“How Do I Get a Good Bio Score on the DAT?” 

 
Easy - use all of DAT Bootcamp’s biology resources together. 

1. The Bootcamp Bio Notes (what you’re reading now) is a concise, comprehensive bio 
resource that is easy to print off and study from. It assumes you have a background 
in bio. It covers all the high-yield DAT biology concepts in 120 pages. 
2. Bootcamp’s Bio Academy covers the same information as the Bio Notes, but is 
more explanatory, goes into more details, and includes illustrations and videos. If 
you’re rusty on a chapter and need more information, I recommend these. 
3. Bootcamp Bio Flashcards + Chrome extension - these are great for getting a little 
more bio in each day. 
4. DAT Bootcamp Bio Question Bank - Do these after reviewing a chapter, read the 
explanations, and watch the videos.  
5. DAT Bootcamp Bio Practice Tests - Use these at the end to tie everything together. 

You can read more about using the Bootcamp Bio Notes together with Bio Academy here. 
Using all these resources together will help you get a good score in bio 

“Lastly, I want Bootcamp to be perfect for you”

If you have any feedback or questions, please email us at [email protected]! Your 

feedback is invaluable to improving these notes for future generations of pre-dental 
students.  

Happy studying! 😃 

- Ari and the DAT Bootcamp team   

 

Table of Contents 
 
Chapter 1: Molecules and Fundamentals of Biology 3

Chapter 2: Cells and Organelles 8

Chapter 3: Cellular Energy 13

Chapter 4: Photosynthesis 20

Chapter 5: Cell Division 23

Chapter 6: Molecular Genetics 29

Chapter 7: Heredity 37

Chapter 8: Microscopy & Lab Techniques 45

Chapter 9: Diversity of Life 50

Chapter 10: Plants 60

Chapter 11.1: Circulatory System 66

Chapter 11.2: Respiratory System 71

Chapter 11.3: Human Immune System 77

Chapter 11.4: Nervous System 81

Chapter 11.5: Muscular System 87

Chapter 11.6: Skeletal System 90

Chapter 11.7: Endocrine System 93

Chapter 11.8: Digestive System 98

Chapter 11.9: Excretory System 101

Chapter 11.10: Integumentary System 103

Chapter 12: Reproduction and Developmental Biology 104

Chapter 13: Evolution 111

Chapter 14: Ecology 116

Chapter 15: Animal Behavior 120

 

   

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Chapter 1: Molecules and Fundamentals of  Memorize: 

Biology   
  ● Ribose - a five carbon monosaccharide. 
Table of Contents   ● Fructose - a six carbon monosaccharide. 
  ● Glucose - a six carbon monosaccharide. 
● Biological Chemistry   ● Glucose and fructose are isomers of each 
● Carbohydrates   other (same chemical formula, different 
● Proteins   arrangement of atoms). 
● Lipids    
● Nucleic Acids   Disaccharides contain two monosaccharides 
● Biological Hypothesis and Theories  joined together by a glycosidic bond. It is the 
  result of a dehydration (condensation) reaction, 
Biological Chemistry  where a water molecule leaves and a covalent 
  bond forms. A hydrolysis reaction is the 
Basic terminology:  opposite, through which a covalent bond is broken 
  by the addition of water.  
● Matter - anything that takes up space and has   
mass.   Memorize: 
● Element - a pure substance that has specific   
physical/chemical properties and can’t be  ● Sucrose - disaccharide made of glucose + 
broken down into a simpler substance.  fructose. 
● Atom - the smallest unit of matter that still  ● Lactose - disaccharide made of galactose + 
retains the chemical properties of the element.  glucose.. 
● Molecule - two or more atoms joined together.  ● Maltose - disaccharide made of glucose + 
● Intramolecular forces - attractive forces that  glucose.  
act on atoms within a molecule.   
● Intermolecular forces - forces that exist  Polysaccharides contain multiple 
between molecules and affect physical  monosaccharides connected by glycosidic bonds 
properties of the substance.   to form long polymers.  
● Monomers - single molecules that can   
potentially polymerize.  Memorize: 
● Polymers - substances made up of many   
monomers joined together in chains.  ● Starch - form of energy storage for plants and 
  is an alpha (α) bonded polysaccharide. Linear 
Carbohydrates  starch is called amylose; the branched form is 
  amylopectin. 
Carbohydrates contain carbon, hydrogen, and  ● Glycogen - form of energy storage for humans 
oxygen atoms (CHO). They can come in the form  and is an alpha (α) bonded polysaccharide. It 
of monosaccharides, disaccharides, and  has much more branching than starch. 
polysaccharides.  
 
Monosaccharides are carbohydrate monomers 
with an empirical formula of (CH2O)n. “n” 
represents the number of carbons.  
 
   

 
Adapted from: https://commons.wikimedia.org/w/index.php?curid=30131154 
 
   

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● Cellulose - structural component in plant cell  Protein structure: 

walls, and is a beta (β) bonded polysaccharide.   
Linear strands packed rigidly in parallel.  1. Primary structure - sequence of a.a.. 
● Chitin - structural component in fungi cell walls  2. Secondary structure - intermolecular forces 
and insect exoskeletons. It is a beta (β)  between the polypeptide backbone (not 
bonded polysaccharide with nitrogen added  R-groups) due to hydrogen bonding. Forms 
to each monomer.   α-helices or β-pleated sheets. 
  3. Tertiary structure - three-dimensional 
Proteins  structure due to interactions between R-groups. 
  Can create hydrophobic or hydrophilic 
Proteins contain carbon, hydrogen, oxygen, and  spaces based on the R-groups. Disulfide 
nitrogen atoms (CHON). These atoms combine to  bonds are created by covalent bonding 
form amino acids, which link together to build  between the R-groups of two cysteine a.a.’s. 
polypeptides (or proteins). A proteome refers to  4. Quaternary structure - multiple polypeptide 
all the proteins expressed by one type of cell  chains come together to form one protein. 
under one set of conditions.    
  Proteins can also be classified based on structure 
Amino acids (a.a.) are the monomers of proteins  as fibrous, globular, or intermediate. When 
and have the structure shown below:  looking at protein composition, they can be simple 
  (amino acids only) or conjugated (amino acids + 
other components).  
 
Protein denaturation describes the loss of 
protein function and higher order structures. Only 
the primary structure is unaffected. Proteins will 
denature as a result of high or low 
temperatures, pH changes, and salt 
concentrations. For example, cooking an egg in 
 
high heat will disrupt the intermolecular forces in 
Adapted from: https://commons.wikimedia.org/w/index.php?curid=41348719 
  the egg’s proteins, causing it to coagulate. 
There are twenty different kinds of amino acids,   
each with a different “R-group”.  Protein functions: 
 
Polypeptides are polymers of amino acids and are 
joined by peptide bonds through dehydration 
(condensation) reactions. Hydrolysis reactions 
break peptide bonds. The polypeptide becomes an 
amino acid chain that contains two end terminals 
on opposite sides. 
 
The N-terminus (amino terminus) of a 
polypeptide is the side that ends with the last 
amino acid’s amino group.  
 
The C-terminus (carboxyl terminus) of a 
polypeptide is the side that ends with the last 
amino acid’s carboxyl group. 
 
   
     

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Catalysts increase reaction rates by lowering   

the activation energy of a reaction. The  An enzyme kinetics plot can be used to visualize 
transition state is the unstable conformation  how inhibitors affect enzymes. Below are a few 
between the reactants and the products. Catalysts  terms used to describe the plot: 
reduce the energy of the transition state. Catalysts   
do not shift a chemical reaction or affect  1. The x-axis represents substrate 
spontaneity.   concentration [X] while the y-axis represents 
  reaction rate or velocity (V).  
Enzymes act as biological catalysts by binding to  2. Vmax is the maximum reaction velocity. 
substrates (reactants) and converting them into  3. Michaelis Constant (KM) is the substrate 
products.   concentration [X] at which the velocity (V) is 
  50% of the maximum reaction velocity 
● Enzymes bind to substrates at an active site,  (Vmax). 
which is specific for the substrate that it acts  4. Saturation occurs when all active sites are 
upon. Most enzymes are proteins.  occupied, so the rate of reaction does not 
● The specificity constant measures how  increase anymore despite increasing substrate 
efficient an enzyme is at binding to the  concentration (causes graph plateaus). 
substrate and converting it to a product.   
● The induced fit theory describes how the  Competitive inhibition → KM increases, while Vmax 
active site molds itself and changes shape to fit  stays the same 
the substrate when it binds. The “lock and   
key” model is an outdated theory of how  Noncompetitive inhibition → KM stays the same, 
substrates bind.  while Vmax decreases 
● A ribozyme is an RNA molecule that can act   
as an enzyme (a non-protein enzyme). 
● A cofactor is a non-protein molecule that helps 
enzymes perform reactions. A coenzyme is an 
organic cofactor (i.e. vitamins). Inorganic 
cofactors are usually metal ions. 
● Holoenzymes are enzymes that are bound to 
their cofactors while apoenzymes are enzymes 
that are not bound to their cofactors. 
● Prosthetic groups are cofactors that are 
tightly or covalently bonded to their enzymes. 
● Protein enzymes are susceptible to 
denaturation. They require optimal 
temperatures and pH for function.   
  Adapted from: https://commons.wikimedia.org/w/index.php?curid=49924777 

Competitive inhibition occurs when a   

competitive inhibitor competes directly with the   
substrate for active site binding. The rate of   
enzyme action can be increased by adding more     
substrate. 
 
Noncompetitive inhibition occurs when the 
noncompetitive inhibitor binds to an allosteric 
site (a location on an enzyme that is different from 
the active site) that modifies the active site. In 
noncompetitive inhibition, the rate of enzyme 
action cannot be increased by adding more 
substrate.  

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Lipids  Cholesterol is also a lipid molecule that is a 

  component of the cell membranes and is 
Lipids contain carbon, hydrogen, and oxygen  amphipathic. It is the most common precursor to 
atoms (CHO), like carbohydrates. They have long  steroid hormones (lipids that have four 
hydrocarbon tails that make them very  hydrocarbon rings). Cholesterol is also the starting 
hydrophobic.   material for vitamin D and bile acids.  
   
Triacylglycerol (triglyceride) is a lipid molecule  Factors that influence membrane fluidity: 
with a glycerol backbone (three carbons and   
three hydroxyl groups) and three fatty acids (long  1. Temperature - ↑ temperatures increase 
hydrocarbon tails). Glycerol and the three fatty  fluidity while ↓ temperatures decrease it.  
acids are connected by ester linkages.  2. Cholesterol - holds membrane together at 
  high temperatures and keeps membrane fluid 
Saturated fatty acids have no double bonds and  at low temperatures. 
as a result pack tightly (solid at room temperature).   3. Degrees of unsaturation - saturated fatty 
  acids pack more tightly than unsaturated fatty 
Unsaturated fatty acids have double bonds.  acids, which have double bonds that may 
They can be divided into monounsaturated fatty  introduce kinks.  
acids (one double bond) and polyunsaturated   
fatty acids (two or more double bonds).  Lipoproteins allow the transport of lipid 
  molecules in the bloodstream due to an outer coat 
of phospholipids, cholesterol, and proteins.  
 
● Low-density lipoproteins (LDLs) - have low 
protein density and work to deliver cholesterol 
to peripheral tissues. Sometimes considered 
“Bad cholesterol” - can cause vessel blockage 
and heart disease. 
● High-density lipoproteins (HDLs) - have high 
protein density and take cholesterol away from 
peripheral tissues.Considered “Good 
cholesterol” because they deliver cholesterol 
to the liver to make bile (reduces blood lipid 
 
levels).  
https://commons.wikimedia.org/w/index.php?curid=5560145 
   
Cis-unsaturated fatty acids have kinks that cause  Waxes are simple lipids that have long fatty acid 
the hydrocarbon tails to bend. As a result, they do  chains connected to monohydroxy alcohols 
not pack tightly.  (contain a single hydroxyl group) through ester 
Trans-unsaturated fatty acids have straighter  linkages. Used mainly as hydrophobic protective 
hydrocarbon tails, so they pack tightly.  coatings. 
   
Phospholipids are lipid molecules that have a  Carotenoids are lipid derivatives containing long 
glycerol backbone, one phosphate group, and  carbon chains with conjugated double bonds and 
two fatty acid tails. The phosphate group is polar,  six-membered rings at each end. They function 
while the fatty acids are nonpolar. As a result, they  mainly as pigments. 
are amphipathic (both hydrophobic and 
hydrophilic). Furthermore, they spontaneously 
assemble to form lipid bilayers.  
 

