group of cells or tissues performing an overall function. For
example: the heart is an organ that pumps blood within the cardiovascular system.
Tissue: (in multicellular organisms). A group of cells performing a specific function. For example heart
muscle tissue is found in the heart and its unique contraction properties aid the heart’s functioning as a
pump. .
Cell: The fundamental unit of living things. Each cell has some sort of hereditary material (either DNA or
more rarely RNA), energy acquiring chemicals, structures, etc. Living things, by definition, must have the
metabolic chemicals plus a nucleic acid hereditary information molecule.
Organelle: A subunit of a cell, an organelle is involved in a specific subcellular function, for example the
ribosome (the site of protein synthesis) or mitochondrion (the site of ATP generation in eukaryotes).
Molecules, atoms, and subatomic particles: The fundamental functional levels of biochemistry.
Figure 12. Organization levels of life, in a graphic format. Images from Purves et al., Life: The Science of
Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com), used with permission.
It is thus possible to study biology at many levels, from collections of organisms (communities), to the
inner workings of a cell (organelle).
CELLS: ORIGINS
Origin of the Earth and Life
Scientific estimates place the origin of the Universe at between 10 and 20 billion years ago. The theory
currently with the most acceptance is the Big Bang Theory, the idea that all matter in the Universe existed
in a cosmic egg (smaller than the size of a modern hydrogen atom) that exploded, forming the Universe.
Recent discoveries from the Space Telescope and other devices suggest this theory smay need some
modification. Evidence for the Big Bang includes:
1) The Red Shift: when stars/galaxies are moving away from us the energy they emit is shifted to the red
side of the visible-light spectrum. Those moving towards us are shifted to the violet side. This shift is an
example of the Doppler effect. Similar effects are observed when listening to a train whistle– it will
sound higher (shorter wavelengths) approaching and lower (longer wavelengths) as it moves away.
Likewise red wavelengths are longer than violet ones. Most galaxies appear to be moving away from
ours.
2) Background radiation: two Bell Labs scientists discovered that in interstellar space there is a slight
background radiation, thought to be the residual afterblast remnant of the Big Bang. Click here for
additional information from sites dealing with the Big Bang, or here for a Powerpoint slideshow about the
Big Bang.
Soon after the Big Bang the major forces (such as gravity, weak nuclear force, strong nuclear force, etc.)
differentiated. While in the cosmic egg, scientists think that matter and energy as we understand them did
not exist, but rather they formed soon after the bang. After 10 million to 1 billion years the universe
became clumpy, with matter beginning to accumulate into solar systems. One of those solar systems,
ours, began to form approximately 5 billion years ago, with a large “protostar” (that became our sun) in
the center. The planets were in orbits some distance from the star, their increasing gravitational fields
sweeping stray debris into larger and larger planetesimals that eventually formed planets.
The processes of radioactive decay and heat generated by the impact of planetesimals heated the Earth,
which then began to differentiate into a “cooled” outer cooled crust (of silicon, oxygen and other
relatively light elements) and increasingly hotter inner areas (composed of the heavier and denser
elements such as iron and nickel). Impact (asteroid, comet, planetismals) and the beginnings of volcanism
released water vapor, carbon dioxide, methane, ammonia and other gases into a developing atmosphere.
Sometime “soon” after this, life on Earth began.
Where did life originate and how?
Extra-terrestrial: In 1969, a meteorite (left-over bits from the origin of the solar system) landed near
Allende, Mexico. The Allende Meteorite (and others of its sort) have been analyzed and found to contain
amino acids, the building blocks of proteins, one of the four organic molecule groups basic to all life. The
idea of panspermia hypothesized that life originated out in space and came to Earth inside a meteorite.
Recently, this idea has been revived as Cosmic Ancestry. The amino acids recovered from meteorites are
in a group known as exotics: they do not occur in the chemical systems of living things. The ET theory is
now not considered by most scientists to be correct, although the August 1996 discovery of the Martian
meteorite and its possible fossils have revived thought of life elsewhere in the Solar System.
Supernatural: Since science is an attempt to measure and study the natural world, this theory is outside
science (at least our current understanding of science). Science classes deal with science, and this idea is
in the category of not-science.
Organic Chemical Evolution: Until the mid-1800’s scientists thought organic chemicals (those with a CC skeleton) could only form by the actions of living things. A French scientist heated crystals of a mineral
(a mineral is by definition inorganic), and discovered that they formed urea (an organic chemical) when
they cooled. Russian scientist and academecian A.I. Oparin, in 1922, hypothesized that cellular life was
preceeded by a period of chemical evolution. These chemicals, he argued, must have arisen spontaneously
under conditions exisitng billions of years ago (and quite unlike current conditions).
Figure 1. Ingredients used in Miller’s experiments, simple molecules thought at the time to have existed
on the Earth billions of years ago. Image from Purves et al., Life: The Science of Biology, 4th Edition, by
Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.
In 1950, then-graduate student Stanley Miller designed an experimental test for Oparin’s hypothesis.
Oparin’s original hypothesis called for : 1) little or no free oxygen (oxygen not bonded to other elements);
and 2) C H O and N in abundance. Studies of modern volcanic eruptions support inference of the
existence of such an atmosphere. Miller discharged an electric spark into a mixture thought to resemble
the primordial composition of the atmosphere. Miller’s atmosphere contents are shown in Figure 1. From
the water receptacle, designed to model an ancient ocean, Miller recovered amino acids. Subsequent
modifications of the atmosphere have produced representatives or precursors of all four organic
macromolecular classes. His experimental apparatus is shown in Figure 2.
Figure 2. A diagrammatic representation of Miller’s experimental apparatus. Image from Purves et al.,
Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com), used with permission.
