Lecture 1

Biology The scientific study of life

Cell Theory All living things have cells, basic building block, all cells come from
other cells
Domain The classification of all tings into 3 different groups. Bacteria / Archaea /
Eukarya
Eukaryote Has a nucleus and is more complex
Evolution Happens when populations of organisms with inherited variations are
exposed to environmental factors that favor the success of some individuals over
others
Natural selection Explains the main mechanism whereby all species of
organisms change, or evolve
Prokaryote Has no nucleus and is less complex
Reductionism Reduce complex studies to study the simpler components
Science Is to know
Scientific Method Observation > Question > Hypothesis > Prediction > Test or
experiment
Lecture 2
Atom The smallest particle on and element, made up of protons, neutrons and
electrons
Chemical Bond - An attraction between two atoms, resulting from a sharing of
outer-shel electrons or the presence of opposite charges on the atoms. The bonded
atoms gain complete outer electron shells.
Chemical Reaction - A process leading to chemical changes in matter; involves the
making and/or breaking of chemical bonds.
Compound More than one element combined
Covalent Bond - A type of strong chemical bond in which two atoms share one or
more pairs of valence electrons.
Electron Shell A path whereby the electrons travel
Electron - A subatomic particle with a single negative charge. One or more
electrons move around the nucleus of an atom.
Element Is a substance that cannot be broken down to other substances by
ordinary chemical means.
Hydrogen Bond - A type of weak chemical bond formed when the slightly positive
hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly
negative atom of a polar covalent bond in another molecule.
Ion - An atom that has gained or lost electrons, thus acquiring a charge.
Ionic Bond - A chemical bond resulting from the attraction between oppositely
charge ions.
Isotope An element with more or less nuetrons
Molecular Formula - A type of molecular notation indicating only the quantity of
the constituent atoms. (Atoms present) example H20 has 2 hydrogens & 1 oxygen.
Molecule - Two or more atoms held together by covalent bonds.
Neutron - An electrically neutral particle (a particle having no electrical charge),
found in the nucleus of an atom.

Product - An ending material in a chemical reaction.

Proton - A subatomic particle with a single positive electrical charge, found in the
nucleus of an atom.
Reactant - A starting material in a chemical reaction.
Structural Formula - A type of molecular notation in which the constituent atoms
are joined by lines representing covalent bonds. (Shows bonds - these are covalent
bonds represented by a --) So H-H
Valence Last or outer
Lecture 3
Acid - A substance that increases the hydrogen ion concentration of a solution.
Adhesion - The attraction between different kinds of molecules. Clinging of one
substance to another
Base - A substance that reduces the hydrogen ion concentration of a solution.
Buffer - A substance that consists of acid and base forms in a solution and that
minimizes changes in pH when extraneous acids or bases are added to the solution.
Cohesion - The binding together of like molecules, often by hydrogen bonds.
Heat - The total amount of kinetic energy due to molecular motion in a body of
matter. Heat is energy in its most random form.
Hydrogen Ion - A single proton with a charge of 1+. The dissociation of a water
molecule (H2O) leads to the generation of hydroxide ion (OH-) and a hydrogen ion
(H+).
Hydrophilic - Any substance that has an affinity for water (Water-loving)These
substances are dominated by ionic or polar bonds.
Hydrophobic - Substances that have no affinity for water (Water-aversions).
Tending to coalesce and form droplets in water.
Molarity - A common measure of solute concentration, referring to the number of
moles of solute per liter of solution.
Mole (Mol) - Just like a dozen always = 12, Mole is always 6.02 x 10 (23)
(6200000000000000000000000)The number of grams of a substance that equals its
molecular weight in daltons and contains Avogadro's number of molecules.
pH - A measure of hydrogen ion concentration equal to -log [H+] and ranging in
value from 0 to 14.
Polar Molecule - A molecule (such as water) with opposite charges on opposite
sides.
Solute - A substance that is dissolved in a solution.
Solution - A liquid that is a homogeneous mixture of two or more substances.
Solvent - The dissolving agent of a solution. Water is the most versatile solvent
known.
Temperature - A measure of the intensity of heat in degrees, reflecting the average
kinetic energy of the molecules.
Lecture 4
Alcohol - Organic compounds with hydroxyl groups, names typically end in -ol.
Aldehyde - When the carbonyl group is on the end of the skeleton.
Amine - Organic compounds with amino groups.

