Bio 301E

Handout 1 - Diversity of Cells and Organisms

Aug 26-31

1. What are some properties common to all living organisms that distinguish them from nonliving entities?
All living organisms share seven common properties of life: they must be made of
cells, be able to reproduce, contain DNA, obtain and use energy, respond (or react) to their
environment in some way, and must maintain homeostasis. Organism must contain the cell,
which is the most basic unit of life, and can be either unicellular (containing only one cell) or
multicellular (containing many cells). Living things can reproduce either sexually, when two
parent organisms combine genetic material to produce the offspring, or asexually, when a
single organism can divide or bud to create its offspring without additional species. Living
things share a Universal Genetic Code, which makes up part of the DNA. Growth refers to two
processes: increase in the number of cells and increase in the size of cells. Development
refers to changes in the organism, which occur through its life span, including cell
differentiation, organ development, aging and death. Energy is used by all living things for
growth, development, and reproduction. Life processes which results in building the
organism is known as anabolism, and life process where energy is extracted by breaking
down substances is called catabolism. Something which causes an organism to react to its
environment is known as a stimulus (stimuli) and the ability of organism to react is called
irritability. Lastly, organisms must maintain homeostasis, which is an internal stable set of
internal conditions allowing the chemical reactions of life to occur.
2. What is meant by the term biodiversity? List some arguments that people use in favor
of preserving species biodiversity. What is extinction? What are the major threats to the
earths biodiversity today?
Biodiversity refers to the variety of life in a particular habitat or ecosystem. More
largely, biodiversity is the variety of life on the entire Earth. Biodiviersity is important to
humans because it helps to create sustainability in ecosystems, which we need to
survive. Additionally, biodiversity ensures that we have ample variety of food choices.
Medically, more biodiversity allows for more potential drugs to be discovered. Extinction
is when a species or family of organisms die out and seize to exist. Several recent events
threaten the life of many organisms and cause concern for their extinction. Perhaps the
most concerning is the rise of global warming. Global warming threatens the environment
of many plants and animals, such as the polar bears and their icy homes. Scientists fear
that the earths temperature will increase to such a level that many animals will no longer
be able to thrive on earth.
3. All organisms on earth have some chemistry in common - all use ATP as an energy
currency molecule; all use DNA as an information storage molecule; all use enzymes and
other proteins to control rates of specific cell processes. Be familiar with these systems, and
tell why this adds to the evidence suggesting that all life on earth evolved from a common
origin.

Energy-storing Molecules

Electrons Carriers
Oxidized
Form
NAD+
FAD
NADP+

Generated In
Electron Transport Chain,
Fermentation
Electron Transport Chain
Calvin Cycle

Reduced
Form
NADH
FADH2
NADPH

Generated in
Glycolysis, Preparing Pyruvate, Krebs
Cycle
Krebs Cycle
Light-dependent Reactions

Adenosine Triphosphate (ATP)

Process that Generates ATP
Substrate-level phosphorylation
Chemiosmosis (using ATP synthase)

Utilized During
Glycolysis, Krebs Cycle
Oxidative Phosphorylation, Light-
dependent Reactions

Other Key Molecules to Know

Molecule
Glucose
Phosphofructokinase
Glyceraldehyde-3-Phosphate
Pyruvate

Why You Should Know It

Substrate for cellular respiration
Enzyme that is key to regulation of glycolysis (and cellular
respiration); phosphorylates fructose-6-P
Intermediate in glycolysis, product of Calvin cycle
Product of glycolysis and substrate that is converted to acetylCoA
for the Krebs cycle

Acetyl CoA
Oxaloacetate

Starting material for Krebs cycle

Accepts the two carbons from acetyl CoA in the first step of the
Krebs cycle

Citrate
ATP Synthase

Product of the first step of the Krebs cycle

An integral membrane protein that generates ATP using the flow of
protons down their gradient
Substrate for first step of Calvin cycle
Enzyme that catalyzes the first step of Calvin cycle
Product of the first step of Calvin cycle