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H-bond to T (using two hydrogen bonds) and G 

can only H-bond to C (using three hydrogen 
bonds). RNA is single-stranded after being copied 
from DNA during transcription. In RNA, U binds to 
A, replacing T. MicroRNA, or miRNA, are small RNA 
  molecules that can silence gene expression by 
Adapted from: https://commons.wikimedia.org/w/index.php?curid=1828495 and  base pairing to complementary sequences in 
 
https://commons.wikimedia.org/w/index.php?curid=4052606
  mRNA. 
Nucleic Acids   
  Fundamentals of Biology 
Nucleic acids contain carbon, hydrogen, oxygen,  Modern cell theory: 
nitrogen, and phosphorus atoms (CHONP). They   
contain nucleotide monomers that build into DNA  1. All lifeforms have one or more cells. 
(deoxyribonucleic acid) and RNA (ribonucleic  2. The cell is the basic structural, functional, and 
acid) polymers.   organizational unit of life. 
  3. All cells come from other cells (cell division). 
Nucleosides contain a five-carbon sugar and a  4. Genetic information is stored and passed down 
nitrogenous base. Nucleotides contain a  through DNA.  
five-carbon sugar, a nitrogenous base, and a  5. An organism’s activity is dependent on the total 
phosphate group.. Deoxyribose sugars (in DNA)  activity of its independent cells. 
have a hydrogen at the 2’ carbon while ribose  6. Metabolism and biochemistry (energy flow) 
five-carbon sugars (in RNA) have a hydroxyl group at  occurs within cells, 
the 2’ carbon.   7. All cells have the same chemical composition 
  within organisms of similar species. 
Adenine (A), thymine (T), cytosine (C), and   
guanine (G) are the nitrogenous bases found in  The central dogma of genetics states that 
DNA. The uracil (U) nucleotide replaces T in RNA.  information is passed from DNA → RNA → 
  proteins. There are a few exceptions to this (eg. 
A and G are purines that have a two-ringed  reverse transcriptase and prions). 
structure, while C, U, and T are pyrimidines that   
have a one-ringed structure.  The RNA World Hypothesis states that RNA 
  dominated Earth’s primordial soup before there 
PUR As Gold = PURines are Adenine and Guanine  was life. RNA developed self-replicating 
  mechanisms and later could catalyze reactions, 
CUT the PY = Cytosine, Uracil, and Thymine are  such as protein synthesis, to make more complex 
PYrimidines.  macromolecules. Since RNA is reactive and 
  unstable, DNA eventually became a better way of 
Phosphodiester bonds connect the phosphate  reliably storing genetic information. 
group of one nucleotide (at the 5’ carbon) to the   
hydroxyl group of another nucleotide (at the 3’    
carbon). A series of phosphodiester bonds create   
the sugar-phosphate backbone, with a 5’ end 
(free phosphate) and a 3’ end (free hydroxyl).  
Nucleic acid polymerization proceeds as 
nucleoside triphosphates are added to the 3’ end of 
the sugar-phosphate backbone. 
 
DNA is an antiparallel double helix, in which two 
complementary strands with opposite 
directionalities (positioning of 5’ ends and 3’ ends) 
twist around each other. Furthermore, A can only 

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Chapter 2: Cells and Organelles  Peripheral membrane proteins are found on the 
  outside of the bilayer, and they are generally 
Table of Contents   hydrophilic. Below are some possible functions: 
   
● Cell Membrane  ● Receptor - trigger secondary responses within 
● Crossing Cell Membranes  the cell for signaling. (Note: if a receptor 
● Organelles   proteins transmits a signal all the way through 
● Cytoskeleton  the lipid bilayer, it is considered an integral 
● Extracellular Matrix  protein) 
● Cellular Tonicity and Cell Circulation   ● Adhesion - attaches cells to other things (eg. 
  other cells) and act as anchors for the 
Cell Membrane  cytoskeleton. 
  ● Cellular recognition - proteins which have 
Cell membranes hold cellular contents and are  carbohydrate chains (glycoproteins). Used by 
mainly composed of phospholipids, cholesterol,  cells to recognize other cells.  
and proteins:   
  The fluid mosaic model describes how the 
1. Phospholipids - glycerol backbone, one  components that make up the cell membrane can 
phosphate group (hydrophilic), and two fatty  move freely within the membrane (“fluid”). 
acid tails (hydrophobic). Amphipathic  Furthermore, the cell membrane contains many 
because the molecules have both polar and  different kinds of structures (“mosaic”).  
nonpolar parts, allowing them to form a lipid   
bilayer in an aqueous environment.   The fluidity of the cell membrane can be affected 
  by:  
 
● Temperature - ↑ temperatures increase 
fluidity while ↓ temperatures decrease it.  
● Cholesterol - holds membrane together at 
high temperatures and keeps membrane fluid 
at low temperatures. 
● Degrees of unsaturation - saturated fatty 
acids pack more tightly than unsaturated fatty 
acids, which have double bonds that may 
  introduce kinks. Trans-unsaturated fatty acids 
https://commons.wikimedia.org/w/indeg.php?curid=30131169  pack more tightly than cis-unsaturated fatty 
  acids (which have a more severe kink).  
2. Cholesterol - has four fused hydrocarbon   
rings and is a precursor to steroid hormones. 
Also amphipathic and helps regulate 
membrane fluidity. 
3. Membrane proteins - are either integral or 
peripheral membrane proteins.  
 
Integral (transmembrane) proteins traverse the 
entire bilayer, so they must be amphipathic. Their 
nonpolar parts lie in the middle of the bilayer while 
their polar ends extend out into the aqueous 
environment on the inside and outside of the cell. 
Usually assist in cell signaling or transport. 
   
Adapted from: https://commons.wikimedia.org/w/index.php?curid=49923679 

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Crossing Cell Membranes 

 
Cells must regulate the travel of substances 
across the cell membrane. There are 3 types of 
transport across the cell membrane: 
 
1. Simple diffusion - flow of small, uncharged, 
nonpolar substances (eg. O2 and CO2) across 
the cell membrane down their concentration 
gradient (high to low) without using energy.   
● Osmosis is a type of simple diffusion that 
involves water molecules (water is polar, 
but is small enough to cross the 
membrane).   
2. Facilitated transport - integral proteins allow   
larger, hydrophilic molecules to cross the cell  ● Secondary active transport uses free 
membrane.   energy released when other molecules 
● These proteins can be uniporters (single  flow down their concentration gradient 
substance, single direction), symporters  (gradient established by primary active 
(two substances, same direction), or  transport) to pump the molecule of interest 
antiporters (two substances, opposite  across the membrane.  
directions).    
● Also, they can also be classified as channel  Cytosis refers to the bulk transport of large, 
proteins (open tunnels that face both sides  hydrophilic molecules across the cell membrane 
of bilayer) and carrier proteins (bind to  and requires energy (active transport 
molecule on one side and changes shape to  mechanism).  
bring it to the other side).    
● Passive diffusion is a type of facilitated  Endocytosis involves the cell membrane wrapping 
transport that is performed by channel  around an extracellular substance, internalizing it 
proteins, bringing molecules down their  into the cell via a vesicle or vacuole. Below are 
concentration gradient without energy  different forms of endocytosis: 
use (similar to simple diffusion, but a   
protein channel is used). Examples include  ● Phagocytosis - cellular eating around solid 
porins for hydrophilic molecules and ion  objects.  
channels for ions.   ● Pinocytosis - cellular drinking around 
3. Active transport - substances travel against  dissolved materials (liquids). 
their concentration gradient and require the  ● Receptor-mediated endocytosis - requires 
consumption of energy by carrier proteins.   the binding of dissolved molecules to 
● Primary active transport uses ATP  peripheral membrane receptor proteins, 
hydrolysis to pump molecules against their  which initiates endocytosis.  
concentration gradient. For example, the   
sodium-potassium (Na+/K+) pump  Exocytosis is the opposite of endocytosis, in which 
establishes membrane potential (discussed  material is released to the extracellular 
in later chapters).   environment through vesicle secretion.  
 
   

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Organelles  Parts of the nucleus: 

 
 
● The nucleoplasm is the cytoplasm of the 
nucleus.  
● The nuclear envelope is the membrane of the 
nucleus. It contains two phospholipid bilayers 
(one inner, one outer) with a perinuclear 
space in the middle.  
● Nuclear pores are holes in the nuclear 
envelope that allow molecules to travel in and 
out of the nucleus. 
● The nuclear lamina provides structural 
support to the nucleus, as well as regulating 
DNA and cell division. 
● The nucleolus is a dense area that is 
responsible for making rRNA, and producing 
ribosomal subunits (rRNA + proteins).  
 
Ribosomes are not considered to be organelles; 
Adapted from: https://commons.wikimedia.org/w/indeg.php?curid=20664784  they work as small factories that carry out 
  translation (mRNA → protein). They are 
  composed of ribosomal subunits.  
Organelles are cellular compartments enclosed by   
phospholipid bilayers (membrane bound). They  Eukaryotic ribosomal subunits (60S and 40S) 
are located within the cytosol (aqueous  assemble in the nucleoplasm and are then 
intracellular fluid) and help make up the  exported from the nucleus to form the complete 
cytoplasm (cytosol + organelles).   ribosome in the cytosol (80S). (Note: S does not 
  refer to mass, but to sedimentation characteristics) 
Only eukaryotic cells contain membrane-bound   
organelles. Prokaryotes do not, but they have  Prokaryotic ribosomal subunits (50S and 30S) 
other adaptations, such as keeping their genetic  assemble in the nucleoid and form the complete 
material in a region called the nucleoid (more on  ribosome in the cytosol (70S).  
this in later chapters).     
  Free-floating ribosomes make proteins that 
The nucleus primarily functions to protect and  function in the cytosol while ribosomes embedded 
house DNA. DNA replication and transcription  in the rough endoplasmic reticulum (rough ER) 
(DNA → mRNA) occurs here.   make proteins that are sent out of the cell or to the 
 
cell membrane.  
 
The rough endoplasmic reticulum (rough ER) is 
continuous with the outer membrane of the 
nuclear envelope and is “rough” because it has 
ribosomes embedded in it. Proteins synthesized 
by the embedded ribosomes are sent into the 
lumen (inside of the rough ER) for modifications 
(eg. glycosylation). Afterwards, they are either sent 
out of the cell or become part of the cell 
membrane.  
 
The smooth endoplasmic reticulum (smooth 
 
Adapted from: https://commons.wikimedia.org/w/index.php?curid=6197500  ER) is not continuous with other membranes. Its 

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main function is to synthesize lipids, produce  Mitochondria are the powerhouses of the cell, 
steroid hormones, and detoxify cells.   producing ATP for energy use through cellular 
The Golgi apparatus is made up of cisternae  respiration (chapter 3).  
(flattened sacs) that modify and package   
substances. Vesicles come from the ER and reach  Chloroplasts are found in plants and some 
the cis face (side closest to ER) of the Golgi  protists. They carry out photosynthesis (chapter 4). 
apparatus. Vesicles leave the Golgi apparatus from   
the trans face (side closest to cell membrane).   Centrosomes are organelles found in animal cells 
  containing a pair of centrioles. They act as 
Lysosomes are membrane-bound organelles that  microtubule organizing centers (MTOCs) during 
break down substances (through hydrolysis)  cell division (chapter 5).  
taken in through endocytosis. Lysosomes contain   
acidic digestive enzymes that function at a low  Cytoskeleton 
pH. They also carry out autophagy (the   
breakdown of the cell’s own machinery for  The cytoskeleton provides structure and function 
recycling) and apoptosis (programmed cell death).  within the cytoplasm.  
   
Vacuoles:   Microfilaments are the smallest structure of the 
  cytoskeleton, and are composed of a double helix 
● Transport vacuoles - transport materials  made of two actin filaments. They are mainly 
between organelles.   involved in cell movement and can quickly 
● Food vacuoles - temporarily hold endocytosed  assemble and disassemble. Below are some of 
food, and later fuse with lysosomes.    their functions: 
● Central vacuoles - very large in plants and   
have a specialized membrane called the  1. Cyclosis (cytoplasmic streaming) - ‘stirring of 
tonoplast (helps maintain cell rigidity by  the cytoplasm’; organelles and vesicles travel 
exerting turgor). Function in storage and  on microfilament “tracks”. 
material breakdown).  2. Cleavage furrow - during cell division, actin 
● Storage vacuoles - store starches, pigments,  microfilaments form contractile rings that split 
and toxic substances.  the cell. 
● Contractile vacuoles - found in single-celled  3. Muscle contraction - actin microfilaments 
organisms and works to actively pump out  have directionality, allowing myosin motor 
excess water.  proteins to pull on them for muscle 
  contraction.  
The endomembrane system is a group of   
organelles and membranes that work together to  Intermediate filaments are between 
modify, package, and transport proteins and  microfilaments and microtubules in size. They are 
lipids that are entering or exiting a cell. It includes  more stable than microfilaments and mainly help 
the nucleus, rough and smooth ERs, Golgi  with structural support. For example, keratin is 
apparatus, lysosomes, vacuoles, and cell  an important intermediate filament protein in skin, 
membrane.  hair, and nails. Lamins are a type of intermediate 
  filament which helps make up the nuclear lamina, 
Peroxisomes perform hydrolysis, break down  a network of fibrous intermediate filaments that 
stored fatty acids, and help with detoxification.  supports the nucleus.  
These processes generate hydrogen peroxide,   
which is toxic since it can produce reactive  Microtubules are the largest in size and give 
oxygen species (ROS). ROS damage cells through  structural integrity to cells. They are hollow and 
free radicals. Peroxisomes contain an enzyme  have walls made of tubulin protein dimers. 
called catalase, which quickly breaks down  Microtubules also have functions in cell division, 
hydrogen peroxide into water and oxygen.   cilia, and flagella.  
   