Amino Group - A functional group that consists of a nitrogen atom bonded to two
hydrogen atoms; can act as a base in solution, accepting a hydrogen ion and
acquiring a charge of 1+.
Carbonyl Group - (=CO) consists of an oxygen atom joined to the carbon skeleton
by a double bond. A functional group present in aldehydes and ketones and
consisting of a carbon atom double-bonded to an oxygen atom.
Carboxyl Group - Consists of a carbon atom with a double bond with an oxygen
atom and a single bond to a hydroxyl groupA functional group present in organic
acids and consisting of a single carbon atom double-bonded to an oxygen atom and
also bonded to a hydroxyl group.
Carboxylic Acid - Compounds with carboxyl groups.
Enantiomer - molecules that are mirror images of each otherThey are like lefthanded and right-handed versions. Possible if there are four different atoms or
groups of atoms bonded to a carbon. Usually one if biologically active, and the other
inactive.
Functional Group - A specific configuration of atoms commonly attached to the
carbon skeletons of organic molecules and usually involved in chemical reactions.
Geometric Isomer - compounds with the same covalent partnerships that differ in
their spatial arrangement around a carbon-carbon double bond
Hydrocarbon - organic molecules that consist of only carbon and hydrogen atoms
Hydroxyl Group - A functional group consisting of a hydrogen atom joined to an
oxygen atom by a polar covalent bond. Molecules possessing this group are soluble
in water and are called alcohols.
Isomer - compounds that have the same molecular formula but different structures
and therefore different chemical properties.The three types of isomers are:
structural isomers, geometric isomers, and enantiomers.
Ketone - When the carbonyl group is NOT on the end of the skeleton.
Phosphate Group - A functional group important in energy transfer.
Structural Isomer - One of several organic compounds that have the same
molecular formula but differ in covalent arrangements of their atoms.
Sulfhydryl Group - A functional group consisting of a sulfur atom bonded to a
hydrogen atom (-SH).
Thiol - Organic molecules with sulfhydryl groups
Lecture 5
ATP - (Adenosine Triphosphate) An adenine-containing nucleoside triphosphate that
releases free energy when its phosphate bonds are hydrolyzed. This energy is used
to drive endergonic reactions in cells.
Amino Acid - An organic molecule possessing both carboxyl and amino groups.
Amino acids serve as the monomers of proteins.
Carbohydrate - A sugar (monosaccharide) or one of its dimers (disaccharides) or
polymers (polysaccharides)
Condensation Reaction - A reaction in which two molecules become covalently
bonded to each other through the loss of a small molecule, usually water; also called
a dehydration reaction.

Dehydration Reaction - A chemical reaction in which two molecules covalently

bond to each other with the removal of a water molecule.
Denaturation - In proteins, a process in which a protein unravels and loses its
native conformation, thereby becoming biologically inactive. In DNA, the separation
of the two strands of the double helix. Denaturation occurs under extreme
conditions of pH, salt concentration, and temperature.
Deoxyribonucleic Acid (DNA) - A double-stranded, helical nucleic acid molecule
capable of replicating and determining the inherited structure of a cell's proteins.
Deoxyribose - The sugar component of DNA, having one less hydroxyl group than
ribose, the sugar component of RNA
Disaccharide - A double sugar, consisting of two monosaccharides joined by
dehydration synthesis
Double Helix - The form of native DNA, referring to its two adjacent polynucleotide
strands wound into a spiral shape.
Fat - A biological compound consisting of three fatty acids linked to one glycerol
molecule
Fatty Acid - A long carbon chain carboxylic acid. Fatty acids vary in length and in
the number and location of double bonds; three fatty acids linked to a glycerol
molecule form fat.
Gene - A discrete unit of hereditary information consisting of a specific nucleotide
sequences in DNA (or RNA, in some viruses).
Glucose
Hydrolysis - A chemical process that lyses, or splits, molecules by the addition of
water.
Lipid - One of a family of compound, including fats, phospholipids, and steroids, that
are insoluble in water
Macromolecule - A giant molecule formed by the joining of smaller molecules,
usually by a condensation reaction. Polysaccharides, proteins, and nucleic acids are
macromolecules.
Monomer - The subunit that serves as the building block of a polymer
Monosaccharide - The simplest carbohydrate, active alone or serving as a
monomer for disaccharides and polysaccharides. Also known as simple sugars, the
molecular formulas of monosaccharides are generally some multiple of CH2O
Nucleic Acid - A polymer (polynucleotide) consisting of many nucleotide
monomers; serves as a blueprint for proteins and through the actions of proteins, for
all cellular activities. The two types are DNA and RNA
Nucleotide - The building block of a nucleic acid, consisting of a five-carbon sugar
covalently bonded to a nitrogenous base and a phosphate group.
Phospholipids - A molecule that is a constituent of the inner bilayer of biological
membranes, having a polar, hydrophilic head and a non-polar, hydrophobic tail.
Polymer - A long molecule consisting of many similar or identical monomers linked
together.
Polypeptide - A polymer (chain) of many amino acids linked together by peptide
bonds.
Polysaccharide - A polymer of up to over a thousand monosaccharides, formed by
dehydration reactions.