The primordial Earth was a very different place than today, with greater amounts of energy, stronger
storms, etc. The oceans were a “soup” of organic compounds that formed by inorganic processes
(although this soup would not taste umm ummm good). Miller’s (and subsequent) experiments have not
proven life originated in this way, only that conditions thought to have existed over 3 billion years ago
were such that the spontaneous (inorganic) formation of organic macromolecules could have taken place.
The simple inorganic molecules that Miller placed into his apparatus, produced a variety of complex
molecules, shown below in Figure 3.
Figure 3. Molecules recovered from Miller’s and similar experiments. Images from Purves et al., Life:
The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com), used with permission.
The interactions of these molecules would have increased as their concentrations increased. Reactions
would have led to the building of larger, more complex molecules. A pre-cellular life would have began
with the formation of nucleic acids. Chemicals made by these nucleic acids would have remained in
proximity to the nucleic acids. Eventually the pre-cells would have been enclosed in a lipid-protein
membrane, which would have resulted in the first cells.
Biochemically, living systems are separated from other chemical systems by three things.
The capacity for replication from one generation to another. Most organisms today use DNA as the
hereditary material, although recent evidence (ribozymes) suggests that RNA may have been the first
nucleic acid system to have formed. Nobel laureate Walter Gilbert refers to this as the RNA world.
Recent studies suggest a molecular
The presence of enzymes and other complex molecules essential to the processes needed by living
systems. Miller’s experiment showed how these could possibly form.
A membrane that separates the internal chemicals from the external chemical environment. This also
delimits the cell from not-cell areas. The work of Sidney W. Fox has produced proteinoid spheres, which
while not cells, suggest a possible route from chemical to cellular life.
Fossil evidence supports the origins of life on Earth earlier than 3.5 billion years ago. The North Pole
microfossils from Australia, illustrated in Figure 4, are complex enough that more primitive cells must
have existed earlier. From rocks of the Ishua Super Group in Greenland come possibly the earliest cells,
as much as 3.8 billion years old. The oldest known rocks on Earth are 3.96 billion years old and are from
Arctic Canada. Thus, life appears to have begun soon after the cooling of the Earth and formation of the
atmosphere and oceans.
Figure 4. Microfossils from the Apex Chert, North Pole, Australia. These organisms are Archean in age,
approximately 3.465 billion years old, and resemble filamentous cyanobacteria. Image from
http://www.astrobiology.ucla.edu/ESS116/L15/1515%20Apex%20Chert.jpg.
These ancient fossils occur in marine rocks, such as limestones and sandstones, that formed in ancient
oceans. The organisms living today that are most similar to ancient life forms are the archaebacteria. This
group is today restricted to marginal environments. Recent discoveries of bacteria at mid-ocean ridges
add yet another possible origin for life: at these mid-ocean ridges where heat and molten rock rise to the
Earth’s surface.
Archaea and Eubacteria are similar in size and shape. When we do recover “bacteria” as fossils those are
the two features we will usually see: size and shape. How can we distinguish between the two groups: the
use of molecular fossils that will point to either (but not both) groups. Such a chemical fossil has been
found and its presence in the Ishua rocks of Greenland (3.8 billion years old) suggests that the archeans
were present at that time.
Is there life on Mars, Venus, anywhere else?
The proximity of the Earth to the sun, the make-up of the Earth’s crust (silicate mixtures, presence of
water, etc.) and the size of the Earth suggest we may be unique in our own solar system, at least. Mars is
smaller, farther from the sun, has a lower gravitational field (which would keep the atmosphere from
escaping into space) and does show evidence of running water sometime in its past. If life did start on
Mars, however, there appears to be no life (as we know it) today. Venus, the second planet, is closer to
the sun, and appears similar to Earth in many respects. Carbon dioxide build-up has resulted in a
“greenhouse planet” with strong storms and strongly acidic rain. Of all planets in the solar system, Venus
is most likely to have some form of carbon-based life. The outer planets are as yet too poorly understood,
although it seems unlikely that Jupiter or Saturn harbor life as we know it. Like Goldilocks would say
“Venus is too hot, Mars is too cold, the Earth is just right!”
Mars: In August 1996, evidence of life on Mars (or at least the chemistry of life), was announced. Click
here to view that article and related ones. The results of years of study are inconclusive at best. The
purported bacteria are much smaller than any known bacteria on Earth, were not hollow, and most could
possibly have been mineral in origin. However, many scientists consider that the chemistry of life appears
to have been established on Mars. Search for martian life (or its remains) continues.
Terms applied to cells
Heterotroph (other-feeder): an organism that obtains its energy from another organism. Animals, fungi,
bacteria, and mant protistans are heterotrophs.
Autotroph (self-feeder): an organism that makes its own food, it converts energy from an inorganic source
in one of two ways. Photosynthesis is the conversion of sunlight energy into C-C covalent bonds of a
carbohydrate, the process by which the vast majority of autotrophs obtain their energy. Chemosynthesis is
the capture of energy released by certain inorganic chemical reactions. This is common in certain groups
of likely that chemosynthesis predates photosynthesis. At mid-ocean ridges, scientists have discovered
black smokers, vents that release chemicals into the water. These chemical reactions could have powered
early ecosystems prior to the development of an ozone layer that would have permitted life to occupy the
shallower parts of the ocean. Evidence of the antiquity of photosynthesis includes: a) biochemical
precursors to photosynthesis chemicals have been synthesized in experiments; and b) when placed in
light, these chemicals undergo chemical reactions similar to some that occur in primitive photosynthetic
bacteria.
