CHAPTER 1: BIOLOGY

1.1
Biology: Scientific Study of Life
Life is characterized by the following properties and processes:
Order: Life is characterized by ordered structures
Reproduction: Organisms reproduce their own kind
Growth and Development: Inherited Info from DNA controls growth and development patterns
Response to the environment: Environmental stimuli
Energy Processing: Take in energy and use it for power
Regulation: Mechanisms to maintain internals
Evolutionary Adaptation: evolve over generations with heritable traits best suited to environment have
greater reproductive success
Cell:
A basic unit of living matter separated from its environment by a plasma membrane; the fundamental
structural unit of life.

1.2 Arrangement of Diversity into 3 domains

Each unique form of life is called a species
Given two-part, italicized, scientific name
Name identifies the Genus and the specific species in that Genus
Species -> Genus -> Species
Taxonomy: branch of biology that names and classifies species, arranges into hierarchy.
Kingdom, phylum, class, order, family, genus, species \
Usually divided life into 5 kingdoms, instead we use 3 higher domains (Domain>Kingdom)
1) Bacteria
2) Archaea
3) Eukarya
a. Made of 4 Kingdoms, besides protists, others distinguished via mode of nutrition
b. Protists (Multiple Kingdom) – Mostly single cell organisms
c. Kingdom Plantae – produce food via photosynthesis
d. Kingdom Fungi – decompose organic waste and absorb nutrients into cells
e. Kingdom Animalia – Eat other organisms
Bacteria, Archaea, consit of microorganisms and simple cells.
Archaea lives in hot temperatures
All other organisms are more complex, in domain Eukarya b/c of complex cells called Eukaryotes
emergent properties
New properties that arise with each step upward in the hierarchy of life, owing to the
arrangement and interactions of parts as complexity increases.
THE PROCESS OF SCIENCE
1.4 What is science/?

Science: An approach to understanding the natural world based on verifiable evidence.

Biologists record observations called Data.

Qualitative vs Quantitative

Hypothesis: A testable explanation for a set of observations based on the available data.

Experiment: A scientific test. Often carried out under controlled conditions that involve
manipulating one factor in a system in order to see the effects of changing that factor.

Observation -> Question -> Hypothesis, Prediction -> Test/Experiment -> Results

We can never prove that a hypothesis is true.

Theory is different from a hypothesis:

Theory: A widely accepted explanatory idea that is broader in scope than a hypothesis,
generates new hypotheses, and is supported by a large body of evidence.

Science is based off of hypothesis testing and verifiable evidence. Science is willingness to follow the
evidence and correct itself when new evidence is found.
What is the main requirement for a scientific hypothesis?
It must generate predictions that can be tested by experiments or gathering further observations.

1.5 Hypotheses can be tested using controlled experiments

Controlled Experiments: Manipulation of one component or variable and observe the change

Independent Variable: A factor whose value is manipulated or changed during an experiment to reveal
possible effects on another factor (the dependent variable). MANIPULATED BY RESEARCHER

Dependent Variable: A factor whose value is measured in an experiment to see whether it is influenced
by changes in another factor (the independent variable). Affected by MANIPULATED VARIABLE.

controlled experiment
An experiment in which an experimental group is compared with a control group that varies only
in the factor being tested.
Retrospective study: researchers may interview people or examine death certs/medical records to
id factors that lead to an outcome
Prospective study: researchers start from the beginning, enroll a group of participants called a
COHORT and collect data over a period of time
Correlation is not causation in observational studies, large cohort studies are good.
1.6 Hypotheses can be tested using observational data
Behaviour of species 1 must mean it is similar to species 2

Explain why comparisons of DNA sequences are considered observational and not experimental
data.

Scientists are not manipulating DNA sequences in any type of experiment but are simply
recording and comparing the differences in sequences that they observe.

1.7 The process of science is repetitive, nonlinear and collaborative.

Why is hypothesis testing at the center of the process of science?

Hypothesis testing is central because a core component of science is testable explanations of

nature.

1.8 Biology, tech, society are connected

Technology: The application of scientific knowledge for a specific purpose, often involving industry or
commerce but also including uses in basic research.

How do science and technology interact?

New scientific discoveries may lead to new technologies; new technologies may increase the
ability of scientists to discover new knowledge.
FIVE UNIFYING THEMES IN BIOLOGY
1.9 Theme: Evolution is the core theme of biology
Scientific explanation for the unit and diversity is evolution: Descent with modification; the idea
that living species are descendants of ancestral species that were different from present-day ones; also,
the genetic changes in a population from generation to generation.

