Welcome to General
Cell Biology
Biol&160 A & B
Today
 Introduction-
class roll
 Syllabus/Expectations
 Intro to science & scientific method
 Organization of life
 Cell chemistry and molecules
Syllabus
 Questions?
Study Habits
 Find
out what works best for YOU
 Try different methods
– Combine methods
 Use
shorthand
 Read the chapter BEFORE lecture
and be prepared with any questions
What is science?
To Know

Seeks natural causes to phenomenon
– Therefore limited to things that we can OBSERVE and MEASURE
 Ex: Rate of flow of water over a dam
 Ex: Deity





Explanatory –study of the world around us to explain our
observations
Testable – based on observations or measurements
Reproducible – others must be able to confirm and
duplicate scientific findings
Predictive – we use scientific knowledge to predict
answers to questions
Tentative – each new discovery can change the way we
look at other things we know
What is science
 Observational
science
– What is observed in nature
 Experimental
science
– Usually derived from observational
science
– Attempts to answer/understand specific
questions about what is observed
What is Biology
 Study
of life
– Encompasses
 Ethology
Evolutionary Biology
 Physiology
 Genetics
 Molecular Biology
 Morphology
 Systematics
 Ecology
 And more…..

Hypothesis based science
 Hypothesis-
a tentative statement
that proposes a possible explanation
to some phenomenon or event
 Testable
– may include a prediction
 Simple
and concise
 Falsifiable
– Accept or reject
Scientific Theory



Explanation of something that has been
substantiated by a large amount of data collected
over multiple experiments
Best possible explanation at the time based on
experiments and available data
Theories are altered, revised, adapted or simply
abandoned as new data becomes available
Scientific method
Observation
 Question

– This turns into a testable…
Hypothesis
 Prediction
 Experimentation

– Controlled
– Replication
Analysis of results
 Evaluate hypothesis against results
 Generate Scientific Theory

Reasoning
 Inductive-
Extrapolate general
principles from specific examples
 Deductive-
Extrapolate specific
examples from general principles
Humans are made of cells

Inductive
– Every biological sample for the past 200 years
has been made of cells (specific)
THEREFORE
– All organisms (including humans) are made of
cells (general)

Deductive
IF
– all organisms are made of cells & humans are
organisms (general)
THEN
– Humans are made of cells (specific)
Spontaneous Generation
 Living
things arrive from lifeless
matter
– Air had a “life force”
 Rotting
meat, when left, produced
flies
 Redi’s blowfly experiment
Spontaneous Generation





Observation- Flies spontaneously appear on
rotting meat
Question- Does rotting meat produce flies
Hypothesis- Rotting meat produces flies
Prediction- A flask of rotting meat will produce
flies in 21 days
Experimentation- 3 jars of meat were
subjected to being open, semi-sealed with
parchment paper or sealed while other variables
remained identical
– Control is flask of meat set out with no cover
– Experiment is 2 flasks semi-sealed and sealed
 Analysis
of results-
Presence/absence of
flies was recorded. No flies were present in closed
jars, semi-closed jars had fly eggs on the
parchment
 Evaluate
hypothesis against results-
Reject hypothesis as sealed jars did not produce
flies and semi-sealed jars had fly eggs on the
parchment paper
– Flies came from other flies not from the meat
©Barrons 2009
Experiments & Theories
 Experiments
& hypotheses only test
NEVER prove theories
– The very next experiment may falsify
theory
– Always falsify a hypothesis, not prove it
 Correct-
A sealed jar will not produce
flies
 Not- an unsealed jar will produce
flies
Data Interpretation
A
team of scientists
designed an investigation that
used artificial snakes to test
the following hypotheses.
–
–
–
–
H1: The coral snake’s
bright color pattern
serves to warn off
potential predators.
H2: The king snake
suffers less predation
because it mimics or
looks like the coral snake.
H3: The protection that
king snakes receive by
mimicking coral snake will
depend on the presence
of coral snakes.
Both 1 and 2
Data Interpretation
Biologists
placed artificial
snake mimics in two
different localities to test
the hypothesis that
looking like a poisonous
snake only works where
the poisonous snake is
found:
1. Outside of the coral
snake range—only king
snakes present.
2. Inside the coral snake
range—both coral and
king snakes are present.
Data Interpretation
The
graphed data
__________ the hypothesis
that the effectiveness of
mimic coloration depends
upon the presence of the
poisonous model is:
–
–
–
supports
does not support
is irrelevant to
Data Interpretation
Based
on this data which of
the following is a logical
hypothesis or prediction?
–
–
–
King snakes outside of the
range of coral snakes will
more closely resemble coral
snakes than populations of
king snake living within the
range of coral .
King snakes outside of the
range of coral snakes will
not resemble coral snakes
as closely as populations of
king snakes that live within
the range coral snakes.
Neither prediction is valid.
Why do I care about Hypothesis
testing and scientific method?
 Used
in every day life and decision
making
– Ex: Medical- use scientific method to
determine cause of patients ailment
Organization of Life
Life’s levels of
organization
define the
scope of
biology
Hierarchical organization
 Levels
organized according to
complexity
– “Higher” and “lower” order life forms do
not exist, simply a matter of complexity
 Emergent
properties
– Properties that were not present at the
previous lower level and result from the
specific arrangement and interactions
between components
 “The
whole is greater than the sum of its
parts”
Environmental interactions
Living organisms
and their
environments
form
interconnecting
webs
Environmental Interactions

