BIOL120 MIDTERM REVIEW NOTES
CHAPTER 1 – A PREVIEW OF A CELL
Latin word cellula meaning “little room”
Cell theory: all organisms consist of one or more cells; the cell is the basic
unit of structure for all organisms; all cells arise only from preexisting cells.
Electron microscope designs: transmission electron microscope (TEM)
“black and white sketched images” and scanning electron microscope (SEM)
Prokaryote: no nucleus, single celled organism, cell wall. Ex. Bacteria
Eukaryote: true nucleus, multicelled organism, cell wall depends. Ex protists.
Cytoplasm: everything between plasma membrane and nuclear membrane,
includes all membrane bound organelles.
Cytosol: fluid only component of cytoplasm.
Rough ER: wrapped around nucleus, studded with ribosomes, takes RNA
transcripts, proteins for export.
Smooth ER: synthesize lipids and steroids, metabolize carbohydrates and
steroids (but not lipids), and regulate calcium concentration, drug
metabolism and attachment of receptors on cell membrane proteins. Lacks
Golgi apparatus: collection, packing, distribution
Lysosomes: cell “stomachs”, enzymes to digest four macromolecules/worn
out organelles, material brought into cell by phagocytosis.
Mitochondria and chloroplasts contain DNA for some of their own proteins,
both have double layers of membranes.
Nucleus: dense core in centre, consists of protons, neutrons, membrane
CHAPTER 2 – WATER & CARBON: THE CHEMICAL BASIS OF LIFE
C, H, N, O make up 96% of all matter found in organisms.
Cohesion: binding between like molecules. Water molecules stay together
because of the hydrogen bonds that form between individual molecules.
Adhesion: binding between unlike molecules. Usually analyzed in regard to
interactions between a liquid and a solid surface, ie water adheres to
surfaces that have any polar or charged components.
Surface tension: makes water surface act as if it had an elastic membrane.
Acids are proton donors (increase [H+] in solution) and bases are proton
acceptors (decrease [H+] in solution). A chemical reaction that involves
transfer of protons is called an acid-base reaction. This is important because
the transfer of protons changes the charge of donor and acceptor, this means
the charge changes reactivity with respect to hydrogen bonding. Ex blood
pH = -log[H+]. [H+] = 10^-pH
Electrons in outer shells have more potential energy than do electrons in
inner shells, because negative charges in outer shells are farther from the positive charges in the nucleus. If the opportunity arises, an electron residing
in an outer electron shell will fall into a lower electron shell closer to the
positive charges of the protons in the nucleus.
Thermodynamics: relations between forms of energy, interconversions of
forms of energy. First Law of Thermodynamics: Energy can be transferred
and transformed but cannot be created or destroyed. Second Law of
Thermodynamics: energy tends to spontaneous disperse from being
localized, in order to become spread out or disordered. Entropy = disordered.
Exergonic reaction: results in net release of energy. Thermodynamically
favourable, spontaneous, energy used or lost as heat, less complex products.
Endergonic reaction: requires energy input, thermodynamically
unfavourable, more complex products.
Reactions tend to be spontaneous if the products have lower potential energy
than the reactants, or when the product molecules are less ordered than the
Reactions occur when reactants collide in a precise orientation and have
enough kinetic energy to overcome repulsion between electrons that come
into contact as bond forms.
Functional groups: in general, the carbon atoms in an organic molecule
furnish a skeleton that gives the molecule its overall shape. All behave
consistently. All are hydrophilic/polar.
Amino R-NH2. Acts as a base- tends to attract protons
Aldehyde R-C=O-H. React with compounds of form H-R2 to produce larger
Carboxyl R-C=0,-OH. Acts as an acid- tends to lose a proton.
Hydroxyl R-OH. Highly polar, makes compounds more soluble through
hydrogen bonding with water, also may act as weak acid and drop a proton.
Phosphate R-P-O-O-O=O. Breaking O-P bonds releases large amount of
Sulfhydryl R-SH. When present in proteins, can form disulfide (S-S) bonds
that contribute to protein structure.