Prokaryotes are among the most primitive forms of life on Earth. Remember that primitive does not
necessarily equate to outdated and unworkable in an evolutionary sense, since primitive bacteria seem
little changed, and thus may be viewed as well adapted, for over 3.5 Ga. Prokaryote (pro=before,
karyo=nucleus): these organisms lack membrane-bound organelles, as seen in Figures 5 and 6. Some
internal membrane organization is observable in a few prokaryotic autotrophs, such as the photosynthetic
membranes associated with the photosynthetic chemicals in the photosynthetic bacterium Prochloron. A
transmission electron micrograph of Prochloron is shown in Figure 5.
Figure 5 Prochloron, an extant prokaryote thought related to the ancestors of some eukarypote
chloroplasts. Image fom http://tidepool.st.usm.edu/pix/prochloron.gif.
Figure 6. The main features of a generalized prokaryote cell. Image from Purves et al., Life: The Science
of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com), used with permission.
The Cell Theory is one of the foundations of modern biology. Its major tenets are:
All living things are composed of one or more cells;
The chemical reactions of living cells take place within cells;
All cells originate from pre-existing cells; and
Cells contain hereditary information, which is passed from one generation to another.
Components of Cells
Cell Membrane (also known as plasma membrane or plasmalemma) is surrounds all cells. It: 1) separates
the inner parts of the cell from the outer environment; and 2) acts as a selectively permeable barrier to
allow certain chemicals, namely water, to pass and others to not pass. In multicellular organisms certain
chemicals on the membrane surface act in the recognition of self. Antigens are substances located on the
outside of cells, viruses and in some cases other chemicals. Antibodies are chemicals (Y-shaped)
produced by an animal in response to a specific antigen. This is the basis of immunity and vaccination.
Hereditary material (both DNA and RNA) is needed for a cell to be able to replicate and/or reproduce.
Most organisms use DNA. Viruses and viroids sometimes employ RNA as their hereditary material.
Retroviruses include HIV (Human Immunodefficiency Virus, the causative agent of AIDS) and Feline
Leukemia Virus (the only retrovirus for which a successful vaccine has been developed). Viroids are
naked pieces of RNA that lack cytoplasm, membranes, etc. They are parasites of some plants and also as
possible glimpses of the functioning of pre-cellular life forms. Prokaryotic DNA is organized as a circular
chromosome contained in an area known as a nucleoid. Eukaryotic DNA is organized in linear structures,
the eukaryotic chromosomes, which are associations of DNA and histone proteins contained within a
double membrane nuclear envelope, an area known as the cell nucleus.
Organelles are formed bodies within the cytoplasm that perform certain functions. Some organelles are
surrounded by membranes, we call these membrane-bound organelles.
Ribosomes are the tiny structures where proteins synthesis occurs. They are not membrane-bound and
occur in all cells, although there are differences between the size of subunits in eukaryotic and
prokaryotic ribosomes.
The Cell Wall is a structure surrounding the plasma membrane. Prokaryote and eukaryote (if they have
one) cell walls differ in their structure and chemical composition. Plant cells have cellulose in their cell
walls, other organisims have different materials cpmprising their walls. Animals are distinct as a group in
their lack of a cell wall.
Membrane-bound organelles occur only in eukaryotic cells. They will be discussed in detail later.
Eukaryotic cells are generally larger than prokaryotic cells. Internal complexity is usually greater in
eukaryotes, with their compartmentalized membrane-bound organelles, than in prokaryotes. Some
prokaryotes, such as Anabaena azollae, and Prochloron, have internal membranes associated with
photosynthetic pigments.
The Origins of Multicellularity
The oldest accepted prokaryote fossils date to 3.5 billion years; Eukaryotic fossils to between 750 million
years and possibly as old as 1.2-1.5 billion years. Multicellular fossils, purportedly of animals, have been
recovered from 750Ma rocks in various parts of the world. The first eukaryotes were undoubtedly
Protistans, a group that is thought to have given rise to the other eukaryotic kingdoms. Multicellularity
allows specialization of function, for example muscle fibers are specialized for contraction, neuron cells
for transmission of nerve messages.
Microscopes
Microscopes are important tools for studying cellular structures. In this class we will use light
microscopes for our laboratory observations. Your text will also show light photomicrographs (pictures
taken with a light microscope) and electron micrographs (pictures taken with an electron microscope).
There are many terms and concepts which will help you in maximizing your study of microscopy.
There are many different types of microscopes used in studying biology. These include the light
microscopes (dissecting, compound brightfield, and compound phase-contrast), electron microscopes
(transmission and scanning), and atomic force microscope.
The microscope is an important tool used by biologists to magnify small objects. There are several
concepts fundamental to microscopy.
Magnification is the ratio of enlargement (or eduction) between the specimen and its image (either
printed photograph or the virtual image seen through the eyepiece). To calculate magnification we
multiply the power of each lens through which the light from the specimen passes, indicating that product
as GGGX, where GGG is the product. For example: if the light passes through two,lenses (an objective
lens and an ocular lens) we multiply the 10X ocular value by the value of the objective lens (say it is 4X):
10 X 4=40, or 40X magnification.
Resolution is the ability to distinguish between two objects (or points). The closer the two objects are, the
easier it is to distinguish recognize the distance between them. What microscopes do is to bring small
objects “closer” to the observer by increasing the magnification of the sample. Since the sample is the
same distance from the viewer, a “virtual image” is formed as the light (or electron beam) passes through
the magnifying lenses. Objects such as a human hair appear smooth (and feel smooth) when viewed with
the unaided or naked) eye. However, put a hair under a microscope and it takes on a VERY different
look!
Working distance is the distance between the specimen and the magnifying lens.
Depth of field is a measure of the amount of a specimen that can be in focus.
Magnification and resolution are terms used frequently in the study of cell biology, often without an
accurate definition of their meanings. Magnification is a ratio of the enlargement (or reduction) of an
image (drawing or photomicrograph), usually expressed as X1, X1/2, X430, X1000, etc. Resolution is the
ability to distinguish between two points. Generally resolution increases with magnification, although
there does come a point of diminishing returns where you increase magnification beyond added resolution
gain.
