Download Life - Ellis Benjamin

The Scientific
Study of Life
A. What is life?
•
•
•
Biology is the scientific study of life
How do you decide what is living?
5 qualities of life:
1.
2.
3.
4.
5.
Organization
Energy use
Maintenance of internal constancy
Reproduction, growth, development
Evolution
1. Life is organized
• Hierarchical
pattern
– Structures within
structures
– Making up an
organism
– Making up the
entire biosphere
• Ex: Google Earth
• With organization come emergent
properties
– Interacting components create new,
complex functions
– Not evident in individual parts
– Explains structure/function relationship
Levels of Organization In Biology
You can start
from the
smallest or the
largest!
•
Atom
•
•
Molecule
Organelle
•
Cell
•
Tissue
•
Organ
•
Organ System
•
Organism
Size & Complexity
• Population
• Community
• Ecosystem
• Biome
• Biosphere
2. Life requires energy
• Constant stream of energy is required to
maintain organized life
• Energy from the environment used to
– Build new structures
– Repair old ones
– Reproduce
• Broad categories of Energy Sources
– Producer/autotroph
• Extract energy and nutrients from nonliving
environment
• Plants and some microbes
– Consumer/heterotrophs
• Eat other organisms for nutrients
• Humans and other animals
– Decomposer
• Obtain energy from wastes or dead organisms
• Fungi and many bacteria
3. Life maintains internal constancy
• Homeostasis – state of internal constancy
or equilibrium
• Your body must maintain an internal
temperature of 37°C (98.6°F)
– Go outside when it’s cold and your body
shivers to keep warm
– On a cold day, your lips and fingertips may
turn blue as blood is diverted from the body
surface
4. Life reproduces itself, grows and
develops
• 2 basic ways
– Asexual – organism produces offspring
virtually identical to itself
• Bacteria, some plants, fungi and animals
– Sexual – genetic material from 2 individuals
unites to form new third individual
• Benefit of tremendous variation
• Widespread among plants, fungi, and animals
– Some organisms can reproduce either way
depending on the conditions
5. Life evolves
• Some organisms seem “perfectly”
suited to their environments—how did
they get that way?
• Adder snake, deep-sea hydrothermal
microorganisms, hummingbirds
Rocks alive!
•
•
Adaptation – inherited characteristic or
behavior that enables an organism to
survive and reproduce successfully in a
given environment
2 important facts
1. Populations produce more offspring than
can survive
2. Sexual reproduction results in genetic
variability
•
Mutations (changes in DNA) occur
• Natural selection – enhanced reproductive
success of certain individuals from a
population based on inherited
characteristics
– Individuals with the better combinations of
genes survive and reproduce
– These individuals make up more of the
population over time
– When the environment changes, different
combinations of traits may be better
• Evolution – change in genetic makeup of
a population
– Natural selection is one mechanism of
evolution
B. Taxonomic hierarchy
describes life’s diversity
• Taxonomy is the classification of life
• Hierarchical
• 2 parts to species name called (binomial
nomenclature)
– Homo sapiens (Genus species)
• The more features 2 organisms share, the
more taxonomic levels they share
The Chemistry of Life
A. Atoms are the “stuff” of life
• EVERYTHING is made of matter and energy!
• Matter – any material that has mass and
takes up space
– Organisms, rocks, oceans, gasses, etc.
• Energy – ability to do work (move matter)
– Moving matter
– Heat, light, and chemical bonds
• Element – pure substance that cannot be
broken down by chemical means into
other smaller substances
– Ex: Pure oxygen (O), carbon (C), sodium (Na)
– 92 natural elements; ~25 synthetic elements
– Periodic table – based on chemical behavior
– Essential Elements – needed for life (~25)
• Bulk elements – make up majority of living things
– CHNOPS (Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorous, Sulfur)
• Trace elements – required in smaller amounts
– Iodine (I), Iron (Fe), etc.
Dmitry Mendeleyev’s Periodic Table of Elements
(well, an abbreviated version)
B. Atoms are particles of elements
• Atom – smallest “piece” of an element that retains all
the characteristics of the element
• An Atom is made of a central core, called the
nucleus, with a less-dense area around it called the
“cloud” or orbit
• Each atom is composed of 3 subatomic particles:
– Proton – positive (+) charge, in nucleus
– Neutron – neutral (0) charge, in nucleus
– Electron – negative (-) charge, around nucleus in cloud
• Very small, (negligible) mass compared to proton or neutron
Using the periodic
table, what element
is this?