Ribulose bisphosphate (RuBP)

Rubisco
3-phosphoglycerate

4. Through what processes could living cells have originated in the abiotic earth? Summarize the
concepts of chemical evolution (before the origin of the first cells) and the endosymbiosis
hypothesis for the origin of eukaryotic cells. How can scientists study how these processes
happened?
The chemical evolution refers to the chemical changes on the primitive Earth that gave
rise ot the first forms of life. The first living things on Earth were prokaryotes with a type of cell
similar to present day bacteria. The chemical and physical conditions of the primitive Earth are
invoked to explain the origin of life, which was preceded by chemical evolution of organic
chemicals. The hypothesis is that life developed from non-living materials eventually, by the
process of natural selection, over hundreds of millions of years, became able to self-replicate and
metabolize. Scientists usually propose a four-stage process of formation for the first life: 1.
formation of small organic molecules (amino acids, nucleic acid bases,) 2. and these combine to
make larger biomolecules (proteins, RNA, lipids,), 3. which self-organized, by a variety of
interactions, into a semi-alive system , 4. that gradually transformed into a more sophisticated
form, a living organism.
The endosymbiosis hypothesis is the theory that explains the origin of eukaryotic cells
from prokaryotes. Both mitochondria and chloroplasts have their own genome, which consists of a
single circular molecule of DNA and resembles that of bacteria. The DNA in neither the
mitochondria nor chloroplasts has histones associated with it. Both the mitochondria and
chloroplast use the DNA to produce many proteins and enzymes required specifically for their own
function. The mitochondria and chloroplasts cannot be formed in a cell that lacks them because
they can only be formed from preexisting mitochondria and chloroplasts. Similar to bacteria, they
replicate their own DNA and direct their own division. A double membrane surrounds both of the
organelles, which, once again, suggests that they were ingested by a primitive host

(learn.genetics.utah.edu). The larger prokaryote did not destroy the smaller, engulfed prokaryote,
indicating that there must have been some advantage to keeping the engulfed prokaryote as an
endosymbiont greater than the advantage brought about by breaking it down. Likewise, the
engulfed prokaryote did not destroy its host, again indicating that there must be some benefit to
being an endosymbiont. One advantage to the two prokaryotes is the ability to generate more
energy. It is possible that the smaller prokaryote is able to provide the larger prokaryote with sugar
in return for energy, or vice versa.
5. What is the overall reaction for aerobic cellular respiration of glucose? What is the overall
reaction of photosynthesis? Be able to relate the cellular processes of cellular respiration overall
and photosynthesis overall to global cycles of nutrients (when we discuss ecosystems).

Cellular Respiration (C6H12O6 + 6O2 6CO2 + 6 H2O + Energy)

Glycolysis (C6H12O6 2C3H3O3 + Energy; occurs in
the cytoplasm)
Input
Glucose
2 NAD+

Krebs Cycle (AKA Citric Acid Cycle,

Tricarboxylic Acid Cycle; Acetyl CoA
2 CO2 + Energy; occurs in mitochondrial
matrix)

Output
2 Pyruvate
2 NADH
4 ATP (gross); 2 ATP
(net)

ADP + Pi

Input
Acetyl CoA
3 NAD+
FAD

ADP + Pi

Output
2 CO2
3 NADH
FADH2
ATP

Electron Transport Chain (Part of

Oxidative Phosphorylation; generates
proton gradient; occurs across the inner
mitochondrial matrix)

Preparing Pyruvate (C3H3O3 CO2 + Acetyl CoA +

Energy; occurs in mitochondrial matrix)
Input
Pyruvate
NAD+

Output
Acetyl CoA + CO2
NADH

Input
NADH

FADH2
O2

Output
NAD+
FAD
2 H2O

Photosynthesis (6CO2 + 6 H2O + Energy C6H12O6 + 6O2)

Light Dependent Reactions (Light Energy
Chemical Energy; occurs across the thylakoid
membrane)
Input
NADP+
ADP + Pi
2 H2O