Scientists employ the metric system to measure the size and volume of specimens. The basic unit of
length is the meter (slightly over 1 yard). Prefixes are added to the “meter” to indicate multiple meters
(kilometer) or fractional meters (millimeter). Below are the values of some of the prefixes used in the
metric system.
kilo = one thousand of the basic unit
meter = basic unit of length
centi = one hundreth (1/100) of the basic unit
milli = one thousandth (1/1000) of the basic unit
micro = one millionth (1/1,000,000) of the basic unit
nano = one billionth (1/1,000,000,000) of the basic unit
The basic unit of length is the meter (m), and of volume it is the liter (l). The gram (g). Prefixes listed
above can be applied to all of these basic units, abbreviated as km, kg, ml, mg, nm….etc. The Greek letter
micron (µ) is applied to small measurements (thoudsandths of a millimeter), producing the micrometer
(symbolized as µm). Measurements in microscopy are usually expressed in the metric system. General
units you will encounter in your continuing biology careers include micrometer (µm, 10-6m), nanometer
(nm, 10-9m), and angstrom (Å, 10-10m).
Light microscopes were the first to be developed, and still the most commonly used ones. The best
resolution of light microscopes (LM) is 0.2 µm. Magnification of LMs is generally limited by the
properties of the glass used to make microscope lenses and the physical properties of their light sources.
The generally accepted maximum magnifications in biological uses are between 1000X and 1250X.
Calculation of LM magnification is done by multiplying objective value by eyepiece value.
To view relatively large objects at lower magnifications we utilize the dissecting microscope (shown in
Figure 7). Common uses of this microscope include examination of prepared microscope slides at low
magnification, dissection (hence the name) of flowers or animal organs, and examinations of the surface
of objects such as pennies and five dollar bills. Magnification on the dissecting microscope is calculated
by multiplying the ocular (or eyepiece) value (usually 10X) by the value of the objective lens (a variable
between 0.7 and 3X). The value of the objective lens is selected using a dial on the body tube of the
microscope.
Figure 7. Parts of a Nikon dissecting microscope. Image courtesy of Nikon Co.
The compound light microscope, shown in Figure 8, uses two ground glass lenses to form the image. The
lenses in this microscope, however, are aligned with the light source and specimen so that the light passes
through the specimen, rather than reflects off the surface (as in the dissecting microscope shown in Figure
7). The compound microscope provides greater magnification (and resolution), but only thin specimens
(or thin slices of a specimen) can be viewed with this type of microscope.
Figure 8. Parts of a Nikon compound microscope. Image courtesy of Nikon Co.
Electron microscopes, two examples of which are shown in Figure 9, are more rarely encountered by
beginning biology students. However, the images gathered from these microscopes reveal a greater
structure of the cell, so some familiarity with the strengths and weaknesses of each type is useful. Instead
of using light as an imaging source, a high energy beam of electrons (between five thousand and one
billion electron volts) is focused through electromagnetic lenses (instead of glass lenses used in the light
microscope). The increased resolution results from the shorter wavelength of the electron beam,
increasing resolution in the transmission electron microscope (TEM) to a theoretical limit of 0.2 nm. The
magnifications reached by TEMs are commonly over 100,000X, depending on the nature of the sample
and the operating condition of the TEM. The other type of electron microscope is the scanning electron
microscope (SEM). It uses a different method of electron capture and displays images on high resolution
television monitors. The resolution and magnification of the SEM are less than that of the TEM although
still orders of magnitude above the LM.
Figure 9. Electron microscopes. The above (left) image of a transmission electron microscope is from
http://nsm.fullerton.edu/~skarl/EM/Equipment/TEM.html. The above right image of a scanning electron
microscope is from http://nsm.fullerton.edu/~skarl/EM/Equipment/SEM.html.
CELLS II: CELLULAR ORGANIZATION
Table of Contents
Life exhibits varying degrees of organization. Atoms are organized into molecules, molecules into
organelles, and organelles into cells, and so on. According to the Cell Theory, all living things are
composed of one or more cells, and the functions of a multicellular organism are a consequence of the
types of cells it has. Cells fall into two broad groups: prokaryotes and eukaryotes. Prokaryotic cells are
smaller (as a general rule) and lack much of the internal compartmentalization and complexity of
eukaryotic cells. No matter which type of cell we are considering, all cells have certain features in
common, such as a cell membrane, DNA and RNA, cytoplasm, and ribosomes. Eukaryotic cells have a
great variety of organelles and structures.
Cell Size and Shape
The shapes of cells are quite varied with some, such as neurons, being longer than they are wide and
others, such as parenchyma (a common type of plant cell) and erythrocytes (red blood cells) being
equidimensional. Some cells are encased in a rigid wall, which constrains their shape, while others have a
flexible cell membrane (and no rigid cell wall).
The size of cells is also related to their functions. Eggs (or to use the latin word, ova) are very large, often
being the largest cells an organism produces. The large size of many eggs is related to the process of
development that occurs after the egg is fertilized, when the contents of the egg (now termed a zygote) are
used in a rapid series of cellular divisions, each requiring tremendous amounts of energy that is available
in the zygote cells. Later in life the energy must be acquired, but at first a sort of inheritance/trust fund of
energy is used.
Cells range in size from small bacteria to large, unfertilized eggs laid by birds and dinosaurs. The realtive
size ranges of biological things is shown in Figure 1. In science we use the metric system for measuring.
Here are some measurements and convesrions that will aid your understanding of biology.