• Atomic number – number of protons in
the in the nucleus
– Arranged on periodic table rows sequentially
• Number of protons = number of electrons
– A “normal” atom is electrically neutral
• Ion – atom that has gained or lost
electrons
– Net negative (anion) or positive charge
(cation)
– Ex: Hydrogen (H+), sodium (Na+), chloride (Cl-)
C. Isotopes have different
numbers of neutrons
• Mass number – total number of protons
and neutrons in nucleus
– Mass of each proton or neutron is 1
– All atoms of an element have the same
atomic number but not necessarily the same
number of neutrons, so the atomic mass
number in the table is the most common or
average
• Isotope – different forms of a single
element with different numbers of neutrons
• (Atomic mass – average mass of all
isotopes is given in table)
• Some isotopes are radioactive and emit
subatomic particles and energy when they
break down into more stable forms
• Half-life – time it takes for half of the atoms
to decay
D. Atoms join together
through Chemical bonds
• Molecule – 2 or more chemically joined
(bonded) atoms
– Diatomic – molecule with 2 atoms of the same
element
• Ex: Oxygen (O2), Nitrogen (N2), Hydrogen (H2)
– Compound – molecule with 2 or more
different elements
• Nitric oxide (NO), water (H2O), methane (CH4)
– Molecular formula – the way we show the different types
of atoms and the number of each type in a molecule
• Ex: CH4 has 4 hydrogen atoms attached to 1
carbon atom
Back to the electrons around the
nucleus of an atom…
• Orbital – most likely location for an
electron relative to the nucleus
– Each holds up to 2 electrons
– Energy shell – group of orbitals that share the same
energy level
• Number of orbitals in a shell determines how
many total electrons the shell can hold
– First shell – one orbital – holds 2 total electrons
– Next 2 shells – 4 orbitals each – each holds 8
electrons total
• Valence shell – outermost occupied energy
shell
– Inert – valence shell full so element is very stable
– To fill partially empty valence shell, atoms will
share, steal, or donate electrons
1. Covalent bonds
• Form when 2 atoms share electrons
• Shared electrons travel around both nuclei
• Ex: Methane (CH4)
– Carbon – 6 electrons total, 4 in valence shell
– Hydrogen – 1 electron total
– 1 carbon shares an electron with each of 4
hydrogen atoms
1. Covalent bonds
1. Covalent bonds
• Single bond – 1 pair of electrons shared
• Double bond – 2 pairs
• Triple bond – 3 pairs
1. Covalent bonds
• Electronegativity – measure of an atom’s ability to
attract electrons
• Nonpolar covalent bond – equal sharing of
electrons
– CH4 example
• Polar covalent bond – unequal sharing of
electrons; has a + charge end and a – charge end
– H2O example
2. Ionic bonds
• Results from the electrical attraction
between 2 ions with opposite charges
• In general, forms between an atom with a
valence shell almost empty and an atom
with a valence shell almost full
• Ex: table salt: NaCl
3. Hydrogen bonds
(Different from covalent and ionic bonds because they form bonds between
atoms to make a molecule; hydrogen bonds weakly bond molecules together!)
• Opposite partial charges on
adjacent polar molecules or
within the same large
molecule attract each other
• Hydrogen is usually the
partially positive member
• Ex: Water molecules
– 2 polar covalent bonds in each
molecule
– Oxygen more electronegative and
pulls electrons away from hydrogens
– Partial positive charge on hydrogen
attracted to slight negative charge on
oxygen in another molecule
E. Water is essential to life:
1. Water is Cohesive & Adhesive
• Cohesion – tendency of water molecules
to stick together
– Based on hydrogen bonding
– Water has a high surface tension that forms a
“skin” strong enough to support small insects
• Adhesion – tendency of water to form
hydrogen bonds with other substances
• Cohesion and adhesion both at work in
capillary action
E. Water is essential to life:
2. Water is a “universal solvent” (at least for polar molecules)
• Water is a solvent – a chemical in which other
substances (called solutes) dissolve
• Solution – one or more solutes dissolved in a
liquid solvent
– Aqueous solution – solvent is water
• Some substances are Hydrophilic
– Substance readily dissolves in water
– Water-loving (salt, ions, etc.)
• Some substances are Hydrophobic
– Substance does not dissolve in water
– Non-Polar substances
– Water-fearing (lipids, etc.)
