Unit 1

 Independent variable: the factor that is intentionally changed, only one

can be changed at a time in an experiment (x-axis)
 Dependent variable: the factor that is affected by the change in the
dependent variable (y-axis)
 Control group: an experiment that is used as a basis of comparison or
reference for a normal or expected outcome (considered a level of
independent variable)
o Negative: includes all variables except the independent variable
o Positive: includes all variables except the IV, plus a variable that
is shown to induce a positive result
 The purpose of the control group is to serve as a baseline of
comparison to help isolate and see the effects of changing the
independent variable.

Macromolecule Table

Macromolecule Monomers Polymers Bonds

Group
Carbohydrates Monosaccharides Polysaccharides Glycosidic bond
Lipids No true monomers No true polymers Ester bond
(Many contain (Phospholipid, (Found in
glycerol and fatty Triglyceride, triglycerides)
acids) Steroid)
Nucleic Acids Nucleotides DNA & RNA Phosphodiester
bond
Proteins Amino acids Polypeptide Peptide bond
Functional Groups

Functional Group Formula Diagram

Hydroxyl OH

Carbonyl CO

Carboxyl COOH

Amino NH2

Phosphate PO4
Methyl CH3

Unit 2

 Bond types
o Ionic: Intramolecular bond that results from the electrical
attraction between ions with opposite charges, the resulting
molecules are salts which dissolve in water
o Covalent: Intramolecular bond between non-metals that share
pairs of electrons
o Hydrogen: Intermolecular bond that is formed from the partial
negative end of one molecule (O, N, F) and the partial positive
end of another molecule with hydrogen
 Polarity: when a molecule displays a difference in electrical charge due
to differences in electronegativity which leads to dipole moment with
atleast one positive and one negative end
o Water is electronegative because oxygen is more electronegative
than water, causing the oxygen to pull on the electrons more,
which leads to an imbalance of charge where the oxygen is
negatively charged and the hydrogens are positively charged
 Water is a universal solvent due to its polarity, where it is able to pull
apart other charged molecules easily due to the large difference in
electronegativity between its oxygen and hydrogens and break them
into their aqueous forms.
 Hydrophobic vs. Hydrophilic
o Hydrophobic: non-polar molecules that do not interact with water
because of water’s polarity, and will instead interact with other
non-polar molecules
o Hydrophilic: polar molecules that interact with other polar
molecules (especially water) due to polarity
 Adhesion vs. Cohesion
o Adhesion: attraction force between different molecules (ex: water
to another molecule)
o Cohesion: attraction force between molecules of the same
substance (ex: water to water)
  pH scale: becomes more basic as the pH increases, (1-14), lower pH
indicates higher hydrogen ion concentrations
 Acid vs. Base
o Acid: hydrogen ion donor
o Base: hydrogen ion acceptor
o A solution at pH 6 contains 100 times more H + ions than a
solution at pH 8
 Buffer: a solution that resists changes in pH
 Solvent vs. Solute
o Solvent: the dissolving medium (usually water)
o Solute: substance being dissolved
 Hydrolysis vs. Condensation
o Hydrolysis: addition of water to break polymer into monomers
o Condensation: removal of water to link monomers together into
polymers
 Unsaturated vs. Saturated fats
o Unsaturated: the hydrocarbon chain has a double bond between
carbons causing a kink in the chain, liquid at room temp (plant
fat (oils))
o Saturated: solid at room temp, all carbons saturated with
hydrogens (animal fat)

Levels of Protein Structure

Structure Description Bonds

Primary Sequence of Covalent peptide
amino acids, not bonds
considered a
polypeptide yet
Secondary Regular repeated Hydrogen bonds
spatial patterns
(alpha helixes,
beta pleated
sheets)
Tertiary Polypeptide Interactions
chain that is bent between R
and folded, groups
resulting in 3D (Disulfide
shape bridges,
hydrogen bonds,
hydrophobic side
chains, van der
Waals
 interactions,
ionic bonds)
Quaternary Two or more Hydrophobic,
polypeptide ionic
chains bound interactions, and
together hydrogen bonds
(Hemoglobin,
collagen)

 Denaturation: unfolding of a protein that causes loss of function due to

factors such as heat, pH, salinity, etc.

