Study Guide for AP Biology Test

Chapter Two: The Nature of Molecules

Matter - any substance in the universe that has mass and occupies space
Atoms - extremely small particles that compose all matter
Electron - negatively charged subatomic particles
Protons - positively charged subatomic particles
Neutrons - neutrally charged subatomic particles
Atomic Number - defined by the number of protons; atoms with the same atomic number have similar chemical properties
Element - any substance that cannot be broken down to any other substance
Atomic Mass - the sum of the masses of its protons and neutrons
Orbitals - positive charges in the nucleus are neutralized by negatively charged electrons located in regions
Dalton - measurement of the mass of atom and subatomic particles
Ions - charged particles
Cations - positive charge; lost an electron
Anions - negative charge; gained an electron
Isotopes - atoms of a single element that possess different numbers of neutrons
Oxidation - the loss of an electron
Reduction - the gain of an electron
Inert - elements possessing all eight electrons in their outer energy level; nonreactive
Compound - a molecule that contains more than one element
Ionic bonds - forms when atoms with opposite charges attract
Covalent bonds - when two atoms share one or more pairs of valence electrons

Properties of Water
• Polar ( + and - ends)
• Cohesive due to hydrogen bonds
• Liquid at Earth's normal temperature
• Forms solutions with solutes (ions, polar molecules)
• Non-polar substances are repelled by water (hydrophobic)
• Solid form (ice) is less dense than liquid
o Bodies of water freeze from surface down
o Freezes in crystalline pattern - allows for spaces in between molecules - less dense
• Relatively high specific heat
o relatively stable
o requires a lot of energy to change temperature
• Vaporization at relatively high temperatures
o H bonds keep molecules stuck together
• Adhesion - attraction to other molecules
o Capillary action - water travels up (against gravity) through veins and roots

Chapter Three: The Chemical Building Blocks of Life

Macromolecules - polymers which consist of long chains of similar subunits
Living systems are made up of four main types of macromolecules - carbohydrates, nucleic acids, proteins (amino acids),
and lipids
Dehydration - removal of OH and a H; removal of a water molecule
Hydrolysis - addition of water molecule, breaking the bond
Carbon:
can form four covalent bonds
and hydrogen have similar electronegativity
Isonomer - molecules that have the same formula but different structure;
structural isonomers differ in structure while sterioisonomers differ in how the structural groups are attached

Carbohydrates - group of molecules that contain carbon, hydrogen and oxygen (1:2:1 ratio)
most important energy-storage molecules
Monosaccharides - simple sugars; glucose, fructose, galactose; contain three to six carbon atoms
Disaccharides - serve as transport molecules; two monosaccarides; effective reservoirs of glucose; sucrose (glucose +
fructose) lactose (glucose + galactose) and maltose
Polysaccharides - long polymers of monosaccharides; starch (storage polysaccharide), cellulose (structural
polysaccharide); amylose & glycogen are starches
chitin - modified form of cellulose
starches - insoluble polysaccharides

Nucleic Acids -
information-carrying devices of cells; a chain of nucleotides linked together by phosphodiester bonds with a nitrogenous
base protruding from each sugars
ex: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
DNA - encodes the genetic information used to assemble proteins
double helix form
RNA - reads the cell's DNA-encoded information and directs synthesis of proteins
Nucleotides - consists of a pentose (five-carbon sugar), a phosphate group, and an organic nitrogenous base

Proteins -
Enzyme catalysis - facilitate specific chemical reactions by stressing chemical bonds
ex: polymerases
Defense - use their shapes to recognize foreign microbes
ex: snake venom
Transport - transports small molecules or ions
ex: hemoglobin (transport iron)
Support - fibers that retain structure
ex: collagen
Motion - contraction through a sliding motion between two kinds of protein filaments
ex: actin and myosin
Regulation - hormones which serve as intercellular messengers; turn on and shut off genes during development
ex: insulin
Storage - binding ions to storage proteins
ex: ferritin and casein; calcium
Amino acids - contain an amino group (out of twenty different aminos) and a carboxyl group with an additional hydrogen
and a functional side group (R)
Amino Acids have Five chemical classes:
Nonpolar amino acids (leucine)
Polar uncharged amino acids (threonine)
Charged amino acids; contains acid or bases that can ionize
Aromatic amino acids (phenylalanine); usually nonpolar
Special function amino acids (methionine)
Peptide bond - covalent bond that links two amino acids
Polypeptide - a chain of amino acids
Protein structure is defined by the following hierarchy:
Primary - refers to amino acid sequence
Secondary - based on hydrogen-bonding patterns that can create helices or planar sheets
Tertiary - refers to the three-dimensional folded shape
Quaternary - formed by the association of two or more polypeptides
Domains - functional units within a larger structure of proteins
exons - sometimes encode functional domains of a protein
Denaturation - the protein's environment is altered and the protein may change its shape or even unfold
Dissociation - the reversible separation of protein subunits from quaternary structure without altering their tertiary
structure