Output
NADPH
ATP
O2

Calvin Cycle (3CO2 + Energy Glyceraldehyde-3Phosphate; occurs in stroma)

Input
3 CO2
6 NADPH
9 ATP

Output
Glyceraldehyde-3-P
6 NADP+
9 ADP + Pi

6. Name the three domains of life and give an example type of organism in each. Distinguish

prokaryotic cells from eukaryotic cells, and relate those terms to the three domains of life.
Describe energy acquisition and cell specialization seen in three major kingdoms of multicellular
organisms.
The three domains of life include eukarya, bacteria, and archaea. Eukarya includes
eukaryotic organisms, such as humans, horses, and dogs. These are organisms with cells that
contain a nucleus as well as membrane-bound organelles. The kingdoms most associated with
Eukarya are the Plantae, Animalia, and Fungi kingdoms. Additionally, Kingdom Protista has had
some of its organisms, such as amoebas and some seaweeds, classified as Eukarya. Although
similar to each other, bacteria (ex. coccus, bacillus, spirrillum) and archae (ex. sulfobus) have a
couple major distinctions. Firstly, archae cell walls do not contain peptidoglycan, which is a
polymer consisting of polysaccharide and peptide chains that are found in bacterial cell walls.
While archae can have a variety of cell walls, some cell walls are made of pseudopeptidoglycan.
The cell membranes of archae have a very unique structure and do not contain lipids. The cell
membrane of archae usually contains linkages, where as bacteria cell membrane contains ester
bonds. Thirdly, archae have three RNA polymerases like eukaryotes, and bacteria have only one
RNA polymerase. Furthermore, archae and bacteria are usually found in very different types of
environments. Bacteria can be found in a variety of locations, but archae is usually found in harsh
environments.
There are several main distinctions between prokaryotic and eukaryotic cells (see
cod.edu for more information):
1. Eukaryotic cells have a true nucleus, bound by a double membrane. Prokaryotic cells have no
nucleus. The purpose of the nucleus is to sequester the DNA-related functions of the big
eukaryotic cell into a smaller chamber, for the purpose of increased efficiency. This function is
unnecessary for the prokaryotic cell, because its much smaller size means that all materials
within the cell are relatively close together. Of course, prokaryotic cells do have DNA and DNA
functions. Biologists describe the central region of the cell as its "nucleoid" (-oid=similar or
imitating), because it's pretty much where the DNA is located. But note that the nucleoid is
essentially an imaginary "structure." There is no physical boundary enclosing the nucleoid.
2. Eukaryotic DNA is linear; prokaryotic DNA is circular (it has no ends).
3. Eukaryotic DNA is complexed with proteins called "histones," and is organized into
chromosomes; prokaryotic DNA is "naked," meaning that it has no histones associated with it,
and it is not formed into chromosomes. Though many are sloppy about it, the term "chromosome"
does not technically apply to anything in a prokaryotic cell. A eukaryotic cell contains a number of
chromosomes; a prokaryotic cell contains only one circular DNA molecule and a varied
assortment of much smaller circlets of DNA called "plasmids." The smaller, simpler prokaryotic
cell requires far fewer genes to operate than the eukaryotic cell.
4. Both cell types have many, many ribosomes, but the ribosomes of the eukaryotic cells are
larger and more complex than those of the prokaryotic cell. Ribosomes are made out of a special
class of RNA molecules (ribosomal RNA, or rRNA) and a specific collection of different proteins.
A eukaryotic ribosome is composed of five kinds of rRNA and about eighty kinds of proteins.
Prokaryotic ribosomes are composed of only three kinds of rRNA and about fifty kinds of protein.
5. The cytoplasm of eukaryotic cells is filled with a large, complex collection of organelles, many
of them enclosed in their own membranes; the prokaryotic cell contains no membrane-bound
organelles which are independent of the plasma membrane. This is a very significant difference,
and the source of the vast majority of the greater complexity of the eukaryotic cell. There is much
more space within a eukaryotic cell than within a prokaryotic cell, and many of these structures,
like the nucleus, increase the efficiency of functions by confining them within smaller spaces
within the huge cell, or with communication and movement within the cell.
7. Distinguish, and be able to apply, two ways by which biologists define species? How do new
species form? What are some reproductive isolating mechanisms keep two species from
interbreeding?
A species is a population or group of population whose members have the potential to