1 meter = 100 cm = 1,000 mm = 1,000,000 µm = 1,000,000,000 nm
1 centimenter (cm) = 1/100 meter = 10 mm
1 millimeter (mm) = 1/1000 meter = 1/10 cm
1 micrometer (µm) = 1/1,000,000 meter = 1/10,000 cm
1 nanometer (nm) = 1/1,000,000,000 meter = 1/10,000,000 cm
Figure 1. Sizes of viruses, cells, and organisms. Images from Purves et al., Life: The Science of Biology,
4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used
with permission.
The Cell Membrane
The cell membrane functions as a semi-permeable barrier, allowing a very few molecules across it while
fencing the majority of organically produced chemicals inside the cell. Electron microscopic
examinations of cell membranes have led to the development of the lipid bilayer model (also referred to
as the fluid-mosaic model). The most common molecule in the model is the phospholipid, which has a
polar (hydrophilic) head and two nonpolar (hydrophobic) tails. These phospholipids are aligned tail to tail
so the nonpolar areas form a hydrophobic region between the hydrophilic heads on the inner and outer
surfaces of the membrane. This layering is termed a bilayer since an electron microscopic technique
known as freeze-fracturing is able to split the bilayer, shown in Figure 2.
Figure 2. Cell Membranes from Opposing Neurons (TEM x436,740). This image is copyright Dennis
Kunkel at www.DennisKunkel.com, used with permission.
Cholesterol is another important component of cell membranes embedded in the hydrophobic areas of the
inner (tail-tail) region. Most bacterial cell membranes do not contain cholesterol. Cholesterol aids in the
flexibility of a cell membrane.
Proteins, shown in Figure 2, are suspended in the inner layer, although the more hydrophilic areas of these
proteins “stick out” into the cells interior as well as outside the cell. These proteins function as gateways
that will allow certain molecules to cross into and out of the cell by moving through open areas of the
protein channel. These integral proteins are sometimes known as gateway proteins. The outer surface of
the membrane will tend to be rich in glycolipids, which have their hydrophobic tails embedded in the
hydrophobic region of the membrane and their heads exposed outside the cell. These, along with
carbohydrates attached to the integral proteins, are thought to function in the recognition of self, a sort of
cellular identification system.
The contents (both chemical and organelles) of the cell are termed protoplasm, and are further subdivided
into cytoplasm (all of the protoplasm except the contents of the nucleus) and nucleoplasm (all of the
material, plasma and DNA etc., within the nucleus).
The Cell Wall
Not all living things have cell walls, most notably animals and many of the more animal-like protistans.
Bacteria have cell walls containing the chemical peptidoglycan. Plant cells, shown in Figures 3 and 4,
have a variety of chemicals incorporated in their cell walls. Cellulose, a nondigestible (to humans
anyway) polysaccharide is the most common chemical in the plant primary cell wall. Some plant cells
also have lignin and other chemicals embedded in their secondary walls.
The cell wall is located outside the plasma membrane. Plasmodesmata are connections through which
cells communicate chemically with each other through their thick walls. Fungi and many protists have
cell walls although they do not contain cellulose, rather a variety of chemicals (chitin for fungi).
Animal cells, shown in Figure 5, lack a cell wall, and must instead rely on their cell membrane to
maintain the integrity of the cell. Many protistans also lack cell walls, using variously modified cell
membranes o act as a boundary to the inside of the cell.
Figure 3. Structure of a typical plant cell. Image from Purves et al., Life: The Science of Biology, 4th
Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with
permission.
Figure 4. Lily Parenchyma Cell (cross-section) (TEM x7,210). Note the large nucleus and nucleolus in the
center of the cell, mitochondria and plastids in the cytoplasm. This image is copyright Dennis Kunkel at
www.DennisKunkel.com, used with permission.
Figure 5. Liver Cell (TEM x9,400). This image is copyright Dennis Kunkel. This image is copyright
Dennis Kunkel at www.DennisKunkel.com, used with permission.
The nucleus
The nucleus, shown in Figures 6 and 7, occurs only in eukaryotic cells. It is the location for most of the
nucleic acids a cell makes, such as DNA and RNA. Danish biologist Joachim Hammerling carried out an
important experiment in 1943. His work (click here for a diagram) showed the role of the nucleus in
controlling the shape and features of the cell. Deoxyribonucleic acid, DNA, is the physical carrier of
inheritance and with the exception of plastid DNA (cpDNA and mDNA, found in the chloroplast and
mitochondrion respectively) all DNA is restricted to the nucleus. Ribonucleic acid, RNA, is formed in the
nucleus using the DNA base sequence as a template. RNA moves out into the cytoplasm where it
functions in the assembly of proteins. The nucleolus is an area of the nucleus (usually two nucleoli per
nucleus) where ribosomes are constructed.
Figure 6. Structure of the nucleus. Note the chromatin, uncoiled DNA that occupies the space within the
nuclear envelope. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer
Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.
Figure 7. Liver cell nucleus and nucleolus (TEM x20,740). Cytoplasm, mitochondria, endoplasmic
reticulum, and ribosomes also shown.This image is copyright Dennis Kunkel at www.DennisKunkel.com,
used with permission.
The nuclear envelope, shown in Figure 8, is a double-membrane structure. Numerous pores occur in the
envelope, allowing RNA and other chemicals to pass, but the DNA not to pass.
Figure 8. Structure of the nuclear envelope and nuclear pores. Image from Purves et al., Life: The Science
of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com), used with permission.
Figure 9. Nucleus with Nuclear Pores (TEM x73,200). The cytoplasm also contains numerous ribosomes.
This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.
Cytoplasm
The cytoplasm was defined earlier as the material between the plasma membrane (cell membrane) and the
nuclear envelope. Fibrous proteins that occur in the cytoplasm, referred to as the cytoskeleton maintain
the shape of the cell as well as anchoring organelles, moving the cell and controlling internal movement
of structures. Elements that comprose the cytoskeleton are shown in Figure 10. Microtubules function in
cell division and serve as a “temporary scaffolding” for other organelles. Actin filaments are thin threads
that function in cell division and cell motility. Intermediate filaments are between the size of the
microtubules and the actin filaments.