Producers
– Organisms that produce organic compounds
from inorganic compounds
 These
organisms are autotrophs
 Photosynthesis, chemosynthesis, etc

Consumers
– Organisms that obtain nutrients from other
organisms
 Heterotrophs

Decomposers
– Decay organic matter, releasing energy back
into the ecosystem
 Saprobes
Common features of all living
forms
 Order/organization
 Regulation
 Growth
& Development
 Energy utilization/processing
 Response to the environment
 Reproduction
 Evolution
In-class Exercise
Get into groups
 Each group identify a scientific question,
hypothesis and experimental outcome for
each scenario

– Don’t worry about figuring out an experiment,
just make up the results of one

Decide if your outcome supports or refutes
your hypothesis
Example
While walking to class today, I notices a
fire hydrant in the middle of the pathway
 Question- Why was the hydrant placed in
the middle of the path
 Hypothesis- The middle of the path was
the most accessible location for the
hydrant
 Experimental outcome- The middle of the
path was not found to be the most
accessible location for a hydrant
 My findings do not support my hypothesis
and thus, my hypothesis is rejected.

Exercise
Scenario 1-While hiking in the forest one
day, you notice that while on the left side
of the trail, the frogs are bright green, but
on the right, they are a mottled greenbrown color.
 Scenario 2- As a nurse, one of your
patients presents with an unusually low
temperature, but no other symptoms
 Scenario 3-You are fishing out in Puget
Sound and find that all the other
fishermen are pulling up salmon, but you
are catching fish.

Cellular Chemistry
Ch 2
Life primarily
consists of
carbon,
hydrogen,
oxygen, and
nitrogen
Rest are
present in
trace amounts
Table 2.1
Trace elements