Unit 3

 Enzymes belong to the protein macromolecule group

 The function of an enzyme is to serve as a catalyst to accelerate
chemical reactions in the cell
 Terms
o Substrate: the reactant that the enzyme acts on
o Active site: the specific region on the enzyme where the
substrate binds
o Allosteric site: a site other than the active site where molecules
can bind to regulate the enzyme’s activity via changing its
structure (conformational change)
 The active site is where the substrate binds to the enzyme where the
reaction is catalyzed. The active site is specific to the substrate.
 Activation energy is the energy needed to start a reaction. Enzymes
lower the activation energy for a reaction to occur.
 Correct surface area to volume ratio is crucial for proper functioning of
the cell because high surface area to volume ratio allows for efficient
transport of materials in and out of cells. As a cell grows, its volume
increases faster than its surface area so larger cells have less efficient
exchange.
 Features common to prokaryotes and eukaryotes
o Plasma membrane
o Cytoplasm
o Ribosomes
 Differences between prokaryotes and eukaryotes
 o Prokaryotes have a nucleoid region whereas eukaryotes have a
nucleus
o Prokaryotes have no membrane bound organelles
 Organelle functions

o Nucleus: Contains DNA; where DNA replication and transcription

occurs
o Ribosomes: Synthesize proteins (free: found in cytoplasm and
make proteins that function within the cytoplasm, bound:
attached to rough ER and create proteins packed in lysosomes or
exported from the cell)
o Rough ER: Protein synthesis and modification for proteins that
will be secreted or membrane-bound
o Smooth ER: Lipid synthesis, detoxification.
o Golgi apparatus: Modifies, sorts, and packages proteins.
o Lysosomes: Break down waste and cellular debris
o Vacuoles: Storage of materials (larger in plant cells), structure of
plant cells via turgor pressure, contain pigments, catabolism, and
aid in removing excess water
o Chloroplasts: Location of photosynthesis, converts light energy
into chemical energy stored in glucose (plants)
o Mitochondria: Where cellular respiration (except glycolysis)
occurs; makes ATP for energy in cells
 Endosymbiont theory: theory that states that mitochondria and
chloroplasts originated as prokaryotic cells which were engulfed by
early eukaryotes
o 1. Both mitochondria and chloroplasts have double membranes
o 2. Both mitochondria and chloroplasts have their own ribosomes
and DNA
o 3. Both mitochondria and chloroplasts can reproduce on their
own independent of cell division
 Fluid mosaic model: describes that the cell membrane is flexible (as
most molecules are free to move around) but contains various types of
biomolecules
o The cell membrane is made of proteins, other molecules, and a
phospholipid bilayer
 Active vs. Passive transport
o Active: requires energy in the form of ATP, flows against the
concentration gradient
 Sodium-potassium pump: uses a membrane protein and
ATP to pump sodium ions out of the cell and potassium ions
into the cell
  Exocytosis: release of materials out of the cell via vessicles
 Endocytosis: intake of materials in the cell (phagocytosis,
pinocytosis, receptor-mediated endocytosis)
o Passive: does not require energy and flows down the
concentration gradient
 Simple diffusion: random movement of particles towards
equillibirum
 Facilitated diffusion: requires a facilitator (usually a
transmembrane protein) which allows diffusion to occur
 Osmosis: fork of simple diffusion in which water moves
across a semi-permeable membrane
 Cytoskeleton
o Microfilaments: smallest, dynamically unstable, usually in
bundles, made from the protein actin; help entire cell or parts of
the cell to move (muscle cells), determine and stabilize cell
shape, create cleavage furrow; found throughout the cytoplasm
and just under the cell wall
o Intermediate filaments: middle in size, many different kinds,
tough-ropelike protein assemblages, more permanent than other
filaments and do not show dynamic instability; anchor cell
structures in place, resist tension and maintain rigidity; found
throughout the cytoplasm and extends from a region around the
nucleus

o Microtubules: largest in size, dynamically unstable, long, hollow,

unbranched cylinders formed from the dimers of the protein
tubulin; forms rigid internal skeleton in some cells and acts as
the framework for spindle formation, extracellular projections
(cilia and flagella), and motor proteins; found in the cytoplasm of
cells and on the cell membrane (cilia and flagella)
 Cell junctions
o Tight junctions: prevent the leakage of extracellular fluid across a
layer of cells (threads); commonly found in cells that form linings
(intestines, blood vessels)
o Desmosomes (anchoring junctions): anchor cells together but
allow materials to move in the matrix (bolts); commonly found in
tissues that are prone to constant mechanical stress (skin, heart
tissue)
o Gap junctions: direct connections between the cytoplasm of two
cells that allow various molecules, ions, and electrical impulses
 to directly pass through cells; found in nerves, cardiac, and
smooth muscles
 Cell walls are found in primarily plant cells but can also be found in
some prokaryotes; the cell wall provides support for the cell and limits
the volume by remaining rigid (allowing efficient exchange),
additionally it can act as a barrier to infection and contributes to form
during growth and development
 Plasmodesmata are plasma membrane-lined channels that connect
adjacent plant cells; these allow for the movement of water, ions, small
molecules, hormones, and some RNA and proteins

