Welcome to General
Cell Biology
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
• Study EVERY day
What is science?
To Know
• Seeks natural causes to phenomenon
– Therefore limited to things that we can OBSERVE
and MEASURE
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Explanatory
Testable
Reproducible
Predictive
Tentative
What is Biology
• Study of life
– Encompasses
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Ethology
Evolutionary Biology
Physiology
Genetics
Molecular Biology
Morphology
Systematics
Ecology
And more…..
Approaches
• Discovery- observational
– Uses inductive reasoning
• Hypothesis-based- experimental
– Uses deductive reasoning
Hypothesis based science
Hypothesis- a tentative statement that
proposes a possible explanation to some
phenomenon or event
– Testable
– Tentative relationship is stated
– Simple and concise
– Falsifiable
• Accept or reject
Prediction vs Hypothesis
• Predictions “guess” what will happen
• Hypothesis presents a relationship, which
explains what will happen
– Specific, testable prediction about what will
happen
Language of a hypothesis
• Contain the dependent and independent
variables
– If leaf color change is affected by (related to)
temperature , then exposing plants to low
temperatures will result in changes in leaf
color.
***If the reader cannot figure out what you
are testing, it is not a hypothesis
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

Can be altered, revised, adapted or
simply abandoned as new data
becomes available
Scientific method
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Observation
Question
Hypothesis
Prediction
Experimentation
– Controlled
– Replication
• Analysis of results
• Evaluate hypothesis
• Generate Scientific Theory
Reasoning
• Inductive- Extrapolate general principles
from specific examples
– A conclusion is arrived at based on a set of
observations
• Deductive- Extrapolate specific
conclusions from general principles
– If A then B
Reasoning
Inductive
All observed crows are black.
Therefore:
All crows are black.
Deductive
All men are mortal
Socrates is a man
Therefore, Socrates is mortal
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- If rotting meat produces flies then any
flask with rotten meat will produce 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
• Analysis of results- 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 semisealed jars had fly eggs on the parchment paper
©Barrons 2009
• What would happen if no control group
was included?
Experiments & Theories
• Experiments & hypotheses only test
NEVER prove theories
– The very next experiment may falsify theory
– Always falsify a hypothesis, not prove it
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
• Understand the world around us
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
• 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
green-brown 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 flounder.
Organization of Life
Life’s levels of
organization
define the
scope of
biology
Hierarchical organization
• Organized according to 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
• Autotrophs
– Organisms that produce organic compounds from
inorganic compounds
• “Producers”
• Photosynthesis, chemosynthesis, etc
• Heterotrophs
– Organisms that obtain nutrients from other organisms
• “Consumers”
• Decomposers
– Decay organic matter, releasing energy back into the
ecosystem
• Saprobes
Common features of all living
forms
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Order/organization
Regulation
Growth & Development
Energy utilization/processing
Response to the environment
Reproduction
Evolution
Cellular Chemistry
Ch 2
Elements of life
– Life primarily
consists of C, H,
O, N
– Rest are present
in small amounts
called trace
elements
Table 2.1
Trace Elements
• Essential to life
• Occur in minute amounts
• common additives to food and
water
• Deficiencies can cause various
physiological conditions
Subatomic Particles
Protons- positive
charge
–
2e–
Found in the nucleus
Electrons- negative
charge
+
+
+
+
Neutrons- neutral
charge
Protons and neutrons
occupy the nucleus
Electron
cloud
–
Nucleus
2 +
Protons
2
Neutrons
2 –
Electrons
Mass
number = 4
Arranged in electron
shells around the
nucleus
Figure 2.4A
Differences in Elements
Atoms of each element
always have the same
number of protons
Electron
cloud
6e–
++
Atomic Number=# protons
Mass Number (atomic
weight) = Protons +
neutrons
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
• Irradiation
– 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
– 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
– Shells are “Full” with either 2 or 8 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
Electronegativity
• Atom’s attraction for shared electrons
– Greater the electronegativity, stronger the pull
on e-
Covalent Bonds
•Pairs of e- shared
between pairs of
atoms
–# of bonds is equal
to additional enecessary to fill the
outer shell
•Polar and Non-polar
Covalent bond Diamond with 4
covalent bonds
info.lu.farmingdale.edu/.../atomicbonds.html
Polarity
• Non-polar covalent- When the atoms exert
a equal pull on the e– Overall charge of 0
• Polar covalent- when the atoms exert an
unequal pull on the e-, bond is
– Overall charge on the more electronegative
atom is partially negative and the less
electronegative atom is partially positive
Polar molecules
• Unequal e- sharing
produces polar bonds
(–)
(–)
O
H
H
(+)
(+)
Figure 2.9
Water Molecule
Non-covalent bonds
• Depend on attractive forces between e- of
opposite charge
– Weak bonds, easily broken and reformed
• Ionic
• Hydrogen
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•
•
Anion has neg chrge
Cation has positive charge
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
Figure 2.7A
Na
Cl
Na+
Sodium ion
Cl–
Chloride ion
Sodium chloride (NaCl)
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
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
Hydrogen Bonds
• Partial + charge
allows shared
attractions with –
charged molecules
• + charged region
always H
(–)
Hydrogen bond
(+)
H
(+)
O
(–)
H
(–)
(+)
(–)
(+)
Figure 2.10
Water and H bonding
1. H2O is asymmetric
2. Each of the two covalent bonds are
highly polarized
3. All three atoms are adept at forming H
bonds
The importance of hydrogen bonding
• Cohesion between H20 molecules
– Droplet formation
– Transportation
• Adhesion to substrate
• Surface tension
• Temperature moderation (body and climatic)
– When heated, most thermal E is consumed in disrupting
the bonds rather than contributing to molecular motion
• Density
– Ice vs. liquid water
Visual representation of a molecule
Molecules can be
represented in
many ways
Table 2.8
Solvent
• Water is the solvent of life dissolving any
charged or polar substances
• Solution
• Aqueous solution
• Solvent
– Dissolving agent
• Solute
– Dissolved substance
Ph Scale
• Some molecules disassociate and release
H+ or 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–
H+ H+
–
OH– OH
+
+
H
H+ H
Neutral solution
OH–
1
2
Lemon juice, gastric juice
3
Grapefruit juice, soft drink
4
Tomato juice
OH–
OH– H+ OH–
OH– OH– –
OH
H+
NEUTRAL
[H+]=[OH–]
6
Human urine
7
Pure water
Human blood
8
Seawater
9
10
Milk of magnesia
11
Household ammonia
12
Household bleach
13
Oven cleaner
Basic solution
•
•
•
•
0-14
7 is neutral
0-6.9 acidic
7.1-14 basic/alkaline
5
OH–
Increasingly BASIC
(Lower concentration of H+)
H+
Increasingly ACIDIC
(Higher concentration of H+)
0 pH scale
14
• Each unit is 10 fold
change in
concentration of H+
ions
• Buffers act to minimize
Ph changes
– React with free H+ of
OH ions
CHEMICAL REACTIONS
Chemical reactions change the composition of
matter
reactants
Figure 2.17A
2 H2
products
O2
2 H2O