E. Water is essential to life:
3. Water regulates Temperature
• Water has the ability to resist temperature
changes
– More heat is needed to raise water’s
temperature than other liquids
– Bodies heat and cool more slowly
• Evaporation – conversion of a liquid into a
vapor
• Water expands
when frozen
– Ice floats
• Ice covering
insulates water
• Lakes do not freeze
from the bottom up
– Cells are prone to
rupture when
frozen
• Adaptations to
make “antifreeze”
or dehydrate
E. Water is essential to life:
4. Water is involved in the chemical reactions of life
CH4 + 2O2 → CO2 + 2H2O
methane + oxygen → carbon dioxide + water
• Chemical reactions – 2 or more
molecules “swap” atoms to yield different
molecules
– Chemical bonds break and new ones form
– Starting materials are reactants
– Products are the resulting material
– Atoms are neither created nor destroyed
F. Acids and bases
+)
• Water can break apart into
a
hydrogen
ion
(H
and a hydroxide ion (OH-)
H2O →H+ + OH-
• In a neutral pH solution, the number of H+ and OHare equal
• Acid – More H+ than OH– Adds H+ to the solution
– Ex: Hydrochloric acid (HCl), sulfuric acid (H2SO4)
• Base – More OH- than H+
– Can happen 2 ways
• Add OH• Absorb H+
– Ex: Sodium hydroxide (NaOH)
F. Acids and bases
• pH scale – gauge of how
acidic or basic a solution is
– Acidic solution less than pH 7
– Alkaline or basic solution pH
greater than 7
– Each unit is a 10-fold change in
H+ concentration
• pH 4 is 10 times more acidic than
pH 5
• Buffer systems are pairs of
weak acids and bases that
resist pH changes
G. Organic molecules
• Chemical compounds that contain both
carbon and hydrogen
– Hydrocarbons consist almost entirely of
carbon and hydrogen (CH4)
• 4 types – carbohydrates, lipids, proteins,
and nucleic acids
• Monomers (single units) linked together to
form polymers
• Linked using dehydration – take water out
• Broken apart by hydrolysis – add water in
1. Carbohydrates
• Organic molecules that consist of carbon, hydrogen and
oxygen (often 1:2:1 ratio)
• Simple sugars – ready source of energy
– Monosaccharides – 5 or 6 carbon atoms
• Same number of carbon atoms can be put together differently to give
very different molecules
• Ex: glucose, fructose, etc.
– Disaccharides
• 2 monosaccharides joined by dehydration synthesis
• Ex: Sucrose = fructose + glucose
– Oligosaccharides – 3-100 monomers
• Attach to proteins on the cell membrane
• Complex carbohydrates – stored energy/structures
– Polysaccharides
• Hundreds of monosaccharides
• Types:
–
–
–
–
Cellulose – plant cell walls
Chitin – exoskeleton of insects, cell walls of fungi
Starch – plant energy storage
Glycogen – animal and fungi energy storage
2. Lipids
•
•
•
•
Do not dissolve in water
Hydrophobic
Large areas with nonpolar bonds
Not polymers; made of monomers
– Unlike other 3 major macromolecules
• Several groups
– Triglycerides, sterols, waxes
– Where do sugar substitutes and fake fats come from? Are they
good for you?? See “Can you relate?” on p. 41
• Triglycerides
– 3 fatty acids bonded to
glycerol
– Use dehydration
synthesis and
hydrolysis
– Saturated fatty acids
have all single bonds
between carbons
• Animal fats, solid
– Unsaturated fatty acids
have at least 1 double
bond between carbons
• Plant-derived, liquid
– Trans fats: unkinked
unsaturated fat tails;
high risk for heart
disease 
2. Lipids
• Sterols
2. Lipids
– 4 interconnected
carbon rings
– Vitamin D, cortisone
– Cholesterol used in
cell membranes and
to make other lipids
– What cholesterol is good and
what is bad in the body?? See
“Can you Relate?” on p. 37
• Waxes
– Fatty acids combined
with either alcohols or
other hydrocarbons
– Forms water-repellent
covering
3. Proteins
• Amino acid is the monomer
– Central carbon atom bonded to hydrogen,
carboxyl group, amino group, and an R group
• R group distinguishes amino acids
• Dehydration synthesis links amino acids
with peptide bonds, hydrolysis break them
apart
• Dipeptide, tripeptide, peptide, polypeptide,
proteins
3. Proteins
3. Proteins
• Protein folding – unique 3D
structure
– Primary (1°) structure – amino
acid sequence determined by
organism’s genetic code (DNA)
– Secondary (2°) structure –
interactions from coils, sheets,
loops
– Tertiary (3°) structure – overall
shape arising from interactions
between R groups and water
– Quaternary (4°) structure –
interactions between multiple
polypeptide subunits (hemoglobin
has 4 subunits)
• Denaturation – loss of
structure means loss of
function (heat, salt, pH)
4. Nucleic acids
• 2 types
– Deoxyribonucleic acid
(DNA)
– Ribonucleic acid
(RNA)
• Nucleotide monomers
– 5 carbon sugar,
phosphate group, and
nitrogenous base
• DNA
–
–
–
–
–
–
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4. Nucleic acids
Deoxyribose sugar
Nitrogen Bases: A, C, G and T (not U)
Double strand in helix shape
Hydrogen bonds hold halves together
A with T, C with G
Strands are complementary (bases join together in pairs)
Genetic code – each group of three DNA bases specifies
one amino acid
• RNA
–
–
–
–
Ribose sugar
Nitrogen Bases: A, C, G and U (not T)
Single stranded
3 Different kinds (messenger, transfer, & ribosomal RNA)
• Enable DNA to be expressed without being damaged
• Function as enzymes
• Adenosine triphosphate (ATP) carries energy
Nitrogenous Bases:
A = Adenine
C = Cytosine
G = Guanine
T = Thymine
U = Uracil
Bases pair up to form base pairs
and link 2 strands of nucleic acid
by hydrogen bonds:
A pairs with T or U
C and G only pair with each other
T is found in DNA only
U is found in RNA only
T & U are very similar in shape
and so fill the same positions in
sequences, just T is only in DNA
and U is only in RNA
4. Nucleic acids
Investigating life:
A left hand from Mars?