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Microtubule Organizing Centers (MTOCs) are  The glycocalyx is a glycolipid/glycoprotein coat 

present in eukaryotic cells and help organize  found mainly on bacterial and animal epithelial 
microtubule extension.   cells. It helps with adhesion, protection, and cell 
  recognition.  
Centrioles are hollow cylinders made of nine  Cell-matrix junctions (connect ECM → 
triplets of microtubules (9x3 array). Centrosomes  cytoskeleton): 
contain a pair of centrioles oriented at 90 degree   
angles to one-another. They replicate during the S  1. Focal adhesions - ECM connects via integrins 
phase of the cell cycle so that each daughter cell  to actin microfilaments inside the cell.  
after cell division has one centrosome.   2. Hemidesmosomes - ECM connects via 
  integrins to intermediate filaments inside the 
Cilia and flagella have nine doublets of  cell.  
microtubules with two singles in the center (9+2   
array). They are produced by a basal body, which  Cell-cell junctions (connect adjacent cells): 
is initially formed by the mother centriole (older   
centriole after S phase replication).   1. Tight junctions - form water-tight seals 
  between cells to ensure substances pass 
  through cells and not between them.  
Extracellular Matrix  2. Desmosomes - provide support against 
  mechanical stress. Connects neighboring cells 
The extracellular matrix (ECM) provides  via intermediate filaments. 
extracellular mechanical support for cells.  3. Adherens junctions - similar in structure and 
  function to desmosomes, but connects 
ECM components:  neighboring cells via actin microfilaments.  
  4. Gap junctions - allow passage of ions and 
● Proteoglycan - a type of glycoprotein that has  small molecules between cells. 
a high proportion of carbohydrates.   
● Collagen - the most common structural protein;  Plant cells contain a few unique cell junctions: 
organized into collagen fibrils (fibers of   
glycosylated collagen secreted by fibroblasts).  1. Middle lamella - sticky cement similar in 
● Integrin - a transmembrane protein that  function to tight junctions. 
facilitates ECM adhesion and signals to cells  2. Plasmodesmata - tunnels with tubes between 
how to respond to the extracellular  plant cells. Allows cytosol fluids to freely travel 
environment (growth, apoptosis, etc.).   between plant cells. 
● Fibronectin - a protein that connects integrin   
to ECM and helps with signal transduction.   Cellular Tonicity and Cell Circulation 
● Laminin - behaves similarly to fibronectin.   
Influences cell differentiation, adhesion, and  Isotonic solutions have the same solute 
movement. It is a major component of the  concentration as the cells placed in them. 
basal lamina (a layer of the ECM secreted by   
epithelial cells).   Hypertonic solutions have a higher solute 
  concentration than the cells placed in them, 
Cell walls are carbohydrate-based structures that  causing water to leave the cell (cell shrivels).  
act like a substitute ECM because they provide   
structural support to cells that either do not have  Hypotonic solutions have a lower solute 
ECM, or have a minimal ECM. They are present in  concentration than the cells placed in them, 
plants (cellulose), fungi (chitin), bacteria  causing water to enter the cell (cell swells up). 
(peptidoglycan), and archaea.  Lysis is the bursting of a cell when too much water 
  enters.    
 
   

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Chapter 3: Cellular Energy  Reaction coupling is the process of powering an 

  energy-requiring reaction with an energy-releasing 
Table of Contents   one. It allows an unfavorable reaction to be 
  powered by a favorable reaction, making the net 
● Bio-thermodynamics  Gibbs free energy negative (-ΔG = exergonic = 
● Adenosine Triphosphate  releases energy + spontaneous).  
● Mitochondria   
● Aerobic Cellular Respiration  Mitochondria 
● ATP Yield of Aerobic Cellular Respiration   
● Fermentation  Mitochondria are organelles that produce ATP 
● Alternative Sources of Energy Generation  through cellular respiration (catabolic process). 
  They have an outer membrane and an inner 
Metabolism refers to all the metabolic pathways  membrane with many infoldings called cristae. 
(series of chemical reactions) that are happening in  The intermembrane space is located between the 
a given organism. Catabolic processes involve  outer and inner membranes while the 
breaking down larger molecules for energy while  mitochondrial matrix is located inside the inner 
anabolic processes involve using energy to build  membrane.  
larger macromolecules.    
   
To break down carbohydrates for energy, cells 
either utilize aerobic cellular respiration 
(consumes oxygen, more energy produced) or 
anaerobic cellular respiration (no oxygen 
needed, but less energy produced).   
 
Adenosine Triphosphate 
 
Adenosine triphosphate (ATP) is an RNA 
nucleoside triphosphate. It contains an adenine 
nitrogenous base linked to a ribose sugar (RNA 
nucleoside part), and three phosphate groups 
connected to the sugar (triphosphate part). 

 
 
   
https://commons.wikimedia.org/wiki/File:Nucleoside_nucleotide_general_format.png 
The endosymbiotic theory states that eukaryotes 
 
developed when aerobic bacteria were 
ATP is used as the cellular energy currency 
internalized as mitochondria while the 
because of the high energy bonds between the 
photosynthetic bacteria became chloroplasts. 
phosphate groups. These bonds release energy 
Some evidence for this theory includes size 
upon hydrolysis (breaking bonds).  
similarities and the fact that mitochondria and 
 
chloroplasts contain their own circular DNA and 
 
ribosomes. 
 
   

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Aerobic Cellular Respiration  Since 2 ATP are used up in the energy investment 
  phase and 4 ATP are produced in the energy payoff 
Aerobic cellular respiration is performed to  phase, a net of 2 ATP is produced per glucose 
phosphorylate ADP into ATP by breaking down  molecule within glycolysis.  
glucose and moving electrons around (oxidation 
and reduction reactions). Aerobic cellular 
respiration involves 4 catabolic processes: 
1. Glycolysis 
2. Pyruvate manipulations 
3. Krebs cycle 
4. Oxidative phosphorylation 
 
1. Glycolysis 
 
Glucose → 2 ATP + 2 NADH + 2 pyruvate 
 
Glycolysis takes place in the cytosol and does not 
require oxygen, so it is also used in fermentation.  
 
Substrate-level phosphorylation is the process 
used to generate ATP in glycolysis by transferring a 
phosphate group to ADP directly from a 
phosphorylated compound.  
 
Glycolysis has an energy investment phase and 
an energy payoff phase: 
1. Hexokinase uses one ATP to phosphorylate 
glucose into glucose-6-phosphate, which 
cannot leave the cell (it becomes trapped by 
the phosphorylation). 
2. Isomerase modifies glucose-6-phosphate into 
fructose-6-phosphate. 
3. Phosphofructokinase uses a second ATP to  Adapted from: https://commons.wikimedia.org/w/index.php?curid=53712885 

phosphorylate fructose-6-phosphate into   

fructose-1,6-bisphosphate.   
4. Fructose-1,6-bisphosphate is broken into   
dihydroxyacetone phosphate (DHAP) and   
glyceraldehyde-3-phosphate (G3P), which   
are in equilibrium with one another.   
5. G3P proceeds to the energy payoff phase so   
DHAP is constantly converted into G3P to   
maintain equilibrium. Thus, 1 glucose molecule   
will produce 2 G3P that continue into the next   
steps.    
6. G3P undergoes a series of redox reactions to   
produce 4 ATP through   
substrate-level-phosphorylation, 2 pyruvate   
and 2 NADH.    
   
   
       

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2. Pyruvate manipulations  3. Krebs cycle 

   
2 pyruvate → 2 CO2 + 2 NADH + 2 acetyl-CoA  2 acetyl-CoA → 4 CO2 + 6 NADH + 2 FADH2 + 2 
  GTP 
Pyruvate dehydrogenase is an enzyme that   
carries out the pyruvate manipulation steps below:  The Krebs cycle is also known as the citric acid 
  cycle or the tricarboxylic acid (TCA) cycle. Like 
1. Decarboxylation - Pyruvate molecules (3  pyruvate manipulations, it also occurs in the 
carbon molecule) move from the cytosol into  mitochondrial matrix and the cytosol for 
the mitochondrial matrix (stays in the cytosol  prokaryotes.  
for prokaryotes), where they undergo   
decarboxylation, producing 1 CO2 and one  1. Acetyl-CoA joins oxaloacetate (four-carbon) 
two-carbon molecule per pyruvate.  to form citrate (six-carbon).  
2. Oxidation - The two-carbon molecule is  2. Citrate undergoes rearrangements that 
converted into an acetyl group, giving  produce 2 CO2 and 2 NADH. 
electrons to NAD+ to convert it into NADH.  3. After the loss of two CO2, the resulting 
3. Coenzyme A (CoA) - CoA binds to the acetyl  four-carbon molecule produces 1 GTP through 
group, producing acetyl-CoA.   substrate-level phosphorylation.  
  4. The molecule will now transfer electrons to 1 
  FAD, which is reduced into 1 FADH2. 
5. Lastly, the molecule is converted back into 
oxaloacetate and also gives electrons to 
produce 1 NADH.  
6. Two acetyl-CoA molecules produce 4 CO2 + 6 
NADH + 2 FADH2 + 2 GTP. 

 
https://commons.wikimedia.org/w/index.php?curid=49924804 
 
 
 
 
 
 
 
 
 
 
 
   
   
     

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4. Oxidative phosphorylation   

 
Electron carriers (NADH + FADH2) + O2 → ATP + 
H2O 
 
The electron transport chain (ETC) and 
chemiosmosis (ions moving down electrochemical 
gradients) work together to produce ATP in 
oxidative phosphorylation. Oxygen acts as a final 
electron acceptor and gets reduced to form water.  
 
ETC goal: Regenerate electron carriers and create 
an electrochemical gradient to power ATP 
production. 
 
The mitochondrial inner membrane is the 
location of the ETC for eukaryotes while the cell   
Adapted from: https://commons.wikimedia.org/w/indeg.php?curid=49924811 
membrane is the location of the ETC for   
prokaryotes.   ATP Yield of Aerobic Cellular Respiration 
   
Four protein complexes (I-IV) are responsible for  Aerobic respiration is exergonic, with a ΔG = -686 
moving electrons through a series of  kcal/mol glucose. 
oxidation-reduction (redox) reactions in the   
ETC. As the series of redox reactions occurs,  The estimated yield is around 1 ATP per 4 
protons are pumped from the mitochondrial matrix  protons.  
to the intermembrane space, forming an   
electrochemical gradient. This is the reason the  NADH produces 3 ATP (NADH from glycolysis 
intermembrane space is highly acidic.  produces less)* 
   
NADH is more effective than FADH2 and drops  *The 2 NADH from glycolysis produce 4-6 ATP 
electrons off directly at complex-I, regenerating  because a varying amount of ATP must be used to 
NAD+.  shuttle these NADH from the cytosol to the 
  mitochondrial matrix. However, prokaryotes do 
FADH2 drops electrons off at protein complex-II,  not need to shuttle their NADH, so they will 
regenerating FAD. However, this results in the  produce 6 ATP. 
pumping of fewer protons due to the bypassing of   
complex-I.   FADH2 produces 2 ATP.  
 
Chemiosmosis goal: Use the proton 
electrochemical gradient (proton-motive force) to 
synthesize ATP. 
 
ATP synthase is a channel protein that provides a 
hydrophilic tunnel to allow protons to flow down 
their electrochemical gradient (from the 
intermembrane space back to the mitochondrial 
matrix). The spontaneous movement of protons 
generates energy that is used to convert ADP + Pi 
into ATP, a condensation reaction that is 
endergonic (requires energy + nonspontaneous = 
+ΔG).  

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  https://commons.wikimedia.org/w/index.php?curid=17293840 

Fermentation   
   
Fermentation is an anaerobic pathway (no  2. Alcohol Fermentation 
oxygen) that only relies on glycolysis by   
converting the produced pyruvate into different  Alcohol fermentation uses the 2 NADH from 
molecules in order to oxidize NADH back to NAD+.  glycolysis to convert the 2 pyruvate into 2 ethanol. 
Regenerating NAD+ means glycolysis can continue  Thus, NADH is oxidized back to NAD+ so that 
to make ATP. Fermentation occurs within the  glycolysis may continue. However, this process has 
cytosol. The two most common types of  an extra step that first involves the 
fermentation are lactic acid fermentation and  decarboxylation of pyruvate into acetaldehyde, 
alcohol fermentation.   which is only then reduced by NADH into ethanol. 
Adapted from: https://commons.wikimedia.org/w/index.php?curid=17301493 
 
1. Lactic acid fermentation 
 
Lactic acid fermentation uses the 2 NADH from 
glycolysis to reduce the 2 pyruvate into 2 lactic 
acid. Thus, NADH is oxidized back to NAD+ so that 
glycolysis may continue. This happens frequently 
in muscle cells and occurs continuously in red blood 
cells, which do not have mitochondria for aerobic 
 
respiration. 
 
