Organismal Biology Notes/Study Guide – Test One
Matter
o Has mass and takes up space
Energy
o All living things require energy
o Energy starts at the sun
 Is transferred by consumption
Levels of organization (smallest to largest)
o Atom
 A particle composed of protons, neutrons, and electrons that cannot be further
broken down by chemical means
o Molecule
 Two or more atoms joined by chemical bonds
o Organelle
 Compartment of a eukaryotic cell that performs a specialized function
o Cell
 The smallest unit of life that can function independently
o Tissue
 Group of cells that interact and provide a specific function
o Organ
 Two or more tissues that interact and function as an integrated unit
o Organ system
 Two or more physically or functionally linked organs
o Multicellular organism
 A living individual
o Population
 A group of the same type of organism living in the same place and time
o Community
 All organisms in a given place and time
o Ecosystem
 The living and nonliving environment
 The community of life, plus soil, rocks, water, air, etc.)
o Biosphere
 Parts of the planet and its atmosphere where life is possible
Producers
o Also called autotrophs
o Extract their energy from the nonliving environment
 Mainly sunlight, but some can get energy from rocks
Consumers
o Also called heterotrophs
o Obtain energy by eating nutrients that make up other organisms
Decomposers
o Consumers that obtain energy from wastes or dead organisms
o Fungi and many bacteria are decomposers
Homeostasis
o The state of internal constancy, or equilibrium
o The conditions inside cells must remain within a constant range, even in the face of
drastic changes in the environment
 Basically, in order to stay alive, a cell must maintain a certain water balance,
take in nutrients, excrete wastes, and regulate its many chemical reactions to
prevent deficiencies or excesses of essential substances
Reproduction
o Asexual
 An organism produces new individuals that are virtually identical to it
 Unicellular organisms produce this way
Example: bacteria
o Doubles itself then divides
o Sexual
 Genetic material from two individuals unites to form a third individual
Has a new combination of inherited traits
Mixes the genes of both parents
Evolution
o Adaptation
 An inherited characteristic or behavior that enables an organism to survive and
reproduce successfully in a given environment
o Natural selection
 The enhanced reproductive success of certain individuals from a population
based on inherited characteristics
Basically, over time, those with the best genes will be able to survive
and the retard ones will die
o Evolution
 A change in the genetic makeup of a population
Taxonomic Hierarchy
o Taxonomy
 Classification of organisms
Domain, kingdom, phylum, class, order, family, genus, and species

Element
o A pure substance that cannot be broken down by chemical means into other substances
o Make up the periodic table
 Chart that lists elements according to their properties
o Bulk elements
 Make up the vast majority of every living cell and are therefore required in large
amounts
Examples: carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus
o Trace elements
 Are not needed in large amounts
 Important in ensuring that vital chemical reactions occur fast enough to sustain
life
Examples: iodine and iron
Atoms
o Smallest unit
o Considered an element
o Composed of subatomic particles
 Protons (positive charge)
 Neutrons (no charge)
 Electrons (negative charge)
o Nucleus composed of protons and neutrons
 Mass number is the total number of protons and neutrons in the nucleus
o Electrons are outside of the nucleus in an orbital
 The atom’s valence shell is its outermost occupied energy cell
Atoms are the most stable when their valence shells are full
o The atomic number is the number of protons
o Our bodies are composed of elements
o All living organisms are composed of carbon
Ion
o An atom, or group of atoms, that have gained or lost electrons and therefore has a net
negative or positive charge
o They form ionic bonds
o Examples: hydrogen, sodium, potassium, and chloride
Isotope
o
Any of the forms of an element, each having a different number of neutrons in the
nucleus
Chemical bonding
o An attractive force that holds atoms together in a molecule
o Molecules
 Two or more elements that are bonded together
o Electronegativity
o

 A measure of an atom’s ability to attract electrons
 One end has more protons and pulls the electrons
 One end is positive, the other negative
Covalent bond
 Atoms share electrons
 Fairly strong bond
 Non-polar covalent bonds
Two atoms share electrons equally
No real change in the charge of the molecule