Figure 10. Actin and tubulin components of the cytoskeleton. Image from Purves et al., Life: The Science
of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com), used with permission.
Vacuoles and vesicles
Vacuoles are single-membrane organelles that are essentially part of the outside that is located within the
cell. The single membrane is known in plant cells as a tonoplast. Many organisms will use vacuoles as
storage areas. Vesicles are much smaller than vacuoles and function in transporting materials both within
and to the outside of the cell.
Ribosomes
Ribosomes are the sites of protein synthesis. They are not membrane-bound and thus occur in both
prokaryotes and eukaryotes. Eukaryotic ribosomes are slightly larger than prokaryotic ones. Structurally,
the ribosome consists of a small and larger subunit, as shown in Figure 11. . Biochemically, the ribosome
consists of ribosomal RNA (rRNA) and some 50 structural proteins. Often ribosomes cluster on the
endoplasmic reticulum, in which case they resemble a series of factories adjoining a railroad line. Figure
12 illustrates the many ribosomes attached to the endoplasmic reticulum. Click here for Ribosomes (More
than you ever wanted to know about ribosomes!)
Figure 11. Structure of the ribosome. Image from Purves et al., Life: The Science of Biology, 4th Edition,
by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with
permission.
Figure 12. Ribosomes and Polyribosomes – liver cell (TEM x173,400). This image is copyright Dennis
Kunkel at www.DennisKunkel.com, used with permission.
Endoplasmic reticulum | Back to Top
Endoplasmic reticulum, shown in Figure 13 and 14, is a mesh of interconnected membranes that serve a
function involving protein synthesis and transport. Rough endoplasmic reticulum (Rough ER) is so-
named because of its rough appearance due to the numerous ribosomes that occur along the ER. Rough
ER connects to the nuclear envelope through which the messenger RNA (mRNA) that is the blueprint for
proteins travels to the ribosomes. Smooth ER; lacks the ribosomes characteristic of Rough ER and is
thought to be involved in transport and a variety of other functions.
Figure 13. The endoplasmic reticulum. Rough endoplasmic reticulum is on the left, smooth endoplasmic
reticulum is on the right. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer
Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.
Figure 14. Rough Endoplasmic Reticulum with Ribosomes (TEM x61,560). This image is copyright
Dennis Kunkel at www.DennisKunkel.com, used with permission.
Golgi Apparatus and Dictyosomes
Golgi Complexes, shown in Figure 15 and 16, are flattened stacks of membrane-bound sacs. Italian
biologist Camillo Golgi discovered these structures in the late 1890s, although their precise role in the cell
was not deciphered until the mid-1900s . Golgi function as a packaging plant, modifying vesicles
produced by the rough endoplasmic reticulum. New membrane material is assembled in various cisternae
(layers) of the golgi.
Figure 15. Structure of the Golgi apparatus and its functioning in vesicle-mediated transport. Images from
Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and
WH Freeman (www.whfreeman.com), used with permission.
Figure 16. Golgi Apparatus in a plant parenchyma cell from Sauromatum guttatum (TEM x145,700).
Note the numerous vesicles near the Golgi. This image is copyright Dennis Kunkel at
www.DennisKunkel.com, used with permission.
Lysosomes
Lysosomes, shown in Figure 17, are relatively large vesicles formed by the Golgi. They contain
hydrolytic enzymes that could destroy the cell. Lysosome contents function in the extracellular
breakdown of materials.
Figure 17. Role of the Golgi in forming lysosomes. Image from Purves et al., Life: The Science of
Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com), used with permission.
Mitochondria
Mitochondria contain their own DNA (termed mDNA) and are thought to represent bacteria-like
organisms incorporated into eukaryotic cells over 700 million years ago (perhaps even as far back as 1.5
billion years ago). They function as the sites of energy release (following glycolysis in the cytoplasm) and
ATP formation (by chemiosmosis). The mitochondrion has been termed the powerhouse of the cell.
Mitochondria are bounded by two membranes. The inner membrane folds into a series of cristae, which
are the surfaces on which adenosine triphosphate (ATP) is generated. The matrix is the area of the
mitochondrion surrounded by the inner mitochondrial membrane. Ribosomes and mitochondrial DNA are
found in the matrix. The significance of these features will be discussed below. The structure of
mitochondria is shown in Figure 18 and 19.
Figure 18. Structure of a mitochondrion. Note the various infoldings of the mitochondrial inner
membrane that produce the cristae. Image from Purves et al., Life: The Science of Biology, 4th Edition,
by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with
permission.
Figure 19. Muscle Cell Mitochondrion (TEM x190,920). This image is copyright Dennis Kunkel at
www.DennisKunkel.com, used with permission.
Mitochondria and endosymbiosis
During the 1980s, Lynn Margulis proposed the theory of endosymbiosis to explain the origin of
mitochondria and chloroplasts from permanent resident prokaryotes. According to this idea, a larger
prokaryote (or perhaps early eukaryote) engulfed or surrounded a smaller prokaryote some 1.5 billion to
700 million years ago. Steps in this sequence are illustrated in Figure 20.
Figure 20. The basic events in endosymbiosis. Image from Purves et al., Life: The Science of Biology,
4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used
with permission.