 
Types of organisms based on ability to grow in 
The Cori cycle is used to help convert lactate back 
oxygen: 
into glucose once oxygen is available again. It 
 
transports the lactate to liver cells, where it can 
● Obligate aerobes - only perform aerobic 
be oxidized back into pyruvate. Pyruvate can then 
respiration, so they need the presence of 
be used to form glucose, which can be used for 
oxygen to survive.  
more ideal energy generation.  
● Obligate anaerobes - only undergo anaerobic 
respiration or fermentation; oxygen is poison 
to them. 
● Facultative anaerobes - can do aerobic 
respiration, anaerobic respiration, or 
fermentation, but prefer aerobic respiration 
because it generates the most ATP.  

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● Microaerophiles - only perform aerobic  lipoproteins or as free fatty acids bound by a 

respiration, but high amounts of oxygen are  protein called albumin.  
harmful to them.    
● Aerotolerant organisms - only undergo  Chylomicrons are lipoprotein transport structures 
anaerobic respiration or fermentation, but  formed by the fusing of triglycerides with proteins, 
oxygen is not poisonous to them.   phospholipids, and cholesterol. They leave 
  enterocytes and enter lacteals, small lymphatic 
Alternative Sources of Energy Generation  vessels that take fats to the rest of the body.  
   
Molecules other than glucose, such as other types  Low-density lipoproteins (LDLs) - low density of 
of carbohydrates, fats, and proteins can be  proteins, considered unhealthy because they 
modified to enter cellular respiration at various  transport cholesterol to the peripheral tissues, 
stages for energy generation.  where it can cause vessel blockage.  
   
1. Other carbohydrates mostly enter during  High-density lipoproteins (HDLs) - high density 
glycolysis. Glycogenolysis describes the release of  of proteins, considered healthy because they bring 
glucose-6-phosphate from glycogen, a highly  cholesterol to the liver to make bile.  
branched polysaccharide of glucose. Disaccharides   
can undergo hydrolysis to release two  When a glycerol molecule travels to the liver, it 
carbohydrate monomers, which can enter  can undergo a conversion to enter glycolysis or 
glycolysis.   make new glucose via gluconeogenesis at the liver.  
 
 
Free fatty acids undergo beta-oxidation to be 
converted into acetyl-CoA. Beta-oxidation 
requires an initial investment of ATP; the fatty 
acid chain is then continuously cleaved to yield 
two-carbon acetyl-CoA molecules (which can be 
used in the Krebs cycle for ATP generation) and 
electron carriers (NADH + FADH2 - produces more 
  ATP).  
 
 
Carbohydrates are the preferred energy source 
3. Proteins are the least desirable energy source 
since they are easily catabolized and are high yield 
because the processes to get them into cellular 
(4 kcal/gram).  
respiration take considerable energy and proteins 
 
are needed for many essential functions in the 
Glycogenesis refers to the reverse process - the 
body.  
conversion of glucose into glycogen to be stored in 
 
the liver when energy and fuel is sufficient. 
They are broken down into amino acids, which 
Glycogen is stored in the liver and muscle cells. 
must first undergo oxidative deamination 
 
(removal of NH3) before being shuttled to various 
2. Fats are mostly present in the body as 
parts of cellular respiration. 
triglycerides. Lipases are required to first digest 
 
fats into free fatty acids and alcohols through a 
Ammonia (NH3) is toxic, so it must be converted 
process called lipolysis. These digested pieces 
into uric acid or urea depending on the species 
then can be absorbed by enterocytes in the small 
and excreted from the body. For example, humans 
intestine and reform triglycerides.  
convert ammonia into urea, which is excreted as 
 
urine.  
Adipocytes are cells that store fat (triglycerides) 
 
and have hormone-sensitive lipase enzymes to 
   
help release triglycerides back into circulation as 

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Chapter 4: Photosynthesis  Photosynthesis and Cellular Respiration 

   
Table of Contents   Photosynthesis and cellular respiration are reverse 
  processes in terms of their overall reactions:
● Objective of Photosynthesis 
● Photosynthesis and Cellular Respiration 
● Leaf Anatomy 
● Light Dependent Reactions of 
Photosynthesis 
● The Calvin Cycle 
● Photorespiration 
● Alternative Photosynthetic Pathways   
 
● Anoxygenic Photosynthesis 
Photosynthesis is non-spontaneous and 
 
endergonic, producing glucose after an input of 
Heterotrophs must get energy from the food they 
solar energy. 
eat, while autotrophs can make their own food. 
 
Photoautotrophs take light energy and convert it to 
Cellular respiration is spontaneous and exergonic, 
chemical energy using photosynthesis.  
breaking down glucose to generate energy in the 
 
form of ATP.  
Photosynthesis reduces atmospheric carbon 
 
dioxide, releases oxygen, and creates chemical 
Photosynthesis 
energy that can be transferred through food 
chains. 
 
Photons (light energy) are used to synthesize 
sugars (glucose) in photosynthesis. 
 
Carbon fixation is the process by which inorganic 
carbon (CO2) is converted into an organic molecule 
(glucose). Photosynthesis takes electrons released 
from photolysis (the process of splitting water 
molecules) and excites them using solar energy. 
These excited electrons are then used to power 
carbon fixation.  
 
 
   

 
Adapted from: https://www.flickr.com/photos/102642344@N02/10187194256 
 
   

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Leaf Anatomy  Light Dependent Reactions of Photosynthesis 

   
Epidermis - an outer layer of cells that provides  The light dependent reactions take place in the 
protection and prevents water loss.  thylakoid membrane and harness light energy to 
  produce ATP and NADPH (an electron carrier) for 
Palisade mesophyll cells - located right below  later use in the Calvin cycle (ATP generated here is 
upper epidermis, has many chloroplasts; this is  not used to power the cell - it is consumed in the 
where most photosynthesis occurs.  Calvin cycle). 
   
Spongy mesophyll cells - found at the bottom of  Photosystems contain special pigments, such as 
the leaf, where the leaf has a lot of spaces for gas  chlorophyll and carotenoids, that absorb photons. 
movement; has some chloroplasts for moderate  The reaction center is a special pair of chlorophyll 
amounts of photosynthesis.  molecules in the center of these proteins. 
  Photosystem II (P680) and Photosystem I (P700) 
Stomata - pores on underside of leaf where gas  are used in photosynthesis.  
can enter and exit.    
  Non-cyclic photophosphorylation is carried out 
Guard cells - surround stomata and control their  by the light-dependent reactions. Below are the 
opening/closing.   important steps of this process: 
   
Chloroplasts are organelles found in plants and  1. Water is split (photolysis), passing electrons 
photosynthetic algae, but not in cyanobacteria.  to photosystem II and releasing protons into the 
They are similar to mitochondria and contain the  thylakoid lumen. 
structures listed below (outermost to innermost).  2. Photons excite electrons in the reaction 
  center of photosystem II, passing the 
Parts of a Chloroplast 
electrons to a primary electron acceptor.  
3. The primary electron acceptor sends the 
excited electrons to the electron transport 
chain (ETC). During the redox reactions within 
the ETC, protons are pumped from the stroma 
to the thylakoid lumen. The electrons are 
then deposited into photosystem I.  
4. Photons excite pigments in photosystem I, 
energizing the electrons in the reaction center 
to be passed to another primary electron 
acceptor.  
5. The electrons are sent to a short electron 
transport chain that terminates with NADP+ 
reductase, an enzyme then reduces NADP+ 
into NADPH using electrons and protons.  
6. The accumulation of protons in the thylakoid 
lumen generates an electrochemical gradient 
that is used to produce ATP using an ATP 
synthase, as H+ moves from the thylakoid 
lumen back into the stroma.  
 
  Cyclic photophosphorylation happens when 
 
photosystem I passes its electrons back to the 
 
first ETC instead of the second ETC. This causes 
   
more proton pumping and more ATP production, 
while no NADPH is generated.    

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The Calvin Cycle  Alternative Photosynthetic Pathways 

   
The Calvin cycle is made up of reactions known as  C3 photosynthesis - normal photosynthesis, 
light-independent reactions because they do not  where three-carbon PGA is produced.  
directly use light energy, but can only occur if the   
light-dependent reactions are providing ATP and  C4 photosynthesis - produces four-carbon 
NADPH.   oxaloacetate; occurs in plants living in hot 
  environments. Carbon dioxide is spatially isolated 
The Calvin cycle takes place in the chloroplast  to prevent photorespiration. Below are the 
stroma of plant mesophyll cells. It fixes carbon  important steps: 
dioxide that enters stomata.   
  1. PEP carboxylase fixes CO2 into a three carbon 
1. Carbon fixation - carbon dioxide combines  PEP molecule, producing oxaloacetate, which 
with five-carbon ribulose-1,5-bisphosphate  is converted into malate in the mesophyll cell. 
(RuBP) to form six-carbon molecules, which  2. Malate is transferred to bundle sheath cells, 
quickly break down into three-carbon  which have lower concentrations of oxygen.  
phosphoglycerates (PGA). This reaction is  3. Malate is decarboxylated to release CO2, 
catalyzed by RuBisCo.   spatially isolating where CO2 is fixed by 
2. Reduction - PGA is phosphorylated by ATP and  RuBisCo. The only drawback is that pyruvate 
subsequently reduced by NADPH to form  is also produced and needs to be shuttled back 
glyceraldehyde-3-phosphate (G3P).   to mesophyll cells using ATP energy.  
3. Regeneration - Most of the G3P is converted  4. Pyruvate is converted back into PEP.  
back to RuBP.   
4. Carbohydrate synthesis - some of the G3P is  CAM photosynthesis - uses temporal isolation 
used to make glucose.  of carbon dioxide to prevent photorespiration in 
  hot environments. Below are the important steps: 
6 CO2 + 18 ATP + 12 NADPH + H+ →    
18 ADP + 18 Pi +12 NADP+ + 1 glucose  1. During the day, stomata are closed to prevent 
  transpiration (evaporation of water from 
Photorespiration  plants). 
  2. During the night, stomata are open to let 
RuBisCo, in addition to fixing carbon dioxide into  carbon dioxide in. Just like in C4 
RuBP, can also cause oxygen to bind to RuBP in a  photosynthesis, PEP carboxylase fixes CO2 
process called photorespiration.  into PEP, producing oxaloacetate and 
  afterwards malate. However, malate is stored 
Photorespiration occurs in the stroma,  in vacuoles instead of being shuttled to 
producing a two-carbon molecule  bundle sheath cells.  
phosphoglycolate that is shuttled to  3. During the next day, the stomata are closed 
peroxisomes and mitochondria for conversion  again and malate is converted back into 
into PGA. However, fixed carbon is lost as carbon  oxaloacetate, which releases CO2 and PEP. 
dioxide in the process. Overall, there is a net loss  Thus, CO2 accumulates in the leaf for use in the 
of fixed carbon atoms and no new glucose is  Calvin cycle through temporal isolation. 
made.    
   
Also called C2 photosynthesis, since two-carbon     
phosphoglycolate is produced. 
 
Hot and dry - stomata are closed to minimize 
water loss, oxygen accumulates inside the leaf 
while carbon dioxide is used up. RuBisCo binds 
oxygen and photorespiration occurs. 

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Chapter 5: Cell Division 

 
Table of Contents  
 
● Key Terms 
● The Cell Cycle 
● Components of Interphase  
● Microtubule Organizing Centers 
● Components of the M Phase 
● Cell Cycle Regulation 
● Binary Fission 
● Meiosis 
● Chromosome and Chromatid Numbers 
During Mitosis and Meiosis   
● Summary Chart  https://commons.wikimedia.org/w/index.php?curid=30131216 

   
A part of cell theory states that all cells arise from  ● Karyokinesis - division of the nucleus.  
pre-existing cells through cell division.   ● Cytokinesis - physical division of the 
  cytoplasm and cell membrane. 
Key Terms  ● Parent cell- one parent cell produces two 
  daughter cells after division.  
● Genome - all the DNA in a cell.  ● Ploidy - describes the number of chromosome 
● Chromosomes - separate DNA molecules that  sets found in the body. Humans are diploid 
make up the entire genome.  because they contain two sets of 
● Homologous chromosome pairs - two  chromosomes (46 chromosomes, 23 pairs), 
different versions of the same chromosome  one from each parent. However, they also 
number. One is inherited from mother and  have haploid cells (gametes) that only contain 
one from father.   one chromosome set (23 chromosomes).  
● Sex chromosomes - one pair in the human 
body; they determine sex. 
● Autosomes - 22 pairs in the human body; they 
are nonsex chromosomes. 
● Gametes - haploid cells (sperm and eggs).  
● Germ cells - diploid cells that divide by meiosis 
to produce gametes.  
● Gametocyte - eukaryotic germ cells that can 
either divide to form more gametocytes or 
produce gametes. 
● Somatic cells - all body cells excluding the 
  gametes. Diploid in humans. 
Adapted from https://commons.wikimedia.org/wiki/File:Meiosis_Overview_new.svg   
 
● Sister chromatids - identical, attached copies   
of a single chromosome that form dyads.    
● Dyads - replicated chromosomes containing   
two sister chromatids that look like an “X”.    
● Centromeres - regions of DNA that connect   
sister chromatids in a dyad.    
● Kinetochores - proteins on the sides of   
centromeres that help microtubules pull sister   
Adapted from: https://commons.wikimedia.org/w/index.php?curid=13308417 
chromatids apart during cell division. 
   