Polar covalent bonds
Electrons not shared equally
Normally two different elements
Hydrogen Bond
o Weakest bond
o Forms easily
o Breaks easily
o
Ionic bonding
o Elements with opposite charges attract and bond to each other
o
Ion
o Has either a positive or a negative charge
o Gains or losses an electron
Water Molecules
o No real charge
o Polar molecules are hydrophilic
 Hydrophilic
Loves water
 Hydrophobic
Does not mix with water
Non-polar molecules are hydrophobic
o Always moving
 The faster they move, the hotter the temperature
 The hotter it gets, the faster bonds break which causes evaporation
 When the molecules stop moving, ice is formed
o Solvent
 Easily dissolved in ions or other molecules
o Solute
 The dissolved substances
o Solution
 Consists of one or more solutes dissolved in a liquid solvent
o Mixture
 Two or more substances mixed together
o Cohesive
 When placed under stress, the molecule does not break
Acids and bases
o pH scale
 looks at the number of hydrogen ions
 the more hydrogen ions, the lower the pH

o
Cells
o
0-14 scale
7 is neutral
0-6 is an acid (acidic)
8-14 is a base (basic or alkaline solution)
Buffer Systems
 Pairs of weak acids and bases that resist pH changes
Basic unit of life
 Smallest unit of life
o Potential to survive on its own
o Requires energy
o Senses and responds to changes in environment
o Capable of reproducing
o All cells have:
 DNA
 Proteins that carry out work
 RNA that makes proteins
 Ribosomes
 Cytoplasm
 Cell membranes
Also called a fluid mosaic
 Complex cell contain organelles
o Each cell starts out with a cell membrane
 The outer layer of the cell
 Composed of phospholipids
Phospholipid bilayer
Acts like a fence with gates
 Also called the plasma membrane
Cell theory
o All organisms are composes of 1+ cells
o The cell is the fundamental unit of life
o All cells come from pre-existing cells
3 domains
o Bacteria
 Lack membrane-bounded nuclei
 Contains a nucleoid where its genetic material congregates
 Cell wall surrounds the cell membrane of most bacteria cells
Protects the cell
Prevents it from bursting
Gives it a distinctive shape
o Round, rod-shaped, spiral, comma-shaped, or spindle-shaped