Lipids - group of molecules that are insoluble in water; high proportion of nonpolar carbon-hydrogen bonds
Triglycerides - a glycerol with three fatty acid chains
Saturated - all the internal carbon atoms in the fatty acid chains are bonded to at least two hydrogens
Unsaturated - fatty acid chain that has double bonds between one or more pairs of successive carbon atoms
Polyunsaturated - fatty acid chains with more than one double bond
Phospholipids naturally form biological membranes due to the nonpolarity of the fatty acid chains

Chapter Four: Cell Structure

Cell Theory -
All organisms are composed of one or more cells, and the life processes of metabolism and heredity occur within these
cells.
Cells are the smallest living things, the basic units of organization of all organisms.
Cells arise only by division of a previously existing cell.
*No additional cells are originating spontaneously at present time (constant since beginning of earth)
Eukaryotic cell is typically 10 to 100 micrometers; prokaryotic cell is typically 1-10 micrometers
Rate of diffusion is affected by:
surface area
temperature
concentration gradient of diffusing substance
distance over which diffusion must occur
Larger cells need to synthesize more macromolecules, have correspondingly higher energy requirements, and produce a
higher quantity of waste
Surface Area-to-Volume Ratio - as size increases, volume increases more rapidly than surface area
All Cells -
bounded by a plasma membrane
filled with a semi-fluid substance called cytoplasm
genetic material found in the central portion of the cell (eukaryotic - is contained in a nucleus)
Prokaryotic Cells
some harvest light through photosynthesis, break down dead organisms, cause disease, etc.
small cells, surrounded by a plasma membrane and encased in a thick cell wall
cell wall is made of peptidoglycan - carbohydrate matrix (polymers of sugar)
protects cell
maintains the shape
prevents excessive intake or loss of water
contain ribosomes
lack cytoskeleton
contains no membrane-bounded organelles
has DNA, enzymes
reactions are not compartmentalized, the cell acts as a whole
can contain flagella - long, thread-like structures (protein fibers that rotate like a screw; flagella makes bacteria motile
Types of Bacteria Cells (Prokaryotic Cells)
Found using the Gram staining procedure
Gram-positive - have think, single layered peptidoglycan cell wall with violet dye
Gram-negative - more complex, multi-layered cell wall that does not retain violet dye; looks red
Archaea -
Difference from Bacteria -
nature of membrane lipids - can include saturated hydrocarbons that are covalently attached to glycerol, creating a
monolayer
create greater thermal stability
replication of DNA and synthesized proteins relate more to eukaryotics
Eukaryotic Cells -
have a extensive endomembrane system - weaves through cell interior and organelles (membrane-bounded ones)
in plant cells - contain a central vacuole (stores proteins, pigments or waste)
contain vesicles - smaller sacs for storage and transport materials
have nuclei; in the nucleus, the DNA is wound tightly around proteins to package into chromosomes
cytoskeleton - supported by an internal protein scaffold
can possess microvilli (finger-like projections), flagella or cilia
nucleolus - region where intensive synthesis of ribosomal RNA takes place
Nucleus - contains chromosomes is surrounded by a double membrane; contains the instruction for protein synthesis and
cell reproduction; contains genetic information
Chromosomes - long threads of DNA that form a protein complex; contains hereditary information used to direct the
synthesis of proteins
Nucleolus - site of genes for rRNA synthesis and ribosome assembly
Ribosomes - small complex assemblies of proteins and RNA; sites of protein synthesis
Endoplasmic reticulum - network of internal membranes; forms transport vesicles and participates in lipid synthesis and
synthesis of the membrane or secreted proteins
Golgi Apparatus - packages proteins for export
Lysosomes - digest worn-out organelles and cell debris; digest material taken in by endocytosis
Microbodies - isolate particular chemical activities from the rest of the cell
glyoxysomes - converts fats to carbohydrates in plant cells
peroxisomes - catalyze the removal of electrons and associated hydrogen molecules
Mitochondria - sites of oxidative metabolism; double-membraned
cristae - the folds of the inner membrane
matrix - inside of the inner membrane
intermembrane space
Chloroplasts - sites of photosynthesis; double membraned
grana - stacked disked membranes that lie in the inner membrane
thylakoids - one of the disks; the surface of the thylakoid contain the light-capturing photosynthetic pigments
Cytoskeleton - network of protein filaments to provide structural support and cell movement
actin filmaments - two chains of the globular protein actin; responsible for cellular movements as contraction, crawling...
microtubules - 13 protofilaments of alpha and beta tubulin subunits; provide organization to the cytoplasm; one positive
end and one negative end
intermediate filaments - stable and do not usually break down; cable-like
Centrioles - barrel-shaped organelles; organize microtubules and is responsible for the spindle reaction
centrosome - region surrounding the pair of centrioles
Kinesin - binds to vesicles and uses ATP to drag the vesicle to the peripherary of the cell
Dynein - binds to vesicles and uses ATP to drag the vesicle to the center of the cell
Flagella - cellular extensions with 9 + 2 arrangement of pairs of microtubules used for motility
Cell Wall - outer layer of chitin or cellulose to provide support and protection