Are essential to life, but occur in
minute amounts
Trace elements are common
additives to food and water
Dietary deficiencies in trace
elements can cause various
physiological conditions
These
Interpreting Data
are the
results of a laboratory
experiment to test
the effect of trace
nutrients on the
productivity of Pacific
Ocean water. After 6
days which nutrient
had the greatest
effect on
productivity?
–
–
–
–
Iron
Manganese
Copper
Zinc
Adapted from Coale, Kenneth H. 1991. Effects of Iron,
Manganese, Copper and Zinc Enrichments on Productivity
and Biomass in the Subarctic Pacific. Limnology and
Oceanography. 36: 1851-1864
Subatomic Particles
Protons- positive
charge
Neutrons- neutral
charge
–
–
2e–
+
+
+
+
Protons and neutrons
occupy the nucleus
Electrons- negative
charge
Arranged in electron
shells around the
nucleus
Electron
cloud
Nucleus
2 +
Protons
2
Neutrons
2 –
Electrons
Mass
number = 4
Figure 2.4A
Differences in Elements
Atoms of each element
always have the same
number of protons
Atomic Number=#
protons
Mass Number (atomic
weight) = Protons +
neutrons
Electron
cloud
6e–
++
Nucleus
6
6
6
Atoms have no overall
charge, thus…
+
Protons
Neutrons
–
Electrons
Figure 2.4B
Mass #
= 12
Thus….
 Number
of protons (+ charge) must
be equal to the number of electrons
(-)
For any element:
Number of Protons = Atomic Number
Number of Electrons = Number of
Protons = Atomic Number
Number of Neutrons = Mass Number Atomic Number
Example
Kr
Krypton
Atomic # = 36
Atomic weight = 84
# Protons=?
# Neutrons=?
# Electrons=?
Compounds
Chemical elements combine in fixed ratios to form
compounds
Different combinations of atoms determine the
unique properties of each compound
Chlorine
Sodium
Figure 2.3
Sodium Chloride
Isotopes
The number of neutrons in an atom may vary
Table 2.4

Variant forms of an element are called isotopes

Some isotopes are radioactive
Isotopes
aX
z
A = mass number
(the total number of protons + neutrons)
Z = atomic number
(the total number of protons)
X = element symbol
Ex: Ordinary hydrogen is written 1H1,
deuterium is 2H1 (heavy water, label in chemistry
experiments)
tritium is 3H1 (radioactive)
Radioactive isotopes
 Particles
that are emitted from the
nuclei as a result of nuclear
instability
Usefulness of radioactive isotopes
 Irradiation
– Material is subjected to radiation for the
purposes of disinfestations,
pasteurization or sterilization
 Research
– Radioactive tracers enable researchers
to follow particular molecules as they
undergo change such as through
photosynthesis
Usefulness of isotopes
 Medical
Diagnosis
– Kidney disorders
– Medical Imaging
 PET
scans
PET scan image of
Parkinson's diseased brain
Brown.edu 2008
Electrons, Electrons, Electrons!
 The
active part of the atom
– They are the only part directly involved
in chemical activity
 Interactions
between electrons
form chemical bonds
 Electron
shells
– Arranged in shells, which may contain
different numbers of electrons
Electron Shells
Electron arrangement determines the chemical properties
of an atom
– Electrons in an atom are arranged in shells, which
may contain different numbers of electrons
Outermost electron shell (can hold 8 electrons)
First electron shell (can hold 2 electrons)
Electron
Hydrogen (H)
Atomic number = 1
Figure 2.6
Carbon (C)
Atomic number = 6
Nitrogen (N)
Atomic number = 7
Oxygen (O)
Atomic number = 8
Electron shells
 Valence
electron shell
– Outermost shell of electrons
– These electrons interact with other
atoms
Outermost electron shell (can hold 8 electrons)
First electron shell (can hold 2 electrons)
Electron
Hydrogen (H)
Atomic number = 1
Figure 2.6
Carbon (C)
Atomic number = 6
Nitrogen (N)
Atomic number = 7
Oxygen (O)
Atomic number = 8
Ions


Created when an atom gains or looses and
electron
Results in an net positive or negative charge
depending on if the atom gained or lost the e-
Ionic Bonds
•Attractions between ions of opposite charge
– An electrical attraction between ions with opposite
charges results in an ionic bond
–
–
+
Transfer of
electron
Na
Cl
Na
Sodium atom
Cl
Chlorine atom
–
Na
Cl
Na+
Sodium ion
Cl–
Chloride ion
Sodium chloride (NaCl)
Figure 2.7A
NaCl
 Na
has 1 e- in the outer shell
 Cl has 7 e- in the outer shell
 Na “donates” its e- to Cl, leaving Na
with only 2 shells and Cl with a full
outer shell
– This moves 1 “unit” of negative charge
from Na to Cl, resulting in a net
electrical charge of +1 for Na and -1 for
Cl
NaCl
 The
atom is now an ion
– Recall that an ion is an atom or
molecule with an electrical charge form
either gaining or loosing electrons
Covalent Bonds
Two
atoms share
one or more pair of
outer e–# of bonds is equal
to additional enecessary to fill the
outer shell
–Valence or bonding
capacity of the atom
Join
atoms into
molecules through
the electron sharing
Covalent bond Diamond with 4
covalent bonds
info.lu.farmingdale.edu/.../atomicbonds.html
Polar molecules
Unequal e- sharing
produces polar
bonds
 Electronegativity