Contain flagella
Tail-like appendages that enable the cell to move
Anchored in the cell wall
o Archaea
 Smaller than most eukaryotic cells
 Lack a membrane-bounded nucleus and other organelles
 Most have cell walls and flagella
 All parts of the Archaea architecture are unique
 Famous as “extremophiles” because they live and survive in such brutal
conditions
o Eukarya
 Large in size
10-100 times greater in size than prokaryotic cells
 The main difference between prokaryotic and eukaryotic cells are that
eukaryotic cells have elaborate systems of internal membranes which create
compartments – organelles – where specialized biochemical reactions occur
Simple cells are in the bacteria and Archaea domains
o Called prokaryotic cells
 Contain NO nucleus
o Can survive without oxygen
Both Prokaryotic and Eukaryotic cells contain:
o Cell membranes
o Cytoplasm/cytosol
 A fluid like material
o Organelles
 Has a certain job within the cell
o Cytoskeleton
 An intricate network of internal protein “tracks” and tubules
 A structural framework with numberous function
 It’s a transportation system, provides support necessary to maintain the cell’s
characteristic 3-d shape and enables cells, or parts of cells, to move
 Helps keep structure
 Helps things move throughout the cell
o Ribosomes
 Make proteins
Proteins
o Proteins in the membrane have diverse functions
 Transport proteins
Are embedded in the phospholipid bilayer create passageways through
which water-soluble molecules and ions pass into or out of the cell
 Enzymes
These proteins facilitate chemical reactions that otherwise would not
proceed quickly enough to sustain life
In some membranes, different enzymes are physically laid out in the
order in which they participate in chains of chemical reactions
Increase the rate in which reactions occur
 Recognition proteins
Carbohydrates attached to cell surface proteins serve as “name tags”
that help the body recognize its own cells
The immune system attacks cells with unfamiliar surface molecules,
which is why transplant recipients often reject donated organs
Prokaryotic Cells
o
o Simplest and most ancient forms of life
o Organisms whose cells lack organelles
Eukaryotic Cells
o
Have a nucleus
 Where the DNA is stored
 Nuclear membrane surrounds it
o Endoplasmic reticulum (ER)
 A network of sacs and tubules composed of membranes
 Rough ER
The membrane surface is studded with ribosomes making proteins that
enter the inner compartment of the ER
Ribosomes make it rough looking
 Smooth ER
Synthesizes lipids and other membrane componenets
Makes lipids to be a part of the phospholipid bilayer
o Golgi body/golgi apparatus
 Packages and processes proteins and lipids
o Vesicles
 Small, little sacks that move throughout the cell
 Tries to digest worn out parts of the cell
o Lysosomes
 Organelles containing enzymes that dismantle captured bacteria, worn-out
organelles, and debris
 Recycling center of the cell
Takes old parts or worn out parts of the cell to digest and transport
o Mitochondria
 Use a process called cellular respiration to extract this needed energy from food
 Nearly all eukaryotic cells have a mitochonrion
 Where energy is made
 ATP = energy
 Requires oxygen
The process of making ATP requires oxygen as well
Plant Cells
o Contain a cell wall and chloroplast that the animal cell does not have
o Photosynthesis happens inside the chloroplast
 Occurs in the thylakoid
 Would not happen without sunlight
o ****A FUNGUS IS NOT A PLANT****
o
Energy
o All energy starts from the sun
o Potential energy
 Stored energy
o Kinetic energy
 Energy in use
o Energy is measured in calories and kilocalories
 Kilocalorie = 1000 calories
Laws of Thermodynamics
o Energy conservation
 Energy cannot be created nor destroyed
 It can be converted into other forms and from one thing to the next
o Energy transfers are inefficient
 Every energy transfer losses some energy as heat
 Metabolism
All reactions in the cell
The cell’s ability to get energy
Absorb or release energy
Endergonic reactions
o Must have energy to start off with
 Example: photosynthesis
o Energy needed to build complex molecules
Exergonic reactions
o Releases energy
o Breaking down complex molecules
Oxidation reduction
o The process of transferring an energized electron from one molecule to another
molecule
o Losing electrons
o Releasing energy
o
Reduction actually means gaining an electron
o
Electron Transport Chain
o Groups of cytochromes align in membranes with other proteins, each accepting an
electron from the molecules before it and passing an electron to the next
o Small amounts of energy are released at each step of an electron transport chain
o The cell uses this energy in other reactions
o
ATP
o Adenosine triphosphate
o Temporary energy storage
o Makes energy for the next reaction
Activation site
o Where substrates attach to enzymes
 They fit like puzzle pieces
o Cells control reaction rates
o
Membrane Transport
o
Passive transport
 Diffusion


o
Osmosis
o Simple diffusion
o Movement across a semipermeable membrane between two
components
Tonicity
o Cell’s ability to cause water movement
 Isotonic
Equal concentration
 Hypotonic
Under
Concentration lower inside cell
 Hypertonic
Over
Concentration higher outside cell
Facilitated Diffusion
Assisted by protein
Active transport
 Requires ATP
 Sodium potassium pump is inside the cell membrane
Helps to move it across the gradient
 Endocytosis
Engulfing large molecules/fluids
 Exocytosis
Uses vesicles to move molecules/fluids out of the cell
Negative feedback
o An excess of a reaction’s product inhibits the enzyme that controls its formation
o Example:
 thermostat
Positive feedback
o A product activates the pathway leading to its own production
o Example:
 Blood Clotting
Noncompetitive inhibition
o Product molecules bind to the enzyme at a site other than the active site, but in a way
that alter the shape of the enzyme so that it can no longer bind substrate
o The inhibitor does not directly compete to occupy the active site
Competitive inhibition
o The product of the reaction binds to the enzyme’s active site, preventing it from binding
substrate
o It is “competitive” because the product competes with the substrate to occupy the
active site
Cellular Respiration
o Cells are breaking down complex molecules to make energy (ATP)
o 3 different types of energy releasing pathways
 Aerobic Respiration
Needs oxygen
Occurs in mitochondria/ starts in cytoplasm

Anaerobic Respiration
Requires no oxygen
Starts with glycolysis
o Pyruvate
 What sugar is broken into
o Goes to Kreb’s cycle

o Then electron transport chain
Can be found in:
o Marshes
o Bogs
o Mud
o Deep sea sediment
o Animal guts