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Asking About
Life
Chapter 1 & 2
The Scientific Method
and
The Chemical
Foundations of Life
Scientists use the scientific
method. The first 2 steps are
observation and asking a
question. Scientists make a
hypothesis that you can devise an
experiment to prove or disprove.
A good experiment tests a
hypothesis under controlled
conditions . A control is a
duplicate experiment in which
everything is the same except
the experimental variable.
Collect data- It must be
quantitative, measure
something (weight) to draw a
conclusion.
Draw conclusion – Accept or
reject a hypothesis according to
a statistical standard you set
before the experiment.
A theory is a group of
statements that explain facts
that hold up to repeated
testing.
All organisms are alike in 8ways:
a) Consist of parts
b) Made of cells
c) Perform chemical reactions
d) Obtain energy from surroundings
e) Respond to environment
f) Mature (grow)
g) Reproduce
h) Share common evolution.
Organisms self-regulate by:
1.Barrier to the outside world.
2.Homeostasis
Cells can be:
1.Eukaryotes- contain a nucleus and
have many organelles.
2.Prokaryotes – no nucleus or
organelles.
Eukaryotes evolved from
prokaryotes.
Evolution occurred in the last 4.5
billion years. Biologists now divide
organisms into 3 domains:
1.Archea – bacteria.(ancient to present)
2.Eubacteria – bacteria.(more recent to
present)
3.Eukarya- 4 kingdoms , Plantae,
Animalia, Fungi, and Protista.
1.4 million kinds of organisms
are identified. Biologists believe
that most species have yet to
be discovered. More species
have become extinct than live
now.
Photo taken at
S.Dakota Museum of
Natural History
Members of species are similar because
they have inherited similar genes made
of DNA . Human DNA contains about
42,000 genes, a set of genes is a
genome.
Species differ in adaptations to
distinct environments which are
inherited, they increase the chance
an individual will live and reproduce
Adaptations are size, form, color,
internal structure, and chemical
properties.
Life is diverse because
diversity of habitats favors
organisms with different adaptations.
Structure is related to function.
Diversity of life resulted from
evolution.
Charles Darwin published “On
the Origin of Species” in 1859.
He proposed a way in which
evolution could work. He
modeled his idea of how
evolution worked on “selective
breeding” of farmers.
EX. Seeds from strong wheat
plants were used to produce the
next years crop.
Darwin saw a similar kind of
selection operate in nature and
called it “natural selection”.
Natural selection depends on the
organisms environment. Darwin
thought this was how organisms
gradually evolved.
Geyser – yellow color due to
archebacteria that live there.
Experimental Design- Biologists use a
lot of individuals. How many should
be used? Using only 10 individuals is
not conclusive because 10 can vary a
lot. The greater the variation the more
individuals are needed. By using
statistics variation can be estimated by
small experimental groups.
Statistics is the mathematics of
collecting and analyzing numerical
data. It has 2 uses:
1.Estimate the actual (true)
probability of something.
2.Help test a hypothesis.
Statistics can measure the probability
that what we measure is real, not a
random effect.
Data in tables, graphs, and other
pictures can suggest new
hypotheses.
Statistics states an assumption
clearly.
EX. In a study of heart attack
rates in men, although the
study refers to all men, only a
sample of men are studied.
The best way to do the study is by
a random sample. Choose the
sample irregardless of race, diet,
and other variables. Of a population
of 100 men choose a sample of 25
randomly. If 33 of the population
eventually have a heart attack how
many of the sample population had
heart attacks?(8)
Flipping a coin 100x gets an
average of 50H : 50T. In 10
flips it is unlikely to get 5H :5T.
Random effects are big in small
samples and small in big
samples.
How do scientists estimate a
value? The mean is the
average. A second measure is
standard deviation, an estimate
of variation in the total
population (not just the
sample).
How can biologists tell if 2
groups differ?
If a sample size is too small,
the sample mean differs from
the population mean.
You can estimate variation in data.
How much individual variation
exists is shown by how far is each
data point from the mean. The
average of these distances is the
standard deviation.