• Unity reflected in
chemistry – same types
of molecules in all
organisms
• Extends to chirality or
symmetry of molecules
• When synthesized in a
lab, a batch is half and
half
• In organisms, proportions
are not equal
– 19 of 20 amino acids are
left-handed
Investigating life:
A left hand from Mars?
• Hypothesis that meteorites carrying just
one form of chiral molecule seeded life on
Earth
• Another hypothesis is that either lefthanded or right-handed molecules formed
had an advantage and prevailed over the
other form
• Pharmaceuticals – thalidomide is chiral
and the right-handed version causes birth
defects
Taxonomic Levels of Hierarchical Classification
• Domain
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• species
Domains and kingdoms
• Domain is the largest taxonomic category
– Only 3 Domains: Bacteria, Archaea, Eukarya
– Eukarya – all eukaryotic cells have nuclei
(houses DNA) and many eukaryotes are
multicellular
– Bacteria and archaea superficially similar –
single celled with DNA free in cell (not in a
nucleus)
– Archaeans different from 2 other domains
• Domain Eukarya divided into 4 kingdoms
– Organisms in these kingdom share a general
strategy for acquiring energy
• Fungi and animals are consumers (what they
consume is different)
• Plants are autotrophs
• Protista is different – artificial “none of the above”
category for organisms that are not plants,
animals, or fungi
C. Scientists study the natural world
• they use the
Scientific method
– General way of
organizing an
investigation
– Framework to consider
ideas and evidence in
a repeatable way
Steps of the Scientific Method:
1. Observations
– May be historical incidents or accidents
– May be based on existing knowledge and
experimental results
– Person may make mental connections among
previously unrelated observations
• Like Darwin
2. Hypothesis
– Tentative explanation based on previous
knowledge
– Must be testable
– Cannot be proven true with 100% certainty
3. Experimentation and data collection
–
–
–
–
Some investigations are discovery based
Some use experiments
Deciphering DNA sequence is discovery based
Demonstrating what that gene does requires
experiments
4. Analysis and peer review
– After collecting data, investigator reevaluates
hypothesis
– “Feedback loop” to rethink hypothesis
– May write a paper
– In peer review other scientists evaluate validity of
methods, data, and conclusions
Experimental design
• Sample size – number of individuals
– Larger number gives more meaningful results
• Variables – changeable element of an
experiment
– Independent variable – manipulated variable
– Dependent variable – shows response
– Standardized variables – held constant for all
subjects
• Controls – provides a basis for
comparison to the experimental group
– High, low, or no (control) fertilizer levels
– Placebo – inert substance resembling
treatment given experimental group
– Double-blind design – neither researchers nor
participants know who received substance
being evaluated until after the data is
tabulated
Fertilizer application level
(independent variable)
Average Yield
(dependent variable)
High
20
Low
17
None (control)
15
• Statistical analysis
– Investigator must decide whether independent
variable affected the dependent variable
– Less variation in the data means it is more
likely that the fertilizer is really responsible for
the difference
– Statistical significance based on sample size
and variation – probability that results arose
purely by chance
D. Theories are comprehensive
explanations
• Theory is an explanation for natural
phenomenon
• Differs from a hypothesis
– Theory broader in scope than a hypothesis
– Hypothesis is tentative, theories reflect
broader agreement
– A good theory is predictive – Darwin predicted
the existence of a then-unknown pollinator
based on his theory
Limitations of scientific inquiry
• Scientific method is neither foolproof nor
easy to implement
• Experimental evidence may lead to
multiple interpretations
• Even the most carefully designed
experiment can fail to provide a definitive
answer
• Researchers may misinterpret
observations or experimental results
E. Can you Relate?
good or bad?
•
•
•
•
•
•
Eggs
Caffeine
Low-carb diets?
Adkins Diet?
Trans fats?
Etc.
• Our views of how good or bad something is for
us changes as we learn more about it!