Instead of digesting the smaller organisms the large one and the smaller one entered into a type of
symbiosis known as mutualism, wherein both organisms benefit and neither is harmed. The larger
organism gained excess ATP provided by the “protomitochondrion” and excess sugar provided by the
“protochloroplast”, while providing a stable environment and the raw materials the endosymbionts
required. This is so strong that now eukaryotic cells cannot survive without mitochondria (likewise
photosynthetic eukaryotes cannot survive without chloroplasts), and the endosymbionts can not survive
outside their hosts. Nearly all eukaryotes have mitochondria. Mitochondrial division is remarkably similar
to the prokaryotic methods that will be studied later in this course. A summary of the theory is available
by clicking here.
Plastids
Plastids are also membrane-bound organelles that only occur in plants and photosynthetic eukaryotes.
Leucoplasts, also known as amyloplasts (and shown in Figure 21) store starch, as well as sometimes
protein or oils. Chromoplasts store pigments associated with the bright colors of flowers and/or fruits.
Figure 21. Starch grains ina fresh-cut potato tuber. Image from http://images.botany.org/set-13/13008v.jpg.
Chloroplasts, illustrated in Figures 22 and 23, are the sites of photosynthesis in eukaryotes. They contain
chlorophyll, the green pigment necessary for photosynthesis to occur, and associated accessory pigments
(carotenes and xanthophylls) in photosystems embedded in membranous sacs, thylakoids (collectively a
stack of thylakoids are a granum [plural = grana]) floating in a fluid termed the stroma. Chloroplasts
contain many different types of accessory pigments, depending on the taxonomic group of the organism
being observed.
Figure 22. Structure of the chloroplast. Image from Purves et al., Life: The Science of Biology, 4th
Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with
permission.
Figure 23. Chloroplast from red alga (Griffthsia spp.). x5,755–(Based on an image size of 1 inch in the
narrow dimension). This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with
permission.
Chloroplasts and endosymbiosis
Like mitochondria, chloroplasts have their own DNA, termed cpDNA. Chloroplasts of Green Algae
(Protista) and Plants (descendants of some of the Green Algae) are thought to have originated by
endosymbiosis of a prokaryotic alga similar to living Prochloron (the sole genus present in the
Prochlorobacteria, shown in Figure 24). Chloroplasts of Red Algae (Protista) are very similar
biochemically to cyanobacteria (also known as blue-green bacteria [algae to chronologically enhanced
folks like myself :)]). Endosymbiosis is also invoked for this similarity, perhaps indicating more than one
endosymbiotic event occurred.
Figure 24. Prochloron, a photosynthetic bacteria, reveals the presence of numerous thylakoids in the
transmission electron micrograph on the left. Prochloron occurs in long filaments, as shown by the light
micrograph on the right below. Image from
http://www.cas.muohio.edu/~wilsonkg/bot191/mouseth/m19p32.jpg.
Cell Movement
Cell movement; is both internal, referred to as cytoplasmic streaming, and external, referred to as
motility. Internal movements of organelles are governed by actin filaments and other components of the
cytoskeleton. These filaments make an area in which organelles such as chloroplasts can move. Internal
movement is known as cytoplasmic streaming. External movement of cells is determined by special
organelles for locomotion.
The cytoskeleton is a network of connected filaments and tubules. It extends from the nucleus to the
plasma membrane. Electron microscopic studies showed the presence of an organized cytoplasm.
Immunofluorescence microscopy identifies protein fibers as a major part of this cellular feature. The
cytoskeleton components maintain cell shape and allow the cell and its organelles to move.
Actin filaments, shown in Figure 25, are long, thin fibers approximately seven nm in diameter. These
filaments occur in bundles or meshlike networks. These filaments are polar, meaning there are differences
between the ends of the strand. An actin filament consists of two chains of globular actin monomers
twisted to form a helix. Actin filaments play a structural role, forming a dense complex web just under the
plasma membrane. Actin filaments in microvilli of intestinal cells act to shorten the cell and thus to pull it
out of the intestinal lumen. Likewise, the filaments can extend the cell into intestine when food is to be
absorbed. In plant cells, actin filaments form tracts along which chloroplasts circulate.
Actin filaments move by interacting with myosin, The myosin combines with and splits ATP, thus
binding to actin and changing the configuration to pull the actin filament forward. Similar action accounts
for pinching off cells during cell division and for amoeboid movement.
Figure 25. Skeletal muscle fiber with exposed intracellular actin myosin filaments. The muscle fiber was
cut perpendicular to its length to expose the intracellular actin myosin filaments. SEM X220. This image
is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.
Intermediate filaments are between eight and eleven nm in diameter. They are between actin filaments
and microtubules in size. The intermediate fibers are rope-like assemblies of fibrous polypeptides. Some
of them support the nuclear envelope, while others support the plasma membrane, form cell-to-cell
junctions.
Microtubules are small hollow cylinders (25 nm in diameter and from 200 nm-25 µm in length). These
microtubules are composed of a globular protein tubulin. Assembly brings the two types of tubulin (alpha
and beta) together as dimers, which arrange themselves in rows.
In animal cells and most protists, a structure known as a centrosome occurs. The centrosome contains two
centrioles lying at right angles to each other. Centrioles are short cylinders with a 9 + 0 pattern of
microtubule triplets. Centrioles serve as basal bodies for cilia and flagella. Plant and fungal cells have a
structure equivalent to a centrosome, although it does not contain centrioles.
Cilia are short, usually numerous, hairlike projections that can move in an undulating fashion (e.g., the
protzoan Paramecium, the cells lining the human upper respiratory tract). Flagella are longer, usually
fewer in number, projections that move in whip-like fashion (e.g., sperm cells). Cilia and flagella are
similar except for length, cilia being much shorter. They both have the characteristic 9 + 2 arrangement of
microtubules shown in figures 26.
Figure 26. Cilia from an epithelial cell in cross section (TEM x199,500). Note the 9 + 2 arrangement of
cilia. This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.