Ex. Average length of worms. a = 3 cm.,
b = 5cm., c = 7cm.
Mean = 5 cm.
To calculate Standard Deviation:
Measure the variation, square the
variation, sum the squares, divide by the
total number of data points minus 1
(degrees of freedom) and take the
square root.
Example Calculation of Standard
Deviation
3 – 5 = (-2) squared = 4, 5 – 5 = 0
squared = 0, 7 – 5 = 2 squared = 4.
The square root of 8/2 = 2.
If the sample size is larger the true
standard deviation is smaller.
If the 3 worms were 5.1 cm, 5.0
cm., and 4.9 cm. the standard
deviation would be the square
root of [(0.1) squared + (0.0)
squared + (-0.1) squared
divided by 2] = the square root
of 0.2.
This standard deviation shows less
variation and is more confident that
5 is the true mean. If variation is
large your sample size is too small,
Knowing standard deviation is
important but only accurate if
numbers are distributed normally
around the mean (bell curve) with
an equal number of data points to
each side of the mean.
When data have a normal
distribution, 68% of data points fall
within 1 S.D., 95% will fall within 2
S.D. (P.16). In a normal distribution
if you know the mean and S.D. of 2
samples you can calculate the
probability that the mean of the
experimental group is different from
the controls.
The Chemical Foundations
(Chapter 2)
Matter occupies space and has mass.
There are 92 naturally occurring
elements made of atoms composed
of neutrons, protons, and electrons.
A molecule is a stable combination
of 2 or more atoms. EX: O2. Most
molecules are compounds, pure
substances formed from 2 or more
different elements. EX: H2O.
Properties of compounds differ from
those of atoms that make them up.
Compounds are described by
formulas, CH4 is methane. Most
matter is a mixture of compounds.
Components of mixtures can be
present in any ratio.
Until the 16th C. chemistry’s
beginnings were alchemists trying to
turn lead to gold.
In the 19th C. chemistry began to
develop. Biologists use chemistry to
learn biology on a molecular level,
Ex: effect of NO, or Ca ++ in muscle
contraction. Matter of non-living
things is unlike matter of living
things.
2 traits of living matter distinguish it:
1. Organization of the nucleus.
2. Limited number of kinds of
molecules that make it up. (contain
carbon).
By the 19th C. chemists could
distinguish elements from
compounds by their properties. The
way a substance breaks down is due
to its structure. John Dalton said
elements were made of atoms.
Each element has a characteristic
mass. C weighs 12x an atom of H.
Weight is the effect of gravity on
mass. The mass of every kind of
atom is nearly a multiple of the
mass of the H atom.
This suggests an atom of C is
composed of 12 particles, each
about the size of one H atom or 1
“dalton”. O is 16 daltons. H2O is 18
daltons.
The internal structure of an atom is
mostly space. In 1910 Ernest
Rutherford bombarded gold foil with
positively charged alpha particles
produced by decay of radium. He
determined most of the mass of the
atom was the nucleus.
The nucleus is about 1/10,000 of
the mass of the entire atom, and is
made up of neutrons and protons.
Electrons revolve around the
nucleus on random paths called
energy shells.
The mass of the atom is determined
by the protons and neutrons. If an
atom has a different number of
neutrons than the most stable form it
is an isotope. Carbon -12 is stable.
Carbon-14 is radioactive. Its
nucleus has 6 protons, and 8
neutrons.
Every 4 seconds, 4 C-14 atoms in
a trillion turn into Nitrogen because
one of the neutrons decomposes
into a proton and an electron (beta
particle) which leaves the nucleus
and begins to orbit. Isotopes that
release beta or other particles are
radioisotopes.
The time required for half of the
atoms of a radioisotope to decay is
its half-life. For Carbon-14 it is
5,710 years. For Uranium – 235 it
is 704 million years.
An atom is most stable when it
contains 8 electrons in its outer
energy orbital. Inert gases already
have this and are chemically inert.
Most atoms have a different number
so they share electrons by covalent
bonds.
Covalent bonds have fixed lengths
and directions. Bond lengths and
angles are constant so every
molecule has a definite size and
shape. A water molecule always has
a angled shape.