Protein - A three-dimensional biological polymer constructed from a set of 20

different monomers called amino acids.
Protein Primary - The primary structure of a protein is its unique sequence of
amino acids.- Lysozyme, an enzyme that attacks bacteria, consists on a polypeptide
chain of 129 amino acids.- The precise primary structure of a protein is determined
by inherited genetic information.
Protein Secondary - The secondary structure of a protein results from hydrogen
bonds at regular intervals along the polypeptide backbone.- Typical shapes that
develop from secondary structure are coils (an alpha helix) or folds (beta pleated
sheets).The structural properties of silk are due to beta pleated sheets.- The
presence of so many hydrogen bonds makes each silk fiber stronger than steel.
Protein Tertiary - Tertiary structure- the polypeptide continues to twist, fold and
orient itself, until it reaches the final shape:- a polypeptide subunit, is determined by
a variety of interactions among R groups and between R groups and the polypeptide
backbone.- These interactions include hydrogen bonds among polar and/or charged
areas, ionic bonds between charged R groups, and hydrophobic interactions and van
der Waals interactions among hydrophobic R groups.
Protein Quaternary - Quarternary structure results from the aggregation of two or
more polypeptide subunits.- Collagen is a fibrous protein of three polypeptides that
are supercoiled like a rope.This provides the structural strength for their role in
connective tissue.- Hemoglobin is a globular protein with two copies of two kinds of
polypeptides.A protein's conformation can change in response to the physical and
chemical conditions.Alterations in pH, salt concentration, temperature, or other
factors can unravel or denature a protein.- These forces disrupt the hydrogen bonds,
ionic bonds, and disulfide bridges that maintain the protein's shape.Some proteins
can return to their functional shape after denaturation, but others cannot, especially
in the crowded environment of the cell.
Purine - One of two types of nitrogenous bases found in nucleotides. Adenine (A)
and guanine (G) are purines.
Pyrimidine - One of two types of nitrogenous bases found in nucleotides. Cytosine
(C), Thymine (T), and Uracil (U) are pyrimidines.
Ribonucleic Acid (RNA) - A type of nucleic acid consisting of nucleotide monomers
with a ribose sugar and nitrogenous bases adenine (A), Cytosine (C), Guanine (G),
and Uracil (U); usually single-stranded; functions in protein synthesis and as the
genome of some viruses.
Ribose - The sugar component of RNA.
Steroids - A type of lipid characterized by carbon skeleton consisting of four rings
with various functional groups attached.
Lecture 6
Cell Wall - A protective layer external to the plasma membrane in plant cells,
prokaryotes, fungi, and some protists. In plant cells, the wall is formed of cellulose
fibers embedded in polysaccharide-protein matrix. The primary cell wall is thin and
flexible, whereas the secondary cell wall is stronger and more rigid and is the
primary constituent of wood.

Centriole - A structure in an animal cell composed of cylinders of microtubule

triplets arranged in a 9+0 pattern. An animal cell usually has a pair of centrioles
involved in cell division.
Centrosome - Material present in the cytoplasm of all eukaryotic cells, important
during cell division; the microtubule-organizing center.
Chloroplast - An organelle found only in plants and photosynthetic protists that
absorbs sunlight and uses it to drive the synthesis of organic compounds from
carbon dioxide and water.
Chromosome - A threadlike gene-carrying structure found in the nucleus. Each
chromosome consists of one very long DNA molecule and associated proteins.
Cilia - ...
Cytoplasm/Cytosol - Cytoplasm: The entire contents of the cell, exclusive of the
nucleus, and bounded by the plasma membrane. Cytosol: The semifluid portion of
the cytoplasm.
Cytoskeleton - A network of microtubules, microfilaments, and intermediate
filaments that branch throughout the cytoplasm and serve a variety of mechanical
and transport functions.
Desmosome - A typed of intercellular junction in animal cells that functions as an
anchor.
Endoplasmic Reticulum - An extensive membranous network in eukaryotic cells,
continuous with the outer nuclear membrane and composed of ribosome-studded
(rough) and ribosome-free (smooth) regions.
Extracellular Matrix - The substance in which animal tissue cells are embedded,
consisting of protein and polysaccharides.
Flagellum - A long cellular appendage specialized for locomotion. The flagella of
prokaryotes and eukaryotes differ in both structure and function.
Gap Junction - A type of intercellular junction in animal cells that allows the
passage of material or current between cells.
Glycoprotein - A protein covalently attached to a carbohydrate.
Golgi Apparatus - An organelle in eukaryotic cells consisting of stacks of flat
membranous sacs that modify, store, and route products of the endoplasmic
reticulum.
Intermediate Filament - A component of the cytoskeleton that includes all
filaments intermediate in sized between microtubules and microfilaments.
Light Microscope - An optical instrument with lenses that refract (bend) visible
light to magnify images of specimens.
Lysosome - A membrane-enclosed sac of hydrolytic enzymes found in the
cytoplasm of eukaryotic cells.
Microfilament - A solid rod of actin protein in the cytoplasm of almost all eukaryotic
cells, making up part of the cytoskeleton and acting alone or with myosin to cause
cell contraction.
Microtubule - A hollow rod of tubulin protein in the cytoplasm of al eukaryotic cells
and in cilia, flagella, and the cytoskeleton.
Mitochondria - An organelle in eukaryotic cells that serves as the site of cellular
respiration.