Cilia and flagella move when the microtubules slide past one another. Both oif these locomotion
structures have a basal body at base with thesame arrangement of microtubule triples as centrioles. Cilia
and flagella grow by the addition of tubulin dimers to their tips.
Flagella work as whips pulling (as in Chlamydomonas or Halosphaera) or pushing (dinoflagellates, a
group of single-celled Protista) the organism through the water. Cilia work like oars on a viking longship
(Paramecium has 17,000 such oars covering its outer surface). The movement of these structures is
shown in Figure 27.
Figure 27. Movement of cilia and flagella. Image from Purves et al., Life: The Science of Biology, 4th
Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with
permission.
Not all cells use cilia or flagella for movement. Some, such as Amoeba, Chaos (Pelomyxa) and human
leukocytes (white blood cells), employ pseudopodia to move the cell. Unlike cilia and flagella,
pseudopodia are not structures, but rather are associated with actin near the moving edge of the cell. The
formation of a pseudopod is shown in Figure 28.
Figure 28. Formation and functioning of a pseudopod by an amoeboid cell. Image from Purves et al.,
Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com), used with permission.
CELL DIVISION: MEIOSIS AND SEXUAL REPRODUCTION
Meiosis
Sexual reproduction occurs only in eukaryotes. During the formation of gametes, the number of
chromosomes is reduced by half, and returned to the full amount when the two gametes fuse during
fertilization.
Ploidy
Haploid and diploid are terms referring to the number of sets of chromosomes in a cell. Gregor Mendel
determined his peas had two sets of alleles, one from each parent. Diploid organisms are those with two
(di) sets. Human beings (except for their gametes), most animals and many plants are diploid. We
abbreviate diploid as 2n. Ploidy is a term referring to the number of sets of chromosomes. Haploid
organisms/cells have only one set of chromosomes, abbreviated as n. Organisms with more than two sets
of chromosomes are termed polyploid. Chromosomes that carry the same genes are termed homologous
chromosomes. The alleles on homologous chromosomes may differ, as in the case of heterozygous
individuals. Organisms (normally) receive one set of homologous chromosomes from each parent.
Meiosis is a special type of nuclear division which segregates one copy of each homologous chromosome
into each new “gamete”. Mitosis maintains the cell’s original ploidy level (for example, one diploid 2n
cell producing two diploid 2n cells; one haploid n cell producing two haploid n cells; etc.). Meiosis, on
the other hand, reduces the number of sets of chromosomes by half, so that when gametic recombination
(fertilization) occurs the ploidy of the parents will be reestablished.
Most cells in the human body are produced by mitosis. These are the somatic (or vegetative) line cells.
Cells that become gametes are referred to as germ line cells. The vast majority of cell divisions in the
human body are mitotic, with meiosis being restricted to the gonads.
Life Cycles
Life cycles are a diagrammatic representation of the events in the organism’s development and
reproduction. When interpreting life cycles, pay close attention to the ploidy level of particular parts of
the cycle and where in the life cycle meiosis occurs. For example, animal life cycles have a dominant
diploid phase, with the gametic (haploid) phase being a relative few cells. Most of the cells in your body
are diploid, germ line diploid cells will undergo meiosis to produce gametes, with fertilization closely
following meiosis.
Plant life cycles have two sequential phases that are termed alternation of generations. The sporophyte
phase is “diploid”, and is that part of the life cycle in which meiosis occurs. However, many plant species
are thought to arise by polyploidy, and the use of “diploid” in the last sentence was meant to indicate that
the greater number of chromosome sets occur in this phase. The gametophyte phase is “haploid”, and is
the part of the life cycle in which gametes are produced (by mitosis of haploid cells). In flowering plants
(angiosperms) the multicelled visible plant (leaf, stem, etc.) is sporophyte, while pollen and ovaries
contain the male and female gametophytes, respectively. Plant life cycles differ from animal ones by
adding a phase (the haploid gametophyte) after meiosis and before the production of gametes.
Many protists and fungi have a haploid dominated life cycle. The dominant phase is haploid, while the
diploid phase is only a few cells (often only the single celled zygote, as in Chlamydomonas ). Many
protists reproduce by mitosis until their environment deteriorates, then they undergo sexual reproduction
to produce a resting zygotic cyst.
Phases of Meiosis
Two successive nuclear divisions occur, Meiosis I (Reduction) and Meiosis II (Division). Meiosis
produces 4 haploid cells. Mitosis produces 2 diploid cells. The old name for meiosis was reduction/
division. Meiosis I reduces the ploidy level from 2n to n (reduction) while Meiosis II divides the
remaining set of chromosomes in a mitosis-like process (division). Most of the differences between the
processes occur during Meiosis I.
The above image is from http://www.biology.uc.edu/vgenetic/meiosis/
Prophase I
Prophase I has a unique event — the pairing (by an as yet undiscovered mechanism) of homologous
chromosomes. Synapsis is the process of linking of the replicated homologous chromosomes. The
resulting chromosome is termed a tetrad, being composed of two chromatids from each chromosome,
forming a thick (4-strand) structure. Crossing-over may occur at this point. During crossing-over
chromatids break and may be reattached to a different homologous chromosome.
The alleles on this tetrad:
ABCDEFG
ABCDEFG
abcdefg
abcdefg
will produce the following chromosomes if there is a crossing-over event between the 2nd and 3rd
chromosomes from the top:
ABCDEFG
ABcdefg
abCDEFG
abcdefg
Thus, instead of producing only two types of chromosome (all capital or all lower case), four different
chromosomes are produced. This doubles the variability of gamete genotypes. The occurrence of a
crossing-over is indicated by a special structure, a chiasma (plural chiasmata) since the recombined inner
alleles will align more with others of the same type (e.g. a with a, B with B). Near the end of Prophase I,
the homologous chromosomes begin to separate slightly, although they remain attac…
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