Ionic bonds are formed when atoms
gain or lose electrons. Atoms take
on + or – charges depending if they
gain (-) or lose (+) electrons. The +
and - charged atoms are held
together by their opposite attraction.
Na (1 e- in the outer shell) reacts
easily with Cl (7 e- in the outer
shell). The atoms become Na+Cl-.
This type of reaction is called
electrostatic (like your hair in the
winter).
Atoms of each element have a
characteristic electronegativity
(tendency to attract electrons). O
and Cl strongly attract electrons ,
Na, K, and Li are least
electronegative and tend to lose
electrons. C has no tendency to
gain or lose.
The larger the difference in
electronegativity of 2 atoms the more
likely to form an ionic, not covalent
bond. C and N form covalent bonds.
In covalent bonds atoms may not
share electrons equally. The cloud
of shared electrons will be closer to
one atom than the other.
In water the shared electrons are more
toward the O than the H’s. This
causes an uneven distribution of
electrical charges and water is said to
be polar. When polar molecules are
close to other polar molecules the –
side of one is attracted to the + side of
the other.
Covalent and ionic bonds are strong
and take a lot of energy to break.
Most chemical reactions in living
organisms take place in water,
different weak interactions bind
molecules together. Alcohol is polar
and mixes easily with water. Oil is
non-polar and separates.
Water makes up 70% of organisms.
Cells are bathed in water and
contain water. Water molecules
form crystals as they freeze and
they take up more room than liquid
water. Ice is less dense so it floats.
Because ice floats ponds freeze
from the top down allowing fish to
survive the winter at the bottom.
Given additional heat water
temperature raises more slowly than
other chemicals which is referred to
as high heat capacity.
Water helps keep our body
temperature within a narrow range
that biochemical reactions need.
Attraction between molecules of
water is called cohesion. Cohesion
produces a high surface tension that
you feel with a “belly flop”.
Water is cohesive because of weak
hydrogen bonds formed between two
polar molecules. When an H atom
attaches to an electronegative atom
like O the bond is polar covalent.
The H end is sort of +, the O end is
sort of -. Hydrogen bonds play an
important role in holding together
DNA strands and bonds in proteins.
Clinging of water molecules to other
material is called adhesion . Water’s
adhesion results from its tendency to
form H bonds with other polar
molecules. Paper is made of the
polar molecule cellulose which
absorbs water well. Oil (nonpolar) is
absorbed poorly by paper.
Because of water’s cohesive and
adhesive properties it moves up
a tube easily by capillary action.
This is important to get water
from roots to leaves in the small
tubes inside of plants.
Water dissolves ionic salt and polar
sugar easily. These substances do
not dissolve easily in non-polar oil.
Some substances have hydrophobic
and hydrophilic ends and are
referred to as amphipathic. The
hydrophobic end repels water and
hydrophilic end attracts water.
Dish soaps do this as well as the
phospholipid cell membranes. The
hydrophilic ends point outward and
hydrophobic tails point inward. In a
water solution electrons stay closer
to the O than to the H. An H atom
may have no electron at all and
become a naked nucleus (H+).
Then the naked H+ can jump to
another water molecule producing
H3O+ (hydronium ion) and leaving
behind an OH- (hydroxide ion).
These charged ions recombine
readily to re-form regular water. A
molecule that gives up and H+ is a
base. One that accepts an H+ is an
acid.
Vinegar has more H+ ions than OHions so it’s an acid. Stomach acid
contains a trillion x more H+ ions
than OH- ions. pH is based on the
logarithm of the concentration of H
ions. Stomach acid has a pH = 1.
Saliva has a pH = 7 (neutral).
Blood pH = 7.4 (slightly basic). If
blood pH decreases to 6.95
(diabetes) the nervous system fails.
Coma and death can result. If pH
increases to 7.7 the nerves
overreact causing muscle spasms
and convulsions. Diseases, injury,
and drugs (diuretics) can cause this
Small changes in pH are normal.
In sea urchins sperm is immobile in
testes at 7.2 but sea water has a
pH of 8.0 which activates them to
swim to an egg.