 

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The Cell Cycle  Microtubule Organizing Centers 

   
The cell cycle is divided into interphase (G1, G0, S,  Microtubule Organizing Centers (MTOCs) are 
and G2) and the M phase. 90% of the cell cycle  present in eukaryotic cells; they organize extension 
happens during interphase. M phase is where  of microtubules, which are made of the protein 
karyokinesis and cytokinesis occur.  tubulin. MTOCs are responsible for forming the 
  spindle apparatus, which guides chromosomes 
DAT Mnemonic for the cell cycle:  during karyokinesis. 
   
Go = Gap Phase 1 (G1) of interphase  Centrosomes are organelles found in animal cells 
Sam = Synthesis Phase (S) of interphase  that contain a pair of centrioles. They act as 
Go = Gap Phase 2 (G2) of interphase  microtubule organizing centers (MTOCs). 
Make = Mitosis of the M phase   
Cake = Cytokinesis of the M phase  Microtubules in the spindle apparatus: 
   
Components of Interphase  1. Kinetochore microtubules - extend from 
  centrosomes and attach to kinetochores on 
1. Gap phase 1 (G1) - cell grows in preparation  chromosomes. 
for cell division. Also checks for favorable  2. Astral microtubules - extend from 
conditions. If favorable, cell will enter S phase.  centrosomes to the cell membrane to orient 
If unfavorable, cell will enter G0 phase.  the spindle apparatus. 
a. G0 phase - cells still carry out their  3. Polar microtubules - extend from the two 
functions but halt in the cell cycle. Cells  centrosomes and connect with each other. 
that do not divide are stuck here.   They push centrosomes to opposite ends of 
2. Synthesis phase (S) - cell replicates its genome  the cell. 
here and moves to G2 phase when completed.   
Centrosome duplicates.   Centrioles are hollow cylinders made of nine 
3. Gap phase 2 (G2) - cell continues to grow and  triplets of microtubules (9x3 array). Centrosomes 
prepare for cell division by checking DNA for  are located near the nucleus and contain a pair of 
any errors after replication. Also checks for  centrioles oriented at 90 degree angles to one 
mitosis promoting factor (MPF), which needs  another (attached to each other by 
to be present in adequate amounts for cell  interconnecting fibers). They replicate during the 
cycle continuation. Organelles are replicated  S phase of the cell cycle so that each daughter cell 
here.   after cell division has one centrosome.  
   

 
  Adapted from: https://commons.wikimedia.org/w/index.php?curid=4008957 

https://commons.wikimedia.org/w/index.php?curid=12800954   
     
   

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The pericentriolar material surrounds the  Cytokinesis is the physical separation of the 
centrioles and is responsible for microtubule  cytoplasm and cell membrane into two daughter 
nucleation (anchoring tubulin to start microtubule  cells.  
extension).    
  In animal cells, cytokinesis begins in late anaphase 
Cilia and flagella have nine doublets of  with the formation of a cleavage furrow. The 
microtubules with two singles in the center (9+2  cleavage furrow is a contractile ring of actin 
array). They are produced by a basal body, which  microfilaments and myosin motors that pinches the 
is initially formed by the mother centriole (older  cell into two. 
centriole after S phase replication) attaching itself   
to the cell membrane. 
 
Components of the M phase 
 
The M phase is the stage in the cell cycle where 
karyokinesis and cytokinesis occur. Mitosis is a 
type of karyokinesis (nuclear division) that involves   
a diploid parent cell dividing into two diploid  Adapted from: https://commons.wikimedia.org/w/index.php?curid=49926273 

daughter cells.   
  In plant cells, cytokinesis begins in telophase with 
Four phases of mitosis:  the formation of a cell plate. The cell plate is 
  created by vesicles from the Golgi apparatus and 
1. Prophase - chromatin condenses into  ends up producing the middle lamella (cements 
chromosomes (X-shaped dyads). The  plant cells together). 
nucleolus and nuclear envelope disappear.   
Spindle apparatus forms.  
2. Metaphase - the spindle apparatus guides 
the chromosomes to the metaphase plate 
(midpoint of cell) in a single file.  
3. Anaphase - kinetochore microtubules 
shorten to pull sister chromatids apart. Now, 
the sister chromatids are considered separate 
chromosomes. Chromosome number   
doubles.  Adapted from: https://commons.wikimedia.org/w/index.php?curid=49926273 

4. Telophase - chromosomes have segregated   

and nuclear membranes reform. In addition,   
nucleoli reappear and chromosomes     
decondense into chromatin. 
 
 
   

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Cell Cycle Regulation  Binary Fission 

   
The cell cycle influences cell division through  Mitosis is used to increase the number of cells in 
limitations to growth and regulation to prevent  an organism, whereas binary fission is used by 
cancerous growth.   archaea, bacteria, and certain organelles to 
  reproduce.  
Functional limitations:   
  During binary fission, organisms will replicate 
● Surface to volume ratio (S/V) - cell division  their genome while cell division is happening (no S 
occurs when volume is too large because cells  phase for DNA replication). Also, there is no spindle 
rely on the surface area of their cell  apparatus. 
membrane for transport of material. Decrease   
in S/V ratio leads to cell division. 
● Genome to volume ratio (G/V) - cell division 
occurs when the volume of the cell is too large 
to be supported by the limited size of the 
genome. Decrease in G/V ratio leads to cell 
division. 
 
Cell specific regulations: 
 
● Cell specific checkpoints - G1 restriction 
point (checks for favorable conditions to grow, 
enters G0 phase if unfavorable), end of G2 
(checks accuracy of DNA replication and MPF 
levels), and M checkpoint (during metaphase, 
checks for chromosomal attachment to spindle 
fibers).  
● Cyclin-dependent kinases (CDKs) - 
phosphorylate certain substrates to signal cell 
cycle progression. Activated by cyclin, a 
protein that cycles through stages of synthesis 
and degradation.  
● Growth factors - bind to receptors in the 
plasma membrane to signal for cell division. 
● Density dependent inhibition - halting of cell   
division when density of cells is high.   Adapted from: https://commons.wikimedia.org/w/index.php?curid=327384 

● Anchorage dependence - cells divide only     

when attached to an external surface.  
 
 
   

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Meiosis   
   
Meiosis produces four haploid daughter cells from  Meiosis II is very similar to mitosis because sister 
one diploid parent cell. It does this by repeating the  chromatids are separated. Two haploid cells divide 
steps of karyokinesis twice. Meiosis can be divided  into four haploid daughter cells.  
into meiosis I (homologous chromosomes   
separate) and meiosis II (sister chromatids  1. Prophase II - chromatin condenses into 
separate).   chromosomes (X-shaped dyads). The nucleolus 
  and nuclear envelope will disappear. Spindle 
Meiosis I (reductional division) produces two  apparatus forms. No crossing over occurs.  
haploid daughter cells through separation of  2. Metaphase II - chromosomes line up 
homologous chromosomes.   single-file at the metaphase plate just like in 
  mitosis.  
1. Prophase I - chromatin condenses into  3. Anaphase II - kinetochore microtubules 
chromosomes (X-shaped dyads). The  shorten to pull sister chromatids apart. Sister 
nucleolus and nuclear envelope will  chromatids become separate chromosomes 
disappear. Homologous chromosomes pair  and chromosome number doubles. 
up and crossing over occurs.  4. Telophase and Cytokinesis II - nuclear 
● Synapsis - the pairing up of homologous  membranes reform, nucleoli reappear, and 
chromosomes to form tetrads (aka  chromosomes decondense into chromatin. 
bivalents).  Four haploid daughter cells are produced in 
● Synaptonemal complex - protein 
structure that forms between 
homologous chromosomes during 
synapsis.  
● Tetrads (bivalents) - pair of two 
homologous chromosomes each with 
two sister chromatids.  
● Chiasmata - where two 
chromosomes of a homologous pair 
cross over during synapsis, causing 
genetic recombination. 
● Genetic recombination - exchange 
of DNA between chromosomes to 
produce genetically diverse offspring. 
2. Metaphase I - tetrads randomly line up 
double-file on the metaphase plate; this 
contributes to genetic diversity.  
3. Anaphase I - kinetochore microtubules 
shorten to separate homologous 
chromosomes from each other. Will not 
begin unless at least one chiasmata has 
formed within each tetrad. 
4. Telophase and Cytokinesis I - after 
tetrads have been pulled to opposite 
poles, nuclear membranes reform. In 
addition, nucleoli reappear and 
chromosomes decondense into 
chromatin. A Cleavage furrow forms in 
animal cells and a cell plate forms in 
plant cells.   total.  

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Adapted from: https://commons.wikimedia.org/w/index.php?curid=49630204 

 
   

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Chromosome and Chromatid Numbers During  Meiosis: 

Mitosis and Meiosis   
  For meiosis I, a human goes through the same 
(Click here for a deeper breakdown)  DNA replication in S phase as mitosis that results 
  in 46 chromosomes and 92 chromatids. 
Mitosis:  However, during metaphase the chromosomes 
  double up as shown below: 
During the S phase of the cell cycle, a human’s 46 
chromosomes are duplicated. Afterwards, there 
are still 46 chromosomes but also 92 chromatids. 
They line up in metaphase individually as shown 
below: 

 
During anaphase of meiosis I, homologous 
chromosomes split up. This results in the same 
total numbers - 46 chromosomes and 92 
chromatids. Each cell will have 23 chromosomes 
and 46 chromatids. 
 
 
During anaphase of mitosis, sister chromatids 
Meiosis II is very similar to mitosis and involves 
split. This produces 92 separate chromosomes, 
chromosomes lining up individually in metaphase. 
which are also counted as 92 chromatids. Each 
During anaphase, sister chromatids are 
separated cell will have 46 chromosomes (46 
separated, resulting in 23 chromosomes (23 
chromatids). These cells are diploid. 
chromatids) in each daughter cell. These cells are 
 
haploid.  
 
 
   
 
   

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Chapter 6: Molecular Genetics 

 
Table of Contents  
 
● Genetic Building Blocks 
● DNA Organization 
● DNA Replication 
● Transcription 
● Prokaryotic Transcriptional Control 
● Eukaryotic Transcriptional Control 
● Eukaryotic Post-Transcriptional 
Modifications 
● Translation 
● Gene Mutations 
● Molecular Genetics of Viruses   
● Molecular Genetics of Bacteria  https://commons.wikimedia.org/w/index.php?curid=34914285 

   
Genetic Building Blocks  In DNA: 
  A binds to T (with two hydrogen bonds) 
Nucleotide - ribose sugar, nitrogenous base, and  G binds to C (with three hydrogen bonds) 
phosphate group.   
 
Nucleoside - ribose sugar and nitrogenous base. 
 

 
https://commons.wikimedia.org/w/index.php?curid=57283844 
 
DNA is a polymer of nucleotides that have 
hydrogen on the ribose sugar’s 2’ carbon. RNA is a 
polymer of nucleotides that have hydroxyl groups 
on the ribose sugar’s 2’ carbon. This is the reason 
 
DNA is called deoxyribonucleic acid, while RNA is  https://commons.wikimedia.org/wiki/File:DNA_chemical_structure.svg 
called ribonucleic acid.    
  In RNA: 
Purines are the double-ringed nitrogenous bases  A binds to U (with two hydrogen bonds) 
adenine and guanine.  G binds to C (with three hydrogen bonds) 
  Since G-C bonds have more hydrogen bonds, a 
Pyrimidines are the single-ringed nitrogenous  higher temperature is needed to break DNA 
bases cytosine, thymine, and uracil.  strands with a larger proportion of G-C bonds. 
 