Darwins theory of evolution: 2 Points

1) Species living today came from succession of ancestors that were different
a. CALLED DESCENT WITH MODIFICATION
b. Explains unity as we descend from a common ancestor
c. Explains diversity as modifications evolved as species diverged from ancestors
2) Mechanism for evolution
a. CALLED NATURAL SELECTION
b. He made 2 observations and 2 inferences
i. OBS 1: Individual Vartiation
1. People in a population vary in traits, many of which seem to be
heritable via passed from parent to offspring
ii. OBS 2: Overproduction of Offspring
1. All species can overproduce to where environment can sustain them,
this leads to competition among offspring.
iii. Inference 1: Unequal reproductive success
1. Individuals with inherited traits best suited to local environment are
likelier to survive and reproduce
iv. Inference 2: Accumulation of favorable traits over time
1. As a result of unequal reproductive success, over generations, higher
proportion of the population will have traits that are advantageous to
environment
v. EX: Bird eats bright colored beetles, this leaves just dark colored ones, over
generations we got nothing but dark colroed beetles b/c they have a higher
chance of surviving.

Species could evolve as a result of changes over a period of time. Different environemts can change a
species.

Explain the cause and effect of unequal reproductive success.

Those individuals with heritable traits best suited to the local environment produce the greatest
number of offspring. Over many generations, the proportion of these adaptive traits increases in
the population.

1.10 Evolution Connection: Artificial selection: The selective breeding of domesticated plants
and animals to promote the occurrence of desirable traits. Explain how humans are agents of
both artificial selection and natural selection We use artificial selection when choosing specific
traits or genes in organisms that we breed. Our intentional and unintentional manipulations
change the environment and thus affect natural selection.
1.11 Theme: Life depends on the flow of information
DNA is the info that is passed on. Made of 2 chains coiled called a HELIX
Strands made from nucleotides
Genes: A discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA (or
RNA, in some viruses). Most of the genes of a eukaryote are located in its chromosomal DNA; a few are
carried by the DNA of mitochondria and chloroplasts.

Genes make proteins, proteins are a building block of cells

Gene transcribed from DNA to an intermediate RNA called mRNA. RNA carries info to
ribosome (protein factory) of cell, RNA is translated into proteins. THIS PROCESS IS CALLED
GENE EXPRESSION: The process whereby genetic information flows from genes to proteins; the
flow of genetic information from the genotype to the phenotype.

How is signaling information involved in the expression of genetic information?

Information from the internal and external environment affects gene expression—where and
when particular genes are activated and proteins made.

1.12 Theme: Structure and function

Correlation of structure and function. EX: structure of a protein correlates with its function
Close match of form and function in structures of life can be explained by natural selection.
Desirable traits mean reproductive success. EX: Red panda has false thumb to grab bamboo
Look at the structure of your hand and explain how its structure supports its function.
The finger joints and opposable digits allow you to manipulate objects.

1.13 Theme: Life depends on the transfer and transformation of energy and matter
In order to function energy is required. Photosynthesis, energy from sunlight is stored as
chemical energy as atoms in CO2 absorbed by the leaves and H2O from the roots are rearranged
into sugar molecules.
Inflow of light energy from sun makes plants, chemical energy of plants consumed by moose.
Moose takes up Co2 from air and absorbs H2O. Decomposers return chemicals to soil. Heat is
lost. But some energy is reused Energy enters as light, exits as heat.
Matter from the air and soil goes to producers, to consumers and decomposers back to air and
soil
Consumers: obtain matter to build new molecules.
Decomposers: Act as recyclers

1.14 Theme: Life depends on interactions within and between systems

Ex: your body works in conjunction to function
Systems biology: An approach to studying biology that aims to model the dynamic behavior of
whole biological systems based on a study of the interactions among the system’s parts.
FIVES THEMES SUMMARY:
Evolution, Information, Structure, Function, Energy/Matter, Interactions
organelle, cells, tissues, organs, organ systems, organisms, populations,
communities, ecosystem, and biosphere

Biology is the scientific study of life. Properties of life include order, reproduction, growth and
development, energy processing, regulation, response to the environment, and evolutionary
adaptation. The cell is the structural and functional unit of life.

1.2 Biologists arrange the diversity of life into three domains.

Taxonomists name species and classify them into broader groups. Domains Bacteria and
Archaea contain organisms with simple cells. Domain Eukarya includes various protists and the
kingdoms Fungi, Plantae, and Animalia.

1.3 In life’s hierarchy of organization, new properties emerge at each level.

Biological organization unfolds as follows: biosphere > ecosystem > community > population
> organism > organ system > organ > tissue > cell > organelle > molecule. Emergent properties
result from the interactions among component parts.
1.4 What is science?
Science uses an evidence-based process of inquiry to investigate the natural world. The scientific
approach involves observations, hypotheses, predictions, tests of hypotheses via experiments or
additional observations, and analysis of data. A scientific theory is broad in scope and supported
by a large body of evidence.

