Unit One: Chemistry of Life 

Structure of Water and Hydrogen Bonding 

➔ Polar molecule: opposite particle charges, hydrogen partially 
positive and oxygen partially negative, unequal distribution 
➔ Hydrophilic: affinity for water, attracts water, water loving 
➔ Hydrophobic: no affinity for water, avoids water 
➔ POLAR + POLAR 
NONPOLAR + NONPOLAR 
➔ Intermolecular bonds: between molecules 
◆ Hydrogen bonds: H bonds with FON 
◆ Give properties of cohesion, adhesion, surface tension, 
specific heat, and evaporative cooling 
➔ Cohesion: attraction of water molecules. Strong cohesive forces are 
present because they form hydrogen bonds with each other 
➔ Adhesion: one substance is attracted to another. Water adheres to 
other molecules. 
➔ Surface Tension: difficulty to break the surface of the water because 
of cohesive forces 
➔ Specific Heat: the amount of heat energy it takes to raise or lower 
the temperature of one gram of substance 1 degree Celsius 
➔ Evaporative Cooling: water has a high heat of vaporization, so the 
water can absorb a lot of heat and leave the surface cooler 
➔ Dissociation of water: ​Hydrogen shifts from one water molecule to 
another. When a molecule is increasing hydronium concentration by 
releasing hydrogen ions into solutions it is an ​acid. ​When a​ ​molecule 
is increasing hydroxide concentration by absorbing or accepting 
Hydrogen ions it is a ​base​.  
◆ PH scale range (0-14) acidic (<7) neutral (7), 
alkaline/basic (>7). Each 1 level on the PH scale is a 
ten-fold change. Most biological fluids are in the range 6-8. 
pH = −log [H+] 
Elements of Life 
➔ An element's properties are retained by the smallest unit of mass 
called an atom. Protons, neutrons, and elections make up atoms.  
➔ The atomic number is the number of protons in the nucleus and the 
atomic mass number is the sum of the protons and neutrons. 
➔ Isotopes: two atoms of an element that have a different number of 
neutrons 
◆ Radioactive isotopes: decay spontaneously and release 
energy 
➔ An electron’s potential energy is called an energy level or election 
shell  
 ➔ Carbon is the building block of the major macromolecules/organic 
molecules 
◆ Tetra-valence 
◆ 4 valence electrons; octet rule 
➔ Functional Groups 
◆ Hydroxyl  
◆ Carbonyl 
◆ Amino Group 
◆ Phosphate Group 
◆ Sulfhydryl Group 
Introduction to Biological Macromolecules 
➔ Covalent: sharing elections; single v. double v. trible bonds 
◆ Structural formula: two longs connecting two atoms 
➔ Electronegativity: atom’s attraction for electrons in covalent bonds.  
➔ Ionic: transfer of electrons/electrostatic attractions between a 
positive and negative ion.  
➔ Metallic Bonds: the attractions between metal ions and delocalized 
electrons 
➔ Polymer: a long molecule composed of many molecules bonded 
together covalently, composed of monomers  
◆ Lipids do not form polymers 
➔ Monomer: small building block molecules that, when combined, make 
a polymer 
➔ Covalent Bonds 
◆ Nonpolar covalent bond: the equal sharing of electrons and 
distribution of charge 
◆ Polar covalent bond: unequal sharing of electrons and 
distribution of charges which causes a partial positive and 
partial negative charge  
◆ Intra v inter molecule bonds 
➔ Dehydration Synthesis: monomers combine to form a polymer 
through a reaction after water is removed.  
➔ Hydrolysis: occurs when polymers are broken down into monomers 
through a reaction due to the addition of water.  
Properties of Biological Macromolecules 
➔ Macromolecules: large molecules composed of two or more polymers 
combined together 
➔ Carbohydrates: sugars and polymers of sugars 
◆ Multiple hydroxyl groups and a carbonyl group 
◆ Monosaccharide: simple sugar, formula that is a multiple of 
CH2O (1:2:1).  
➔ Lipid: the only class of macromolecules that DO NOT form polymers 
◆ Nonpolar and hydrophobic 
◆ Fats: glycerol and three fatty acids joined by an ester bond 
→ triglyceride/triacylglycerol 
◆ Glycerol: three carbon alcohol with a hydroxyl group 
 attached to each carbon 
◆ Fatty acid: long chains of carbon attached to a carboxyl 
group and can be saturated or unsaturated 
● Saturated: no double bonds between carbon atoms, 
saturated with hydrogen atoms; solid at room 
temperature 
● Unsaturated: one or more double bonds and/or 
triple bonds between the carbon atoms; liquid at 
room temperature 
◆ Phospholipids: one of the fatty acids of a triglyceride, 
replaced by a phosphate group 
◆ Steroid: a carbon skeleton made up of 4 fused rings 
● Ex: cholesterol 
➔ Proteins: make up of 20 different monomer amino acids joined by 
peptide bonds, which are covalent bonds 
◆ A slight change at the primary stage can lead to the change 
in both a protein’s structure and functions 
◆ When two amino acids are joined together by dehydration 
synthesis, it is called a dipeptide.  
◆ Polymers of amino acids are polypeptides and are formed 
when many amino acids are joined together 
◆ The folding of one or more polypeptides forms a protein 
◆ Some are polar, nonpolar, acidic, and/or basic 
Structure and Function of Biological Macromolecules 
➔ Disaccharide: two monosaccharides joined together by a covalent 
bond through dehydration synthesis  
◆ Maltose 
◆ Sucrose 
◆ Lactose 
➔ The covalent bond that the monosaccharides are joined together by 
is called a glycosidic bonds, forming disaccharides and 
polysaccharides 
➔ Polysaccharides: polymers of sugars that have functions of storage 
and structure which are determined by the positions of glycosidic 
bonds and the monomers in the sugar polymers 
◆ Starch & Glycogen: storage 
◆ Cellulose & Chitin: structural 
 