 

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DNA Organization  Steps of DNA replication: 

   
Nucleosomes are complexes of DNA wrapped  1. Initiation - creating origins of replication at 
around histone proteins. Each nucleosome has  A-T rich segments of DNA because A-T bonds 
nine histones total. The central core contains two  only have two hydrogen bonds and are easier 
of each histone H2A, H2B, H3 and H4. On the  to split apart.  
outside, a single histone, H1, holds the DNA in  2. Elongation - producing new DNA strands using 
place.  different types of enzymes. 
  ● Helicase unzips DNA by breaking hydrogen 
Chromatin refers to the overall packaging of DNA  bonds between strands, creating a 
and histones. Below are two types of chromatin:  replication fork. 
  ● Single-strand binding proteins bind to 
1. Euchromatin - nucleosomes are “loosely  uncoiled DNA strands, preventing 
packed”, so DNA is readily accessible for  reattachment of the strands to each other.  
transcription.  ● Topoisomerase nicks the DNA double 
2. Heterochromatin - nucleosomes are “tightly  helix ahead of helicase to relieve built-up 
packed”, so DNA is mostly inactive.  tension.  
  ● Primase places RNA primers at the origin 
Histones are positively charged while DNA is  of replication to create 3’ ends for 
negatively charged, allowing proper binding.   nucleotide addition.  
  ● Sliding clamp proteins hold DNA 
Acetylation of histones removes positive charges,  polymerase onto the template strand. 
relaxing DNA-histone attractions and allowing for  ● DNA polymerase adds free nucleoside 
more transcription to happen.  triphosphates to 3’ ends. 
  ● The leading strand is produced 
Deacetylation of histones increases positive  continuously because it has a 3’ end that 
charges, tightening DNA-histone attractions and  faces the replication fork. 
decreasing transcription.  ● The lagging strand is produced 
  discontinuously because its 3’ end is facing 
Methylation of histones adds methyl groups,  away from the replication fork. Thus, many 
either increasing or decreasing transcription.  RNA primers are needed to produce short 
  DNA fragments called Okazaki fragments.  
DNA replication  ● A different DNA polymerase replaces RNA 
  primers with DNA.  
An origin of replication is required to initiate DNA  ● DNA ligase glues separated fragments of 
replication where the DNA strands first separate.  DNA together.  
Organisms with circular DNA such as bacteria  3. Termination - replication fork cannot 
have a single origin of replication while organisms  continue, ending DNA replication.  
with linear DNA such as humans have multiple  ● Telomeres are noncoding, repeated 
origins of replication.   nucleotide sequences at the ends of linear 
  chromosomes. They are necessary in 
DNA undergoes semiconservative replication,  eukaryotes because when the replication 
where each new double helix produced by  fork reaches the end of a chromosome, a 
replication has one “new” strand and one “old”  small segment of DNA from the telomere is 
strand.   not replicated and lost (no RNA primer is 
  present to help produce another Okazaki 
DNA is antiparallel, meaning that the 5’ end  fragment).  
(terminal phosphate group) of one strand is  ● Telomerase is an enzyme that extends 
always next to the 3’ end (terminal hydroxyl  telomeres to prevent DNA loss.  
group) of the other strand and vice versa.    
     

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To review, the G1/S checkpoint regulates cell cycle  Specifically, DNA undergoes transcription to 
transition from the G1 phase into the S phase,  produce single-stranded messenger RNA (mRNA).  
checking for favorable conditions to grow. If   
unfavorable, the cell will remain in G0 phase and  Steps of transcription: 
will not enter the S phase for DNA replication.   
1. Initiation - a promoter sequence (aka 
promoter) next to the gene attracts RNA 
polymerase to transcribe the gene.  
2. Elongation - transcription bubble forms and 
RNA polymerase travels in the 3’ → 5’ direction 
on the template strand. However, it extends 
RNA in the 5’ → 3’ direction.  
3. Termination - a termination sequence (aka 
terminator) signals to RNA polymerase to 
  stop transcribing the gene.  
https://commons.wikimedia.org/w/index.php?curid=9550386 
 
 
 
Transcription 
 
 
Genes are instructions within DNA that code for 
proteins. However, they must first be transcribed 
into RNA before being translated into proteins.  
 

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Prokaryotic Transcriptional Control 

 
In prokaryotes, transcription occurs in the cytosol. 
RNA polymerase opens up DNA, forming a 
transcription bubble.  
 
Before transcription can occur, a sigma factor 
combines with prokaryotic core RNA 
polymerase to form RNA polymerase 
holoenzyme, giving it the ability to target specific 
DNA promoter regions.  
 
An operon is a group of genes that function as a   
single unit that is controlled by one promoter. The  Another operon employed by prokaryotes is the 
operator region is present near the operon’s  trp operon, which is responsible for producing the 
promoter and binds activator/repressor  amino acid tryptophan. It is known as a 
proteins to regulate the promoter.   repressible operon because it codes for 
  tryptophan synthetase and is always active 
The lac operon is an inducible operon (it must be  unless the presence of tryptophan in the 
induced to become active). LacZ, lacY, and lacA  environment represses the operon.   
are the three genes contained within the lac   
operon that encode proteins required for lactose  Tryptophan binds to the trp repressor protein, 
metabolism. The lac operon will only be induced  which then attaches to the operator on the trp 
when glucose is not available as an energy source,  operon to prevent tryptophan production. Thus, 
so lactose must be used.   this is the first level of trp operon regulation. When 
   tryptophan is not present in the environment, the 
The lac repressor protein is the first way that the  trp operon will undergo transcription because the 
lac operon is controlled. This protein is encoded by  trp repressor protein will be inactive.  
an entirely separate gene called lacI, which is  https://commons.wikimedia.org/w/index.php?curid=13443283 

constitutively expressed (always on). Thus, the 

lac repressor protein is always bound to the 
operator, blocking transcription. However, when 
lactose is present it is converted to allolactose. 
Allolactose binds directly to the repressor and 
removes it from the operator, allowing 
transcription to occur.   
 
cAMP levels and catabolite activator protein 
(CAP) are the second level of lac operon regulation. 
cAMP levels are inversely related to glucose levels, 
so when glucose is low, cAMP is high. cAMP binds 
to catabolite activator protein (CAP), which then 
attaches near the lac operon promoter to help 
attract RNA polymerase, promoting transcription.  
 

 
   

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Eukaryotic Transcriptional Control  Eukaryotic Post-Transcriptional Modifications 

   
Unlike in prokaryotes, eukaryotic transcription  Post-transcriptional modification describes the 
occurs in the nucleus and uses RNA polymerase  conversion of pre-mRNA into processed mRNA, 
II to transcribe most genes.   which leaves the nucleus. Below are the three 
  main types of post-transcriptional modification: 
Transcription factors are needed in eukaryotes   
to help RNA polymerase bind to promoters. The  1. 5’ capping - 7-methylguanosine cap is added 
TATA box is a sequence in many promoters that  to the 5’ end of the mRNA during elongation, 
transcription factors can recognize and bind to.   protecting the mRNA from degradation. 
  2. Polyadenylation of the 3’ end - addition of 
● Enhancers are DNA sites that activator  the poly A tail to the 3’ end to prevent 
proteins can bind to; they help increase  degradation. 
transcription of a gene.  3. Splicing out introns - introns are stretches of 
● Silencers are DNA sites that repressor  noncoding DNA that lie between regions of 
proteins can bind to; they decrease  coding DNA (exons). Splicing refers to 
transcription of a gene.   removing introns from pre-mRNA using 
spliceosomes. “Splice signals” present within 
introns signal to the spliceosome where to cut.  
 
snRNAs (small nuclear RNA) and proteins make 
up the functional part of a spliceosome and are 
collectively referred to snRNPs (small nuclear 
RiboNucleic Proteins). 
 
Alternative splicing describes a single pre-mRNA 
having multiple possible spliced mRNA products. 
Thus, the same pre-mRNA can produce many 
different proteins.  

 
Enhancers and silencers can be far upstream or 
downstream from the gene, so DNA from these 
sites are thought to loop around to colocalize 
with RNA polymerase.  
 
The poly A signal is located within the terminator 
sequence and stimulates polyadenylation 
(addition of adenine nucleotides to the 3’ end of 
the mRNA). 
 
  https://commons.wikimedia.org/w/index.php?curid=6882704 
   
     
 
   

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Translation  Ribosomal binding sites for tRNA: 

   
Ribosomes and tRNA (transfer RNA) are  1. A site - A for aminoacyl-tRNA, which first 
important players in translation, the process of  enters at this site.  
converting mRNA into protein products.   2. P site - P for peptidyl-tRNA, which carries the 
  growing polypeptide.  
Ribosomes are made up of one small subunit and  3. E site - E for exit site. The tRNA from the P site 
one large subunit as described below:  is sent here and released from the ribosome.  
 
● Eukaryotes - small (40S) and large (60S) 
subunits form a 80S ribosome. They are 
composed of rRNA (ribosomal RNA) and 
proteins. The subunits are made in the 
nucleolus and assembled once they are 
exported to the cytosol.  
● Prokaryotes - small (30S) and large (50S) 
subunits form a 70S ribosome. They are also 
composed of rRNA and proteins, but are 
assembled together in the nucleoid.  
 
A codon is a group of three mRNA bases (A, U, G, 
 
or C) that code for an amino acid or terminate 
The ribosome catalyzes the formation of a peptide 
translation. There are 64 codon combinations 
bond between the polypeptide in the P site and 
total but only 20 amino acids, so degeneracy is 
the newly added amino acid in the A site. 
present (multiple codons code for the same amino 
Afterwards, the polypeptide is transferred to the A 
acid).  
site’s tRNA and the ribosome shifts one codon 
 
down the mRNA. The A site will now be empty and 
Memorize these codons →  
ready to accept another aminoacyl-tRNA. The tRNA 
Start codon: AUG (methionine)  
from the P site will be transferred to the E site and 
Stop codons: UAA, UAG, UGA (end translation, do 
will leave the ribosome.  
not code for any amino acid) 
 
 
An anticodon is a group of three tRNA bases (A, 
U, G, or C) that base pairs with a codon. Each tRNA 
carries an amino acid to be added to the growing 
protein.  
 
 
Aminoacyl-tRNA refers to a tRNA bound to an 
amino acid.  
 
Aminoacyl-tRNA synthetase is the enzyme that 
attaches an amino acid to a specific tRNA using the 
energy from ATP.    
  Adapted from: 
  https://commons.wikimedia.org/wiki/File:Codon-Anticodon_pairing.svg 
   
   

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Mutations   
 
   

A DNA mutation is a heritable change in the 

DNA nucleotide sequence that can be passed 
down to daughter cells.   
 
Three main types of DNA mutations:  
 
1. Base substitutions (point mutations) - 
one nucleotide is replaced by another. 
Below are various effects they may have: 
● Silent mutations - no change in 
amino acid sequence. Due to “third 
base wobble”, mutations in the DNA 
sequence that affect the third base of 
a codon can still result in the same 
amino acid being added to the   
https://commons.wikimedia.org/w/index.php?curid=12481467
protein. Relies on the degeneracy   
(redundancy) of translation.    
● Missense mutations - single change in   
amino acid sequence. Can either be   
conservative (mutated amino acid similar 
to unmutated) or non-conservative 
(mutated amino acid different from 
unmutated).  
● Nonsense mutations - single change in 
amino acid sequence that results in a stop 
codon. Results in early termination of 
protein.  
2. Insertions - adding nucleotides into the DNA 
sequence - can shift the reading frame.  
3. Deletions - removing nucleotides from the 
DNA sequence - can shift the reading frame.  
 
Factors that contribute to DNA mutations: 
 
● DNA polymerase errors during DNA 
replication. 
● Loss of DNA during meiosis crossing over. 
● Chemical damage from drugs. 
● Radiation. 
 
Factors that prevent DNA mutations: 
 
● DNA polymerase proofreading by DNA 
polymerase.  
● Mismatch repair machinery that checks 
uncaught errors.  
● Nucleotide excision repair that cuts out     
damaged DNA and replaces it with correct 
DNA using complementary base pairing. 

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Molecular Genetic of Viruses  Molecular Genetics of Bacteria 

   
Viruses are not living because they must infect  Bacteria are asexual and divide by binary fission, 
living cells to multiply.   so they only receive genes from one parent cell 
  and do not increase genetic diversity through 
The capsid is a viral protein coat that is made of  reproduction. 
subunits called capsomeres. Some viruses also   
have a phospholipid envelope that they pick up  Instead, they must increase genetic diversity 
from the host cell membrane.   through horizontal gene transfer, which 
  describes the transfer of genes between individual 
Two viral life cycle types:  organisms. Below are the three methods of 
  horizontal gene transfer: 
1. Lysogenic cycle - virus is considered dormant   
because it inserts its own genome into the  1. Conjugation - bacteria use a cytoplasmic 
host’s genome and does not harm the host.  bridge called a pili to copy and transfer a 
Each time the host genome undergoes  special plasmid known as the F plasmid 
replication, so does the viral genome.   (fertility factor). If a bacteria contains an F 
2. Lytic cycle - virus takes over host to replicate  plasmid, it is referred to as F+. If not, it is 
and does cause harm to the host. The viral  referred to as F-. To review, plasmids are 
particles produced can lyse the host cell to  circular DNA pieces that are independent from 
find other hosts to infect.  a bacteria’s single circular chromosome.  
2. Transformation - bacteria take up 
extracellular DNA. Bacteria are referred to as 
competent if they can perform transformation. 
Electroporation is the process of using 
electrical impulses to force bacteria to become 
competent. 
3. Transduction - viruses transfer bacterial DNA 
between different bacterial hosts. This occurs 
when a bacteriophage enters the lysogenic 
cycle in its host and carries bacterial DNA 
along with its own genome upon re-entering 
the lytic cycle.  

 
It is important to note that viruses can switch 
between the lysogenic and lytic cycles. For example, 
favorable conditions can stimulate a virus in the 
lysogenic cycle to replicate and enter the lytic 
cycle.  
 