1.5 Hypotheses can be tested using controlled experiments.

The use of control and experimental groups can demonstrate the effect of a single variable.
Hypotheses can be tested in humans with clinical trials, as well as retrospective or prospective
observational studies.

1.6 Hypotheses can be tested using observational data.

Scientists tested hypotheses about the evolutionary relationships of red pandas. Recent studies
comparing DNA sequences classify the red panda as the only living species in its family.

1.7 The process of science is repetitive, nonlinear, and collaborative.

Forming and testing hypotheses is at the core of science. This endeavor is influenced by three
spheres: exploration and discovery; analysis and feedback from the scientific community; and
societal benefits and outcomes.

1.8 Biology, technology, and society are connected in important ways. Technological advances
stem from scientific research, and research benefits from new technologies.
Five Unifying Themes in Biology (1.9–1.14)
1.9 Theme: Evolution is the core theme of biology.
Darwin synthesized the theory of evolution by natural selection.

1.1-3 Full Alternative Text

1.10 Evolution is connected to our everyday lives.
Evolutionary theory is useful in medicine, agriculture, and conservation. Human-caused
environmental changes are powerful selective forces that affect the evolution of many species.

1.11 Theme: Life depends on the flow of information.

DNA is responsible for heredity and for programming the activities of a cell by providing the
blueprint for proteins. Information from the external and internal environment includes the
stimuli, signals, and pathways that regulate body processes and gene expression.

1.12 Theme: Structure and function are related.

Structure is related to function at all levels of organization.

1.13 Theme: Life depends on the transfer and transformation of energy and matter.
Energy flows through an ecosystem in one Energy flows through an ecosystem in one direction
—entering as sunlight, converted to chemical energy by producers, passed on to consumers, and
exiting as heat. Ecosystems are characterized by the cycling of matter from the atmosphere and
soil through producers, consumers, decomposers, and back to the environment.
1.14 Theme: Life depends on interactions within and between systems.
Emergent properties are the result of interactions between the components of a system. Systems
biologymodels the complex behavior of biological systems.
Chapter 2: Atoms and Compounds
Matter: Occupies space and has mass. Matter
makes up everything.
Element: cannot be broken into other
substances.
92 elements found in nature.
Compound: substance containing two or
more different elements
Humans need 25 elements for life essentials
Plants need 17 elements for life essentials
Oxygen, Carbon, Hydrogen, Nitrogen,
Calcium, Phosphorous 99% of body.
O,C,H,N make proteins, carbs and lipids.
Ca and P are major players in bones and
teeth
1% remaining is K, S, Na, Cl and Mg for
nerve signaling and chemical reactions
TRACE elements: Boron, Chromium,
Cobalt, Copper, Fluorine, Iodine, Iron,
Manganese, Molybedenum, Selenium, Silicon, Tin, Vanadium, Zinc, Iron is 0.004%. Fe is trace
need by all forms of life. Iodine is needed only for verterbrates (animals with backbones)

2.2 Trace elements are common additives to food and water

Iodine is needed for thyroid gland to produce hormones. Iodine deficiency = goiter. Bad if
deficient during fetal development and childhood.
Iron found in cereal. Fluorine found in small amounts in water sources.

2.3 Atoms consist of protons, neutrons and electrons

Atom is smallest unit of matter that retains properties of an element.
Subatomic Particles
Protons, Electron, Neutron
All atoms of an element have the same atomic number = # of protons
Mass number = sum of protons + neutrons in nucleus
Protons/Neutrons = 1 dalton of masss
Atomic mass = mass number
Isotopes = same # of protons, diff # of neutrons

2.4 Raduioactive Isotopes can help or harm us

Research can use CO2 containing isotope Carbon 14 to study photosynthesis
Labeled C14 in CO2 can be used to trace the sequence of molecules made by plants in
converting Co2 to sugar in plants
Medical Diagnosis and Treatment:
Isotopes can tag chemicals to accumulate in the body. After injection of tracer, camera can see
and produce an image.
PET scan can be used to produce images of areas of the body with metabolic activity. Can
diagnose heart disorders and cancer and brain. Isotopes of glucose and oxygen can be used w/
PET scan used for Alzheimer screening. Alzheimers b/c of plaque deposits of beta amyloid
protein. PIB is a radioactive label that binds to plaques. Can be detected on a PET scan.
Dangers:
Chernboyl, Fukushima.
Radon, radioactive gas, causes lung cancer. Due to uranium under buildings.