CHAPTER 3 – PROTEIN STRUCTURE & FUNCTION
Proteins are made of 21 different amino acid building blocks, which all have a
common backbone structure: a central carbon bonded to an amino functional
group, a carboxyl, a hydrogen, and a R group (side chain).
The R groups vary – may be H, ring structure, contain carboxyl, sulfhydryl,
hydroxyl, or amino acid functional groups (more reactive). Affect solubility,
Non polar side chains: no charged or electronegative atoms to form hydrogen
bonds, not soluble, bury themselves in peptide chains to “hide” from water.
Charged polar side chains: partial charges form hydrogen bonds, soluble.
Uncharged polar side chains: contain acids or bases, soluble. Polymerization: the process of linking monomers. Amino acids polymerize to
Condensation/dehydration reactions: newly formed bond results in loss of
Hydrolysis: opposite of condensation/dehydration. Breaks polymers apart by
adding a water molecule. Dominates because it increases entropy and is
energetically favourable (lowers potential energy). This is why
polymerization reactions are expected to proceed slowly.
Peptide bond: Between a carboxyl group of one amino acid and the amino
group of another. Side chains are present, has directionality, flexible. End of
the sequence that has the free amino group is on the left and is called N-
terminus, and the end with the free carboxyl group appears on the right hand
side and is called the C-terminus.
Primary structure: polypeptide chain. Changes in primary structure affect
protein function: one single amino acid mutation causes a change. Ex sickle
cell anemia (abnormally shaped red blood cells). Caused by a single amino
acid mutation in hemoglobin.
Secondary structure: created in part by hydrogen bonding. Distinctively
shaped sections of proteins are stabilized largely by hydrogen bonding that
occurs between the carboxyl oxygen of one amino acid residue and the
hydrogen on the amino group of another. Created by interactions between
atoms that are part of the protein’s peptide bonded backbone. Alpha helix or
beta pleated sheet shape.
Tertiary structure: A result of interactions between R groups or between R
groups of the peptide backbone. Each contact between R groups causes the
peptide -bonded backbone to bend and fold in a precise way. Twisted, folded
and coiled polypeptides. Include interactions between alpha helices and
beta-pleated sheets. Four types of interactions: hydrogen bonds between
hydrogen atoms and carboxyl group/hydrogen and atoms with partial
negative charges in side chains. Van der Waals interactions, water molecules
interact with hydrophilic side chains and force hydrophobic side chains to
coalesce. Once hydrophobic side chains are close to each other, they are
stabilized by the electrical forces (van der Waals)- weak attracts occur
because the constant motion of electrons gives molecules a tiny asymmetry
in charge that changes with time. Covalent bonds form between sulfur atoms
when a reaction occurs between sulfur containing R groups (disulfide bonds
“bridges”). Ionic bonds form between groups that have full and opposing
charges. Tertiary structure depends on primary and secondary structure.
Quaternary structure: The combination of polypeptide subunits gives
proteins a quaternary structure. Based on tertiary structure, primary
structure. Produced by combinations of tertiary structures.
Folding may release enough free energy to be exergonic and occur
spontaneously. Proteins can unwind, or become denatured, by treating with
compounds (pH, salt concentration, temperature) that break hydrogen bonds
and disulfide bonds. Enzymes catalyze reactions. Catalysts lower activation energy of a reaction
and increases rate of reaction.
Enzymes bring reactant molecules called substrates together in precise
orientation so the electrons involved can interact.
A collision between reactants creates a combination of old and new bonds
called transition state.
Amount of free energy required to reach the transition state is called the
activation energy of the reaction. Reactions happen when reactants have
enough kinetic energy to reach the transition state. The Ek is a function of the
temperature; this is why reactions tend to proceed faster at higher
The location where substrates bind and react are the enzyme’s active site.
This is where the catalysis occurs.
Interactions with R groups at the active site stabilize the transition state and
thus lower the activation energy required for the reaction to proceed.
Enzyme cofactors, which can be metal ions or small organized molecules