Nuclear Lamina - A netlike array of protein filaments that maintains the shape of
the nucleus.
Nucleolus - A specialized structure in the nucleus, formed from various
chromosomes and active in the synthesis of ribosomes.
Nucleus - An atom's central core, containing protons and neutrons. The
chromosome-containing organelle of a eukaryotic cell. A cluster of neurons.
Organelle - One of several formed bodies with specialized functions, suspended in
the cytoplasm of eukaryotic cells.
Peroxisome - A micro-body containing enzymes that transfer hydrogen from
various substrates to oxygen, producing and then degrading hydrogen peroxide.
Plasma Membrane - The membrane at the boundary of every cell that acts as a
selective barrier, thereby regulating the cell's chemical compositions.
Plasmodesmata - An open channel in the cell wall of a plant through which strands
of cytosol connect from an adjacent cell.
Prokaryotic Cell - A type of cell lacking a membrane-enclosed nucleus and
membrane-enclosed organelles. Organisms with prokaryotic cells (bacteria and
archaea) are called prokaryotes.
Ribosome - A cell organelle constructed in the nucleolus and functioning as the site
of protein synthesis in the cytoplasm; consists of RNA and protein molecules, which
make up two subunits. - Rough ER looks rough because ribosomes (bound
ribosomes) are attached to the outside, including the outside of the nuclear
envelope.
Rough ER - That portion of the endoplasmic reticulum studded with ribosomes.
Smooth ER - That portion of the endoplasmic reticulum that is free of ribosomes. Smooth ER looks smooth because it lacks ribosomes.
Tight Junction - A type of intercellular junction in animal cells that prevents the
leakage of material between cells.
Vacuole - ...
Vesicle - A sac made of membrane inside of cells.
Lecture 7
Active Transport - The movement of a substance across a biological membrane
against its concentration or electrochemical gradient with the help of energy input
and specific transport proteins.
Amphipathic Molecule - A molecule that has both a hydrophilic region and a
hydrophobic region.
Concentration Gradient - An increase or decrease in the density of a chemical
substance in an area. Cells often maintain concentration gradients of ions across
their membranes.
Cotransport - The coupling of the "downhill"diffusion of one substance to the
"uphill" transport of another against its own concentration gradient.
Diffusion - The spontaneous tendency of a substance to move down its
concentration gradient from a more concentrated to a less concentrated area.
Endocytosis - The cellular uptake of macromolecules and particulate substances by
localized regions of the plasma membrane that surround the substance and pinch off
to form an intracellular vesicle.

Exocytosis - The cellular secretion of macromolecules by the fusion of vesicles with

the plasma membrane.
Facilitated Diffusion - The spontaneous passage of molecules and ions, bound to
specific carrier proteins, across a biological membrane down their concentration
gradients.
Gated Channel - A protein channel in a cell membrane that opens or closes in
response to a particular stimulus.
Hypertonic Solution - In comparing two solutions, referring to the one with a
greater solute concentration.
Integral Protein - Typically a transmembrane protein with hydrophobic regions that
completely spans the hydrophobic interior of the membrane.
Isotonic Solutions - Having the same solute concentration as another solution.
Ligand - A molecule that binds specifically to a receptor site of another molecule
Osmosis - The diffusion of water across a selectively permeable membrane.
Passive Transport - The diffusion of a substance across a biological membrane.
Peripheral Protein - A protein appendage loosely bound to the surface of a
membrane and not embedded in the lipid bilayer.
Phagocytosis - A type of endocytosis involving large, particulate substances,
accomplished mainly by macrophages, neutrophils, and dendritic cells.
Pinocytosis - A type of endocytosis in which the cell ingests extracellular fluid and
its dissolved solutes.
Receptor-Mediated Endocytosis - The movement of specific molecules into a cell
by the inward budding of membranous vesicles containing proteins with receptor
sites specific to the molecules being take in; enables a cell to acquire bulk quantities
of specific substances.
Selective Permeability - A property of biological membranes that allows some
substances to cross more easily than others.
Sodium-Potassium Pump -A special transport protein in the plasma membrane of
animal cells that transport sodium out of the cell an potassium into the cell against
their concentration gradients.
Transport Protein - A transmembrane protein that helps a certain substance or
class of closely related substances to cross the membrane.