– Atom’s attraction
for shared electrons
– Greater the
electronegativity,
stronger the pull on (+)
e-
(–)
(–)
O
H
H
(+)
Figure 2.9
Water Molecule
Polar molecules
 If
the atoms exert a equal pull on the
e-, bond is non-polar covalent
– Overall charge of 0
 If
the atoms exert an unequal pull on
the e-, bond is polar covalent
– Overall charge on the more
electronegative atom is partially
negative and the less electronegative
atom is partially positive
Polar molecules
(–)
(–)
 Polar
molecules
have an
unequal
distribution of
charges
O
H
H
(+)
(+)
Figure 2.9
Water Molecule
Visual representation of a molecule
– Molecules can be
represented in
many ways
Table 2.8
Hydrogen Bonds
 Partial
+ charge
allows shared
attractions with
– charged
molecules
 + charged
region always H
(–)
Hydrogen bond
(+)
H
(+)
O
(–)
H
(–)
(+)
(–)
(+)
Figure 2.10
The importance of hydrogen bonding

Cohesion between H20 molecules
– Droplet formation
– Transportation
Adhesion to substrate
 Surface tension
 Temperature moderation (body and climatic)

– H bonds absorb a great deal of energy before
breaking, thus, a lot of energy is required before an
increase in temp occurs

Density
– Ice vs. liquid water
Solvent
Water is the solvent of life dissolving any
charged or polar substances
 Solution
 Aqueous solution
 Solvent

– Dissolving agent

Solute
– Dissolved substance

EX: Salt water
– Water is the solvent and salt the solute
Ph Scale
 Some
H20 molecules disassociate
into H+ and OH A compound that releases (donates)
H+ ions in solution is an acid
– Increases the net H+ ions in solution
A
compound that accepts (removes)
H+ ions in solution is a base
– Increases the net OH- ions in solution
Ph Scale
H+
H+ OH– H+
OH– H+ H+
H+ H+
Acidic solution
OH–
OH–
OH–
H+ H+
–
OH– OH
H+ H+ H+
Neutral solution
OH–
OH–
OH– H+ OH–
OH– OH– –
OH
H+
NEUTRAL
[H+]=[OH–]
1
2
Lemon juice, gastric juice
3
Grapefruit juice, soft drink
4
Tomato juice
5
6
Human urine
7
Pure water
Human blood
8
Increasingly BASIC
(Lower concentration of H+)
H+
Increasingly ACIDIC
(Higher concentration of H+)
0 pH scale
Seawater
9
10
Milk of magnesia
11
Household ammonia
12
Household bleach
13
Oven cleaner
Basic solution
14
0-14
 7 is neutral
 0-6.9 acidic
 7.1-14
basic/alkaline

Each unit is 10 fold
change in
concentration of H+
ions
 Buffers act to
minimize Ph
changes

CHEMICAL REACTIONS
Chemical reactions change the composition
of matter
reactants
Figure 2.17A
2 H2
O2
products
2 H2O
Interpreting Data
This
is the general equation for photosynthesis—the
process of capturing sunlight energy and converting
it to chemical energy. Which of the following are the
reactants of this reaction?
– C6H12O6 and O2.
– CO2 and H2O.
Interpreting Data
Earth’s
oceans are immense. Small floating
plants called phytoplankton contribute to ocean
productivity. As ocean productivity (the rate of
photosynthesis) goes up what would you predict
would happen to global carbon dioxide levels?
– CO2 levels should also go up.
–
CO2 levels should go down
–
CO2 levels should remain constant.