Retroviruses (eg. HIV) have an RNA genome that  https://commons.wikimedia.org/w/index.php?curid=25517403
infects host cells. They contain an enzyme called   
reverse transcriptase, which converts their RNA     
into cDNA (complementary DNA). The cDNA can 
integrate into the host genome and enter the 
lysogenic cycle. 
   

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Chapter 7: Heredity  ● Hemizygous - only one allele is present. For 

  example, men only have one X and one Y 
Table of Contents   chromosome (not homologous), which contain 
  hemizygous genes.  
● Key Heredity Terms  ● Penetrance - proportion of individuals who 
● Patterns of Inheritance  have the phenotype associated with a specific 
● Gene Defects  allele. Can be complete penetrance or 
● Mendel’s Laws  incomplete penetrance. As shown below, Bb 
● Nondisjunction and Aneuploidies  individuals all have brown eyes only when 
● Crosses  there is complete penetrance.  
● Pedigree Analysis   
● Creating Genetic Diversity 
● Gene Linkage 
● Epigenetics 
 
Heredity is the passing of traits from parents to 
offspring. These traits can be passed down 
sexually (mating in animals) or asexually (binary 
fission in bacteria).  
 
Key Heredity Terms 
 
● Genome - all the DNA within a cell.  
● Gene - sequence of DNA that codes for a trait.  
● Locus - location of a gene on a chromosome. 
Plural is gene loci. 
● Allele - one variation of a gene.    
● Wild-type allele - normal allele that is most   

common in nature. Can turn into a mutant  ● Expressivity - describes the degree of a certain 
allele.  phenotype for a given genotype. All of the 
● Mutation - heritable change in DNA.  children of this couple have genotype Hh for 
● Genotype - genetic composition of an  medium thick hair, but because of expressivity, 
organism.  just how medium thick (or medium thin) the 
● Phenotype - observable traits that result from  hair is varies. 
a genotype. 
● Dominant alleles - mask the expression of 
recessive alleles. Typically represented by 
uppercase letters (“A”).  
● Recessive alleles - only show up in a 
phenotype if dominant alleles are not present. 
Typically represented by lowercase letters (“a”). 
● Homologous pairs - two different copies of 
the same chromosome in a diploid organism. 
One from each parent. Each copy is very 
similar, except for minor nucleotide variations 
that generate unique alleles. 
● Heterozygous - one dominant allele and one 
recessive allele in its homologous pair.  
● Homozygous - same allele in both homologs. 
Can be homozygous dominant or   
homozygous recessive.  

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Patterns of Inheritance  Epistasis is when one gene affects the expression 

  of a different gene. (Ex. baldness gene covers up 
Incomplete dominance is when one allele is not  the genes for hair color). 
completely expressed over its paired allele. The   
heterozygous will have an intermediate state. (Ex. 
red x white = pink). 
 

   
Adapted from: https://commons.wikimedia.org/w/index.php?curid=45105028  Adapted from: https://commons.wikimedia.org/w/index.php?curid=30382414 
   
Codominance is when the heterozygous genotype  Pleiotropy describes when one gene is 
expresses both alleles. (Ex. red x white = red +  responsible for many traits. (Ex. cystic fibrosis is a 
white spots).   disease with many symptoms caused by a single 
  gene). 
Multiple alleles describe when there are more   
allele options than just two. (Ex. ABO blood typing  Polygenic inheritance is when many genes are 
- A, B, O alleles).   responsible for one trait. This gives the trait 
  continuous variation. (Ex. height, a single trait 
affected by many genes). 
 
The image below displays both pleiotropy and 
polygenic inheritance: 

   
https://commons.wikimedia.org/w/index.php?curid=8395318  https://commons.wikimedia.org/w/index.php?curid=48116318 
   
     

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Gene Defects  Tumor-suppressor genes are genes that become 

  cancerous as a result of loss-of-function 
Haploinsufficiency occurs when one copy of the  mutations, because they are normally needed to 
gene is lost or nonfunctional and the expression of  suppress cancerous growth.  
the remaining copy is not sufficient enough to   
result in a normal phenotype. It can result in an  Tumor-suppressor genes follow the two hit 
intermediate phenotype.  hypothesis, which states that a loss-of-function 
  mutation in both copies of the gene are needed to 
Haplosufficiency describes when the remaining  make it cause cancer. Thus, tumor-suppressor 
copy of the gene is sufficient enough to result in a  genes are haplosufficient. 
normal phenotype.    
  Null alleles come from mutations that cause the 
Proto-oncogenes are genes that can become  alleles to lack normal function. Tumor-suppressor 
oncogenes (cancer-causing genes) due to  genes have null alleles when they become 
gain-of-function mutations. Gain-of-function  cancer-causing. 
mutations can cause too much protein to be   
made or production of an over-active protein;  ● p53 is an important tumor-suppressor gene 
Cancerous growth occurs as a result.  that is known as the guardian of the cell. It is 
Proto-oncogenes are normally involved in cell cycle  upregulated to prevent cells from becoming 
control.   cancerous.  
  ● p21 is another tumor-suppressor gene that 
Proto-oncogenes follow the one hit hypothesis,  inhibits phosphorylation activity in order to 
which states that a gain-of-function mutation in  decrease rampant cell division. 
one copy of the gene turns it into an oncogene.   ● Retinoblastoma gene (RB) is a 
  tumor-suppressor gene that codes for a 
  retinoblastoma protein, which prevents 
    excessive cell growth during interphase.  
 
   

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Mendel’s Laws  3. Law of independent assortment - 

  homologous chromosomes line up 
Gregor Mendel studied genetics and proposed  independently during metaphase I of meiosis 
three laws:  so that alleles separate randomly (this 
  increases genetic variability). Metaphase II is 
1. Law of dominance - dominant alleles mask  different, during which sister chromatids are 
the expression of recessive alleles. Mendel  pulled apart instead. The law of independent 
studied plant height to come to this conclusion.   assortment can produce 223 options (23 
homologous chromosome pairs split). 
 
Under the law of independent assortment, if we 
consider a 6 chromosome diploid organism 
(haploid number is 3), the 6 chromosomes could 
assort with: 
 
Trial 1: All paternal on one side, all maternal on 
the other: 

 
Resulting in daughter cells that look like this: 

 
Trial 2: However, they also could randomly align 
like this: 

 
   
2. Law of segregation - homologous gene copies  Resulting in daughter cells that look like this: 
separate during meiosis (specifically anaphase 
I). Thus, Aa individuals will produce gametes 
with “A” or “a” alleles.  
 
 
 
 
   

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Nondisjunction and Aneuploidies  3. Single nondisjunction of sister chromatids 

  during mitosis 
Nondisjunction is the improper segregation of   
chromosome pairs during anaphase; it produces  46 chromosomes in diploid parent cell 
daughter cells with an incorrect number of  →  
chromosomes.   47, 45 chromosomes in diploid daughter cells 
   
1. Single nondisjunction of homologous 
chromosomes during meiosis I 
 
46 chromosomes in diploid parent cell 
→  
24, 24, 22, 22 chromosomes in haploid daughter 
cells 
 

 
https://commons.wikimedia.org/w/index.php?curid=66665255 
 
  Aneuploidy refers to an abnormal number of 
Adapted from: https://commons.wikimedia.org/w/index.php?curid=26233546  chromosomes in the daughter cells. After 
  fertilization, trisomy (3 chromosomes copies) or 
2. Single nondisjunction of sister chromatids  monosomy (1 chromosome copies) can occur.  
during meiosis II   
  Down syndrome is a trisomy of chromosome #21 
46 chromosomes in diploid parent cell  (each diploid cell has 47 chromosomes total).  
→   
24, 22, 23, 23 chromosomes in haploid daughter  Turner syndrome is a monosomy of the X 
cells  chromosome in females (each diploid cell has 45 
  chromosomes total). Affected individuals have 
physical abnormalities and sterility. 
 
Klinefelter’s syndrome is a trisomy of the sex 
chromosomes in males, giving them XXY (each 
diploid cell has 47 chromosomes total). Individuals 
usually have disorders in intellectual, physical, and 
reproductive development.  
 
 
 
 
 
Adapted from: https://commons.wikimedia.org/w/index.php?curid=26233546 
   
 

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Crosses  On the other hand, a dihybrid cross examines the 

  inheritance of two genes on separate 
A cross refers to when two organisms are mated  chromosomes. Although the genotype ratio is 
to produce offspring.   complex in the F2 generation, just remember that 
  the phenotype ratio (both dominant:one 
A test-cross pairs an individual of unknown  dominant and one recessive:one dominant and 
genotype with one that is homozygous recessive. By  one recessive:both recessive) should be 
looking at the offspring from a test-cross, we can  (9:3:3:1).   
determine the unknown genotype.   
  Punnett squares are used to visualize these 
True-breeding organisms are homozygous for all  crosses but are too complex for dihybrid crosses. 
the traits of interest.  Thus, one-gene cross ratios can be used to solve 
  these questions faster. Below are the single allele 
The F1 generation (aka filial 1 hybrid) is the first  crosses you should memorize: 
generation cross between true-breeding parents   
with different alleles. The offspring are all  1. Homozygous x homozygous = 1/1 AA or 
heterozygous.  1/1 Aa or 1/1 aa 
   
The F2 generation (aka filial 2 hybrid) is the  2. Homozygous x heterozygous = ½ AA (or 
second generation cross between the  aa) and ½ Aa 
heterozygous offspring from the F1 generation.   
This is where Mendel’s three laws can be studied.   3. Heterozygous x heterozygous = ¼ AA, ½ 
  Aa, ¼ aa  
If these two generations are studied under   
monohybrid crosses, then only a single gene is  Multiple-locus crosses can then be solved using 
examined. In the F2 generation, the genotype ratio  these single allele crosses. As shown below, RrYy 
(AA:Aa:aa) should be (1:2:1) and the phenotype  individuals cross with each other. The Rr single 
ratio (dominant:recessive) should be (3:1).  cross probabilities can be multiplied with the Yy 
  single cross probabilities to get the dihybrid 
offspring probabilities shown on the right. 
 

 
Adapted from: https://commons.wikimedia.org/w/index.php?curid=6070182 

   
Adapted from: https://commons.wikimedia.org/w/index.php?curid=49926348     

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Pedigree Analysis  Creating Genetic Diversity 

   
Pedigree charts are used to track inherited traits  Crossing over also creates genetic diversity and 
over many generations to see inheritance  occurs during prophase I of meiosis. Homologous 
patterns. Females are represented by circles, and  chromosomes join together to form tetrads (aka 
males are represented by squares. Individuals  bivalents) and exchange genetic material at points 
affected by the trait in question are shaded;  referred to as chiasmas. Afterwards, genetically 
unaffected individuals are not shaded.   unique chromatids are produced as a result of 
  crossing over.  
 

 
The pedigree chart shown above has affected 
individuals depicted red and unaffected 
individuals depicted blue. 
 
Recombinant gametes describe the gametes that 
Given that the “affected” trait is autosomal 
receive the genetically unique chromatids (new 
dominant, we can use this chart to solve for the 
combination of alleles), while non-recombinant 
genotype of the affected male in the third 
gametes refer to the gametes that receive 
generation.  
parental chromatids (alleles match parent’s 
 
alleles).  
The logic goes like this; since the male is affected, 
 
we know that he can be heterozygous or 
 
homozygous dominant. However, since his father 
   
is unaffected, the male could not have received an 
“affected” allele from his father. Thus, this 
individual must be heterozygous. The single 
dominant allele came from his mother.  
 
These kinds of questions are frequently asked on 
the DAT, so practice them and use clues from 
parents/offspring to find the answers! 
 
 
   

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Gene linkage  Genomic imprinting refers to genes that are 

  expressed depending on parental origin and are 
Linked genes are found close together on the same  influenced by epigenetic factors. These genes are 
chromosome. By looking at recombination  different from sex-linked traits because they can 
frequencies, we can deduce the relative distance  come from autosomal chromosomes (non-sex 
between these genes.  chromosomes) as well.  
   
One map unit is defined as the chromosomal  X-inactivation is the process by which one of a 
distance that would allow 0.01 crossover events  female’s X chromosomes is inactivated, forming a 
per generation. 20 map units would mean 0.2  Barr body and preventing excess transcription. 
crossover events occur between the two genes per  However, a female carrier may become an 
generation, or that there is a 20% chance of  affected individual for a disease if her unaffected 
recombination.  X chromosome with a normal wild-type allele is 
  inactivated, leaving behind a recessive allele that is 
Recombination frequencies of less than 50%  not covered up. 
mean that the two genes are linked. A random 
assortment of unlinked genes have 50% 
recombinant progeny. 
 
Linkage maps can be drawn out using map units 
to infer the distance between genes on a 
chromosome. 
 
A haplotype is a group of genes that are usually 
inherited together because they are located in 
close proximity to each other. 
 