 
 
 
 
 
 
➔ Levels of Protein Structure 
◆ Primary Structure: a sequence of amino acids, peptide 
 bonds 
◆ Secondary Structure: the result of hydrogen bonding 
between the components of the polypeptide backbone, the 
carboxyl and amino functional groups along the peptide 
chain forming alpha helix or beta-pleated sheets 
◆ Tertiary Structure: the results of interactions between the 
alpha-helix and beta-pleated sheets 
◆ Quaternary Structure: interactions between two or more 
polypeptides chains forming a multi-subunit protein 
➔ Denaturation: proteins are broken down by heat, acids, and high ion 
concentrations, therefore becomes an inactive form of protein 
because it loses is structions 
◆ Sickle-cell disease 
Nucleic Acids 
➔ Nucleic acids: polymers that store, transmit and help express 
hereditary information 
◆ Monomers of nucleic acids are nucleotides → made up of a 
5 carbon sugar, nitrogenous base, and a phosphate group 
➔ Deoxyribonucleic Acid: DNA; genetic material 
◆ Directs its own replication and controls protein synthesis 
➔ DNA 
◆ Deoxyribose 
◆ Double helix 
◆ Sugar phosphate backbone that keeps the nucleotides 
connected with the strand 
➔ RNA 
◆ Ribose  
◆ Single stranded  
◆ A sugar phosphate backbone 
◆ mRNA, tRNA, and rRNA 
➔ Purines and Pyrimidines: two types of nitrogenous bases 
◆ Purines: adenine, guanine; contain a double ring structure 
◆ Pyrimidines: thymine, cytosine, uracil; single ring 
structure 
➔ Chargaff’s Rule 
◆ Adenine pairs with thymine; two hydrogen bonds when 
pairing bases 
◆ Guanine pairs with cytosine; three hydrogen bonds when 
pairing bases 
Unit Two: Cell Structure and Function 
➔ Two types of cells 
◆ Eukaryotic  
◆ Prokaryotic 
Subcellular Components and Function 
➔ Ribosomes: made up of primarily rNA (ribosomal RNA); site of 
translation and are responsible for making all of the proteins for 
 the cell. Ribosomes synthesize proteins according to mRNA 
sequences that they receive during the process of translation 
◆ Free ribosomes: cytosol and make proteins that stay in the 
cell for various functions  
◆ Bound ribosomes: attached to the rough endoplasmic 
reticulum and mainly make proteins for export 
➔ Endoplasmic Reticulum: made up of two parts to serve to make other 
products that the cell needs 
◆ Smooth ER: performs the synthesis of lipids, metabolism of 
carbohydrates, detoxification of drugs and poisons, and 
stores calcium ions 
◆ Rough ER: secretes proteins made by bound ribosomes 
◆ Proteins are moved to the transitional ER, where they are 
wrapped in a transport vesicle to head to the golgi 
apparatus 
➔ Golgi Apparatus: modifies, stores, and sends proteins that come 
from the rough ER 
◆ Glycoproteins are modified 
◆ Two sides on the golgi apparatus, cis and trans face. 
Vesicles enter the golgi apparatus vis the cis face and 
depart via the trans face.  
➔ Mitochondria: double membrane, which is a phospholipid bilayer; 
outer membrane is smooth, while the inner has many folds, called 
cristae. The folds help increase the surface area available for the 
electron transport chain.  
◆ The inside of the inner membrane is called the 
mitochondrial matrix, which is the site of the Krebs Cycle 
◆ Creates ATP for the cell to use via cellular respiration 
◆ Have their own circular DNA 
➔ Lysosomes: hydrolyze most foods, amino acids, and other molecules 
◆ Inner side is extremely acidic 
◆ Digest foods by using phagocytosis or engulfing nutrients 
to digest them 
◆ Hydrolytic enzymes work to break down anything that 
comes into contact with it.  
◆ Used to recycle and digest old or damaged parts.  
◆ Keep hydrolytic enzymes in 
➔ Vacuoles: large vesicles that store many different things, such as 
food or water 
◆ Unicellular eukaryotes have contractile vacuoles to pump 
water out of the cell 
◆ Plants have a large central water vacuole which stores 
water and ions 
➔ Chloroplast: site of photosynthesis 
◆ Have a double membrane and green pigments called 
chlorophyll that allow for the absorption of photons 
 ◆ Made up of the stroma, or liquid filling of the chloroplast, 
and the thylakoids, flat sacs of membranes that allow for 
the absorption of light.  