interbreed in nature and produce viable, fertile offspring, but are unable to produce viable, fertile
offspring with members of other populations. More concisely, species consists of all organisms
that are similar enough to interbreed, no matter where they are found (Audesirk 9). Evolution of
species occurs through changes in a gene pool (microevolution) and diversion and divergence of
a gene pool (macroevolution). Species evolve either through either two patterns of evolution,
anagenesis or cladogenesis. Anagenesis refers to a gradual change of one species into another,
where as cladogenesis means when one gene pool splits and two new species arise.
Reproductive isolation is when barriers exist that prevent the production of viable,
fertile offspring between species. There are two types of reproductive isolation: prezygotic and
postzygotic barriers. Prezygotic barriers (before the zygote) prevent mating or fertilization,
where as postzygotic barriers (after the zygote) prevent the development of zygote into a viable,
fertile adult. Examples of prezygotic barriers include habitat isolation, temporal isolation,
behaviorial isolation, gametic isolation, and mechanical isolation. Habitat isolation is when
species live in the same region but different habitats. Temporal isolation means that organisms
reproduce at different times of the year, which prevents them from being able to breed amongst
each other. Behavioral isolation refers to the different courtship rituals that are used to attract
mates. Gametic isolation means that the sperm cannot fertilize the egg. Lastly, mechanical
isolation indicates morphological differences, which inhibits an organism from being able to breed
with another. Postzygotic barriers include reduced hybrid viability, reduced hybrid fertility, and
hybrid breakdown. Reduced hybrid viability means hybrid offspring do not develop normally, and
repuced hybrid fertility means that hybrid offspring are fertile. Finally, hybrid breakdown indicates
that the offspring of the hybrids (F2 generation) are not viable and/or fertile.
There are two main modes of speciation: allopatric speciation and sympatric
speciation. Allopatric speciation is the geographic separation of a single population, and
sympatric speciation is when one population diverges into two species. Allopatric speciation
requires a geographical barrier, either when a new barrier arises (ex. as water level decreases,
one lake becomes two) or the colonization of a distant land (ex. Galapagos Islands). The
magnitude and type of a barrier in allopatric species depends on the mobility of species. In
sympatric speciation, one population can become two different species either through habitat
differentiation (ex. North American apple maggot fly), polypoloidy, or sexual selection.
Autopolyploiody, the process where an individual belonging to some species doubles its genome,
is common in plants and results in tetraploid species that cannot mate with original diploid
species due to reduced hybrid fertility. Sexual selection is an uncommon, yet important, type of
spympatric specition in which non-random rating results in disruptive selection (such as African
cichlids in Lake Victoria).
8. What is the binomial naming system of organisms devised by Linnaeus? Describe Linnaeus
hierarchical system of classifying organisms. How do classification systems relate to evolutionary
history as hypothesized in phylogenetic trees?

Linnaeus devised the Linnaean taxonomy, which classifies organisms into the three
different kingdoms, divided by classes, families, genera, and then species. Traditional, biological
classification schemes included the idea of ranks, such as species, genus, family, order, class,
etc. In this system (the Linnaean system), for example, there is a Class Reptilia and a Class
Aves. However, the bulk of evidence supports, and the majority of scientists now agree, that the
group Aves belongs within the larger group Reptilia (birds share a most recent common ancestor
with crocodiles, which are generally included in the Class Reptilia). Within a traditional, Linnean
system of classification this means that either the Class Aves is demoted to something below a
class, or that a class (Aves) exists within another class (Reptilia). Problems such as this have
prompted many scientists to propose that a system of naming and classification of biological
diversity be rank-free. Classification systems then only indicate the hierarchical structure of
groups according to the current understanding of their evolutionary history, leaving out rank
labels.