CHEMICAL BONDS
2.5/2.6 Distribution of electrons determines an atoms chemical properties electron shell A level
of electrons at a characteristic average distance from the nucleus of an atom.
SHELLS: 2 8 8
Valence shell determines chemical properties of the atom.
Atoms with unfilled out shells react with other atoms to complete their shells
Chemical bonds are attractions to fulfill this complete shell
Ionic Bond: Transfer of an electron b/w atom
Covalent Bond: Share of electrons b/w atom]
Molecules are 2+ atoms held by covalent bonds. Sharing is not always equal.
Electronegativity measures attraction for shared electron.
Nonpolar covalent: elements w/ 2 same electronegativity, equal share
Polar covalent, negatively charged electrons drawn to more electronegative element. Result is a
dipole of positive charge at one end and negative at other.
4 ways to draw it: Molecule formula: O2
Electron Distribution diagram :c: c:
Structural Formula C-C
Space-filling model: Imagine a 3d shape of the atom OO

Polarity refers to a separation of charges (think of the positive and negative poles of a battery).
Explain why the bonds in a water molecule are polar covalent bonds?
The negatively charged electrons are pulled closer to oxygen, giving it a slight negative charge.
With its electron pulled further away from its positively charged nucleus, the H is slightly
positive.

2.7 Ionic bonds are attractions between ions of opposite charge

If two atoms are so unequal in their attraction for electrons, the more electronegative atom strips
an electron completely away from its partner.
Na becomes positive ion, Cl is more electronegative and steals Na’s electron, becomes negative.
Most drugs are made as salts because they are stable and dry, they dissolve in water easily too.
Explain what holds together the ions in a crystal of table salt.
Opposite charges attract. The positively charged sodium ions and the negatively charged
chloride ions are held together by ionic bonds, attractions between oppositely charged ions.
2.8 Hyrdrogen bonds are weak bonds important in the chemistry of life.
Water is pola, unequal distribution of charges. At 2 H ends of H2O, it is positive, causes
interactions of other hydrogen atoms.
2.9 Chemical reactions make and break chemical bonds
2H2 + O2  2H2O
Reactants to product.
Photosynthesis: CO2 and H2O react with sunlight energy to make glucose C6H12O6 and O2
6Co2 + 6H2o  C6H12O6 +6O2
Matter has been rearranged.
WATERS LIFE SUPPORTING PROPERTIES
2.10 hydrogen bonds make liquid water cohesive.
Hydrogen bonds between water last for trillionths of a second, this results in cohesion. Trees
depend on cohesion to help transport water from roots to leaves. Evaporation exerts a pulling
force on leaf. Force of cohesion force is relatyed all the way to roots.
ADHERSION clinging of one substance to another vs cohesion (between one substance)
Thinness of aplant’s vein enhances the adhesion of water to its cells walls.
Surface tension measures how difficult it is to stretch of breakl the surface of a liquid.
Ex: cohesion makes sweat bead together, adhesion of water helps skin hold beads in place
2.11 Water’s H bonds moderate Temp
Thermal Energy is the energy associated with the random movement of atoms and molecules.
Heast: Thermal energy in transfer from a warmer to a cooler body of matter
Temperature: Intensity of heat, avg eK of molecules or avg speed.
Heat absorbed to break H Bonds. Heat released when H bonds form. When water boils H
bonds break, when it cools H bonds are made.
Heat given off from gradually cooling water warms the air. Why coasts are milder.
Evaporative cooling occurs The process in which the surface of an object becomes cooler during
evaporation, a result of the molecules with the greatest energy changing from the liquid to the gaseous
state.
Molecules with greatest energy :Hotter:” stuff leaves.
High humidty hampers the ability for sweat to evaporate
2.12 Ice floats because it is less dense than water
Ice crystals have fewer molecules than an equal volume of liquid water. Ice is less dense and
floats Water expands as it freezes and becomes farther spaced apart as crystals form
2.13 Water is the solvent of life
Solution is a liquid consisting of 2+ substances mixed
Solvent is water aka the dissolving agent
Solute, the substance that is dissolved aka SALT
Aqueous solution is a solution where water is the solvent
2.14 Chemistry of life is sensitive to acidic and basic conditions
Dissociation to H+ ions and OH- Ions. Can affect proteins.
Acid donates H ions
Base reduces H ions and adds OH to solution to combine with H ions
pH scale.
pH of human is 7.4
7.0 or 7.8 is bad for humans
Buffers minimize changes in pH. Accept H+ when in excess and donate H+ when not enough is
around.
2.15 Scientists study the effects of rising atmospheric CO2 on coral reefs
25% of CO2 is absorbed the ocean. Can harm ocean life
Ocean acidication results in CO2 dissolving in seawater lowering pH. Extra H+ ions in seawater
can make carbonate ions to form bicarbonate ions. Reduces carbonate ion concentration
available to coral other shell building animals.
2.16 Search for ET life centers on the search for water
Mars has an ice cap at both poles and people found water there.