➔ Plasma Membrane 
◆ Semi permeable 
◆ Allows for the creation of a concentration gradient 
Cell Size 
➔ The cells need to maintain a small size in order to have the 
maximum amount of space for the transfer of nutrients and waste 
within the smallest volume of cell. 
➔ As the volume increases, the cell will need more and more nutrients 
to enter, and the higher the surface area, the more nutrients can 
enter.  
➔ The greater the surface area to volume ratio, the more efficient the 
cell becomes 
Plasma Membrane 
➔ Phospholipid bilayer 
◆ Hydrophobic tail: fatty acids, face inward and do not 
interact with water 
◆ Hydrophilic head: comprised of a phosphate group, face the 
outside and inside of the cell, where water is present 
➔ Has glycoproteins and glycolipids 
➔ Given the name: fluid mosaic model; the membrane is fluid and 
somewhat moveable, the proteins embedded in the membrane, which 
serve a variety of functions, create the mosaic portion of the name 
Membrane Permeability 
➔ Selectively permeable; allows some substance to cross easily, while 
others may not be able to cross or may require a special transport 
protein to do so 
◆ Small, non-polar molecules are able to freely cross the 
membrane, while polar or charged molecules require 
transport proteins to cross 
◆ The hydrophobic fatty acids tails are what controls the 
movement of substances; repel charged and polar 
molecules and make it very challenging for them to come 
across 
Membrane Transport 
➔ Simple diffusion: a possessive (no energy) movement of a substance 
from an area of higher concentration to lower concentration. With 
no energy needed, a substance will diffuse down its concentration 
gradient, until equilibrium occurs → passive transport 
➔ Passive transport: large role in getting rid of wastes, importing 
other needed materials. Carbon dioxide and oxygen gas frequently 
rely on simple diffusion in order to enter and exit the membrane 
➔ Facilitated diffusion: a possessive movement of a substance from an 
area of higher to lower concentration, no energy is required for this 
 movement, but a transport protein is needed in order for the 
substance to get across the membrane 
◆ Used by small polar molecule who cannot get across the 
membrane without a transport protein  
◆ When water uses facilitated diffusion, it is called osmosis. 
➔ Active transport: uses energy in the form of ATP to transport 
materials against their concentration gradient. Because of the 
selective permeability of the membrane, concentration gradients 
can form 
◆ May be used for large or bulky molecules or to transport 
large quantities of small molecules → exocytosis and 
endocytosis 
➔ Endocytosis: when a large amount of molecules are entering a cell; 
three kinds 
◆ Phagocytosis: the cell engulfs a large molecule and brings 
it into the cell 
◆ Pinocytosis: the cell “gulps” the surrounding solutes into 
small vesicles that are covered in a layer of protein 
◆ Receptor-Mediated Endocytosis: a receptor binds to a cell. 
When solute binds to the receptor, the plasmid pulls away 
creating a vesicle with the solutes 
➔ Exocytosis: when molecules are secreted from the cell 
◆ A transport vesicle from the golgi apparatus moves along 
the microtubules in the cell unit until it reaches the plasma 
membrane. Then the vesicle fuses with the plasma 
membrane, releasing the contents out of the cell. 
Facilitated Diffusion 
➔ When molecules cannot move easily through the plasma membrane, 
facilitated diffusion occurs. Molecules cannot pass through the 
phospholipid bilayer of the plasma membrane easily when the 
particles are either chargers or polar. 
➔ Facilitated diffusion: form of passive transport which does NOT 
require energy 
➔ Passive transport: occurs when molecules go down the concentration 
gradient 
➔ A concentration gradient is when particles of solute move from a 
highly concentrated area of particles to a less concentrated area of 
particles. This process is aided by proteins located on the plasma 
membrane (membrane proteins) such as transport proteins. 
➔ Channel Proteins: laid throughout the membrane to provide a 
hydrophilic passage through for the molecules to avoid the 