Cellular Respiration
 Overall equation for cellular respiration: C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + ATP
 The final electron acceptor in cellular respiration is oxygen
 Three stages of cellular respiration:
o Glycolysis: occurs in cytoplasm where one glucose and 2 ATP are used to
produce 2 Pyruvate, 4 ATP, and 2 NADH (2 ATP net, ATP produced via
substrate-level phosphorylation)
 Separate step Pyruvate Oxidation oxidizes Pyruvate to create CO2 ,
acetate, and NADH
o Citric acid cycle: occurs in mitochondrial matrix where Acetyl CoA is oxidized to
form 4 CO2 , 2 ATP, 6 NADH, and 2 FADH2 (per glucose); this step also uses
substrate-level phosphorylation
o Oxidative phosphorylation: occurs in mitochondrial inner membrane in two major
event: electron transport chain and chemiosmosis
 ETC: NADH and FADH2 are oxidized and their electrons are passed from
one carrier protein to another, creating a hydrogen ion gradient via active
transport
 Chemiosmosis: hydrogen ions passively transport through ATP synthase
to synthesize ATP through oxidative phosphorylation
 Oxygen is the final electron acceptor, which later joins hydrogen ions to
become water
 NADH & FADH₂ act as electron carriers to bring electrons to the ETC
 Substrate-level phosphorylation is the synthesis of ATP by the direct transfer of a
phosphate group from a intermediate to a molecule of ADP; this occurs in glycolysis and
the citric acid cycle. Oxidative phosphorylation is the use of O2 to oxidize electron
carriers such as NADH in order to add a phosphate group onto a molecule; this occurs in
the ETC and in chemiosmosis
 NADH & FADH₂ donate electrons to the ETC, and the flow of electrons down the ETC
causes H+ ions to be actively pumped from the matrix to the intermembrane space,
hydrogen ions are then diffused through ATP synthase back into the matrix.
 The H+ gradient is important because H+ ions need to be diffused through ATP synthase
to spin the motor in order to add a phosphate group to ADP. Without the creation of a H+
concentration by actively pumping H+ ions from the matrix to the intermembrane space,
the concentrations of H+ ions would be the same on both sides, so H+ ions would not
flow through ATP synthase, thus causing no ATP to be produced.
 Passive vs. Active steps:
o Passive: H+ ions diffuses through ATP synthase (intermembrane space to matrix)
o Active: H+ ions are pumped from matrix to intermembrane space
 Lactic acid fermentation: uses glycolysis to oxidize glucose into pyruvate then reduces
pyruvate via NADH into lactate and regenerates NAD+
 Alchoholic fermentation: uses glycolysis to oxidize glucose into pyruvate; through two
steps, pyruvate is broken into CO2 and acetaldehyde, then acetaldehyde is reduced via
NADH to create ethanol and regenerate NAD+
 Fermentation can occur in bacteria, yeasts, and some animal muscle cells
 In order for fermentation to occur, their environment cannot have oxygen
 NAD+ is regenerated in fermentation in order to allow glycolysis to continue to create
ATP as NAD+ is a reactant in glycolysis
 Obligate anaerobes cannot survive in environments with oxygen whereas facultative
anaerobes can survive in environments with and without oxygen

Photosynthesis

 Autotroph vs Producer vs Photoautotroph

o Autotroph: organism that creates its own food
o Producer: organisms that produce their own organic matter using an external
source of energy, found first in the food chain
o Photoautotroph: organism that creates its own food by utilizing light energy via
photons
 Equation for photosynthesis: 6CO₂ + 6H₂O + light → C₆H₁₂O₆ + 6O₂
 The source of oxygen in photosynthesis is from water H2O
 Flow of electrons in ETC:
o H₂O → Photosystem II → ETC → Photosystem I → NADP⁺ reductase
 Similar to cellular respiration, photosynthesis’s chemiosmosis creates a H+ gradient
because as electrons flow down the ETC, they are reenergized by photons at PSI and
PSII, and the flow of electrons causes H+ ions to be actively transported from the stroma
to the thylakoid space via the cytochrome complex. This higher concentraion of H+ ions
in the thylakoid space then diffuse through ATP synthase to create ATP.
 The final electron acceptor of the light dependent reactions is NADP+

 Light reactions:
o Occurs in the thylakoid membrane
o Inputs: Light, water, ADP, NADP+
o Outputs: O2, ATP, NADPH, H+ ions
 Calvin cycle:
o Occurs in the stroma
o Inputs: CO₂, ATP, NADPH, RuBP
o Outputs: G3P (later becomes glucose with 2 G3P), RuBP, ADP, NADP+