hydrophobic core 
◆ Aquaporins: allow water to diffuse through the membrane; 
essential for plant cells, red blood cells, etc.  
◆ Nerve and muscle cells have gated ion channel proteins to 
enable the flow of charged ions such as sodium and 
 potassium present in the sodium potassium pump of action 
potentials. If a signal such as an electrical signal is 
activated, these channels open their gate to transmit these 
signals through cells. 
➔ Carrier Proteins: alter their shape to allow the flow of molecules 
through the concentration gradient of the membrane similarly to an 
enzyme substrate complex.  
◆ Rate of transport is slower than that of channel proteins 
◆ Provide an easier way for hydrophilic molecules to pass 
through the concentration gradient  
Tonicity and Osmoregulation 
➔ Hypotonic: solution that has less solute than the inside of the cell; 
water will move to where there is more solute, causing the cell to 
expand 
➔ Hypertonic: solution that has more solute in it than there is inside of 
the cell; water will move to where there is more solute, causing the 
water to move outside of the cell, making it shrink 
➔ Isotonic: equal solute in and outside of the cell 
➔ Osmosis: water will attempt to move from an area of high 
concentration to an area of low concentration until there are equal 
amounts of water on both sides of the membrane; allows organisms 
to control their internal solute composition and water potential 
Cell Compartmentalization 
➔ One of the major difference between eukaryotes and prokaryotes is 
the eukaryotes compartmentalize their internal processes in 
membrane-bound organelles 
➔ In eukaryotic cells, after RNA is made from DNA in the process of 
transcription, it moves to the ribosome to go through the process of 
translation. The RNA has to move out of the nucleus to either a 
free-standing ribosome or to the rough endoplasmic reticulum.  
➔ In prokaryotes, RNA is converted to proteins right after being made 
from DNA, as they do not have a nucleus or endoplasmic reticulum. 
This will lead to more differences in transcription and translation, 
which will be discussed in a later unit. 
➔ By reducing the amount of competing space and surface area, and 
also reducing the amount of competing reactions, eukaryotic cells 
are able to be more efficient than prokaryotic cells. 
Origins of Cell Compartmentalization 
➔ Endosymbiotic theory: the current theory of how eukaryotic 
membrane-bound organelles existed in eukaryotic cells 
◆ States that an early ancestor of eukaryotic cells engulfed a 
prokaryotic cell, and the prokaryotic became an 
endosymbiont, a cell living in another cell. These smaller 
cells were capable of producing extra energy for the other 
cell, leading to a selective advantage 
◆ Overtime, cells with an extra cell inside were able to 
 become more able to survive and reproduce quickly 
◆ While prokaryotes generally lack internal membrane bound 
organelles, they still have internal regions with specialized 
structures and functions. These regions are just not 
defined by outer membranes. 

 
 
Other Info On Quarterly 
➔ negative feedback loops (stabilization): brings you closer to the target setpoint; positive feedback loops (amplification): moving away 
from the target setpoint 
➔ Example of positive feedback: release of oxytocin during childbirth which opens up walls for contractions 
➔ Another type of inhibition is one where the inhibitor binds to the allosteric site, but without blocking the active site. This results in a 
change of the active site's shape. 
➔ Action potentials are the unequal distribution of sodium and potassium ions to transmit signals throughout the nervous system. 
➔ Quorum Sensing is when bacteria activate a certain behavior due to sensing population density using signalling molecules and 
receptors 
➔ Cell Signaling 1. signal 2. receptor 3. Response 
➔ Allosteric sites have a separate site from the active site where substrates bind. 
➔ Amphipathic molecules are molecules with both a hydrophobic and hydrophilic region. 
➔ Hormones are used for long distance communication while neurotransmitters are used for shorter distance communication.