Sex-linked traits come from genes located on the 
 
sex chromosomes. Most sex-linked disorders have 
 
X-chromosome linkage. Below are three types of  Epigenetics 
sex-linked traits:   
  Epigenetics does not involve modifying the 
1. X-linked dominant - dominant inheritance on  genetic code, but instead the regulation of when 
the X chromosome. Any offspring (male or  genes are expressed. Epigenetic changes are 
female) that receive the affected allele will end  heritable. Below are some examples of 
up with the disorder.  epigenetic changes: 
2. X-linked recessive - recessive inheritance on   
the X chromosome. For males, only one  ● DNA methylation - causes gene suppression 
affected allele is needed to cause the disorder.  through the addition of methyl groups, 
For females, two affected alleles are needed to  recruiting methyl-binding proteins (MBDs) and 
cause the disorder because females have two  preventing transcription factors from binding. 
X chromosomes.  ● Histone acetylation - causes gene activation 
3. Y-linked - inheritance on the Y chromosome.  and formation of euchromatin (easily 
Can only be passed from father to son. Will  accessible DNA). 
always be expressed whether it is dominant or  ● Histone de-acetylation - causes gene 
recessive because males only have one Y  suppression and formation of 
chromosome.   heterochromatin (hard to access DNA). 
  ● Histone methylation - can upregulate or 
  downregulate gene expression depending on 
    methyl group location and number. 
   
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Chapter 8: Microscopy & Lab Techniques  Types of Optical Microscopes 

   
Table of Contents  1. Stereo microscopes (dissection microscopes): 
● Overview of Microscopy  Use low magnification to view the surface of an 
● Types of Optical Microscopes  object. 
● Types of Electron Microscopes   2. Compound microscopes: have multiple lenses 
● Cellular Biological Lab Techniques  to view simple, one-cell thick, live cells. Without 
● Biological Laboratory Techniques for  fixing and staining, they have poor contrast.  
Nucleic Acids and Proteins  3. Bright field microscopes: compound 
● Genomics  microscopes with a bright light.  
● Miscellaneous Biological Laboratory  4. Phase contrast microscopes: can view thin 
Techniques that are Important for the DAT  samples with live cells. Light is refracted 
  through an annular ring creating a phase shift, 
Overview of Microscopy  leading to high contrast. Large phase shifts can 
  lead to a halo effect (can be reduced with 
Before we can use microscopy, we must first fix  phase plates or thinner samples). 
and stain cells:  5. Fluorescence microscopy: fluorophores 
1. Fixation: getting cells to ‘stick’ to the slide and  (fluorescent chemicals) are used to visualize 
preserving them in their most life-like state.  different parts of the cell. A dichroic filter is 
There are 2 types: heat fixation and chemical  used which allows certain wavelengths of light 
fixation. During heat fixation, cells are placed  to be reflected and others to pass through. 
on top of the slide and then the underside of  Distortions or artifacts decrease the resolution. 
the slide is run over a Bunsen burner. This  6. Confocal laser scanning microscopy: 
heats the cells, preserving and sticking them to  visualizes fluorescent objects. Can be used 
the slide.  without fluorescence tagging. Artifacts are 
2. Staining adds color to cells, making cell  reduced by focusing a beam of UV light onto the 
structures easier to visualize. Staining often kills  sample. This reduces intensity so samples must 
the cells.  be illuminated longer. 
  7. Dark field microscopy: increases contrast 
General Types of Microscopy:  between the sample and the field around it to 
1. Optical microscopy: cells are viewed directly.  allow visualization of unstained live cells. Only 
Light shines on a sample and is magnified via  scattered light is viewed - allows the sample to 
lenses. Can be used to observe living cells.   be viewed against a black background. 
2. Electron microscopy: 
cells are viewed indirectly 
via computer after being 
bombarded with electrons 
which pass through 
magnetic fields in a 
vacuum. Can be used to 
view smaller objects but 
cells must be fixed, 
stained (metal coated) and 
killed.  
 
 
   

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Types of Electron Microscopes  Cellular Biological Lab Techniques 

   
1. Scanning electron microscopy (SEM): high  Techniques to count cells: 
resolution 3D images of the surface of a  1. Hemocytometers (counting chambers): 
dehydrated sample.  gridded slide under microscope. Cells can be 
counted in a known area, and that number can 
be extrapolated to find the full volume of the 
sample. 
2. Colony Forming Units (CFUs): estimates 
number of cells plated on growth medium 
assuming that one cell gives rise to one colony. 
3. Automated cell counting includes electrical 
resistance (counting cells by observing flow of 
electricity) and flow cytometry (cells pass 
through a narrow tube and are detected by 
laser). 
 
Cell fractionation separates cell contents by 
centrifugation. A centrifuge spins contents to 
separate them by mass, density, and/or shape. More 
https://commons.wikimedia.org/wiki/File:Algae_in_Scanning_Electron_Microscope,_m dense particles collect at the bottom (pellet) and 
agnification_5000x.JPG 
 
less dense particles remain as supernatant liquid 
2. Cryo-scanning electron microscopy  on top. 
(cryo-SEM): type of SEM where the sample is 
frozen in liquid nitrogen instead of dehydrated. 
Costly and produces artifacts. 
3. Transmission electron microscopy (TEM): 
high resolution 2D images of the sample’s 
internal structures. 
 

https://commons.wikimedia.org/wiki/File:Chemical_precipitation_diagra
m.svg 
 
● Differential centrifugation: cells are first split 
open to release contents (homogenization). 
Multiple cycles where supernatant is removed 
and spun again allow for fractionation 
(isolation) of each organelle. 
 
https://commons.wikimedia.org/wiki/File:Diplorickettsia_massiliensis_Strain_20B_bac
teria_grown_in_XTC-2_cells_Transmission_electron_microscopy;_staining_with_red_ru
thenium..jpg 
 
4. Electron tomography: not a type of 
microscopy. Sandwiches TEM images to create 
a 3D image of the sample's internal structure. 
 
  Adapted from: https://commons.wikimedia.org/w/index.php?curid=37665969 
   

  ● Density centrifugation: one cycle where 

  organelles are separated by density into layers. 
   

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○ From most dense to least dense: nuclei >  5. Polymerase Chain Reaction (PCR): automated 
mitochondria/chloroplast > ER fragments >  process creating millions of copies of DNA in 3 
ribosomes  steps: 
  I. Denaturation (~95 °C): heating separates 
Biological Laboratory Techniques for Nucleic  DNA into single strands. 
Acids and Proteins  II. Primer annealing (~65 °C): DNA primers 
  hybridize with single strands. 
1. Karyotyping: observing chromosomes under  III. Elongation (~70 °C): nucleotides are added 
light microscope during metaphase. Can be  to the 3’ end of DNA using Taq 
used to diagnose conditions involving  polymerase. 
chromosomal aberrations, breakages, or  6. Bacterial cloning: cloning eukaryotic gene 
aneuploidies (e.g. Down’s syndrome or trisomy  products in prokaryotic cells. Used to produce 
21).  medicine.  
2. DNA sequencing: sequencing nucleotides in  ● Protocol: Processed mRNA for eukaryotic 
fragments of DNA. 2 methods are dideoxy  gene is isolated then treated with reverse 
chain termination or Sanger sequencing  transcriptase to make cDNA → cDNA 
(older) and next generation sequencing  incorporated into plasmid (transfer 
(newer). Can sequence complete genomes  vector) using restriction enzymes and 
piece by piece. In humans single nucleotide  DNA ligase → vector taken up by 
polymorphisms (SNPs) serve as markers for  competent bacterial cells (can undergo 
disease causing genes.  transformation; made competent using 
● Recombinant DNA is produced when  electroporation or heat shock) and undergo 
restriction enzymes cut DNA at  transformation → gene of interest is 
palindromic sequences, generating sticky  found using antibiotic resistance 
ends (have unpaired nucleotides) or blunt  (antibiotic resistant gene attached to target 
ends (have paired nucleotides).  gene) or color change (vectors containing 
  genes making cells blue) methods. 
 
 

● Restriction fragment length 

polymorphisms (RFLPs) are unique 
lengths of DNA from restriction enzymes; 
they allow for comparison between 
individuals by analyzing non-coding DNA  7. Gel electrophoresis: separates DNA 
(coding DNA is highly conserved).  fragments by charge and size. An electric field 
3. DNA fingerprinting: identifies individuals  is applied to agarose gel (top = negative 
through unique aspects of DNA such as RFLPs  cathode, bottom = positive anode). Smaller 
and short tandem repeats (STR’s). Used in  fragments travel further from top of gel. 
paternity and forensic cases.  8. Southern blotting: identifies fragments of 
4. CRISPR: used to edit specific genomic regions  known DNA sequence in a large population of 
of interest by adding or deleting specific  DNA. Electrophoresed DNA is separated into 
targeted sequences of DNA. Used in gene  single strands and identified via complementary 
therapy.  DNA probes. 
9. Northern blotting: identifying fragments of 
known RNA using an RNA probe.   

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  Genomics 
10. Western blotting: quantifies amount of target   
protein in a sample using sodium dodecyl  Genomics is the study of all genes present in an 
sulfate polyacrylamide gel electrophoresis or  organism’s genome and how they interact. 
SDS PAGE (proteins denatured and given   
negative charge proportional to their mass).  1. A genomic library stores the DNA of an 
Treated with primary antibody (binds to  organism’s genome. DNA fragments are 
target protein) and secondary antibody  incorporated into plasmids and can be 
(attached to indicator and binds to primary  screened for by using antibiotic resistance and 
antibody).  color changing techniques. They can then be 
Mnemonic: SNOW DROP  cloned via bacterial cloning. 
  2. DNA microarrays contain thousands of DNA 
  probes that bind to complementary DNA 
  fragments, allowing researchers to see which 
  genes are expressed. 
  ● Protocol: isolate a cell and remove mRNA 
  (active transcription) → synthesize cDNA 
  from mRNA using reverse transcriptase → 
 
hybridize cDNA with DNA probes → 
11. Enzyme-Linked Immunosorbent Assay 
examine microarray for fluorescence → 
(ELISA): determines if a person has a specific 
compare microarray with the sequenced 
antigen. Important to diagnose diseases (e.g. 
genome. 
HIV). Antibodies are placed on a microtiter 
3. Transgenic animals are models used to 
plate with a sample and change color if 
identify the function of a gene. A gene is taken 
antigens are present. 
from one organism and inserted into another. 
12. Pulse chase experiments: useful for studying 
Can be used for mass medication production 
gene expression and the fate of proteins by 
(e.g. clotting factors for hemophiliacs). This 
viewing how a protein moves through a cell. 
process is labor intensive. 
During the pulse phase amino acids are 
4. Reproductive cloning: producing a genetic 
radioactively labeled and then incorporated 
copy of an organism from a somatic cell. A 
into proteins. The chase phase prevents 
multipotent cell must be converted to a 
radioactively labelled protein production. 
totipotent cell. E.g. Dolly the sheep. 
Using simple staining, the radioactive proteins 
● Totipotent cells: can differentiate into an 
can be tracked. 
entire organism (including extraembryonic 
 
membranes). E.g. zygote → morula. 
 
● Pluripotent cells: can differentiate into 
 
the three germ layers (endoderm, 
 
mesoderm, ectoderm). Cannot give rise to 
 
extraembryonic membranes. 
   
● Multipotent cells: can give rise to some of 
the three germ layers - not all. 
 
 
 
 
   

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Miscellaneous Biological Laboratory  Fluorescence Lifetime Imaging Microscopy 

Techniques that are Important for the DAT  (FLIM): provides a quantitative measure of the 
  concentration of various ions, molecules, and gases 
1. Chromatography: separating components of  in a cell. Cell is irradiated with light and fluorescence 
a heterogeneous sample using differential  lifetime is measured. 
solubility. The sample is dissolved in the solvent 
(mobile phase) and placed in an apparatus 
containing the stationary phase. The mobile 
phase climbs up the stationary phase and the 
different components ascend to different 
heights. 

Adapted from: https://commons.wikimedia.org/w/index.php?curid=1175699 

 
2. Fluorescence Recovery After 
Photobleaching (FRAP): quantitative measure 
of how and where biomolecules move in a live 
cell. 
● Protocol: baseline fluorescence is 
measured → area of the sample is 
photobleached → photobleached molecules 
are replaced by unbleached molecules 
overtime due to cell dynamics → area   
gradually recovers fluorescence.  3. Knockout mice: selected gene is ‘knocked out’ 
 
and changes between knockout and wild type 
are observed. 
 

     
 
 

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Chapter 9: Diversity of Life  bacteria have a thin peptidoglycan layer and a 

  second outer membrane. Both are covered by a 
Table of Contents  capsule (a virulence factor protecting the 
● Taxonomy  bacteria from drying out). 
● Prokaryotes   
● Eukaryotes  Gram Positive Bacteria:  
(Click here to see our taxonomy video miniseries)  ● stain dark purple. 
(Click here to download our taxonomy cheat sheet)  ● thick peptidoglycan layer in cell wall. 
  ● no outer membrane. 
Taxonomy  ● very minor periplasm (outside plasma 
  membrane). 
Taxonomy is the science of classifying organisms.  ● No lipopolysaccharide (LPS - an 
endotoxin released when bacteria is 
destroyed). 
● Secrete exotoxins. 
● Contain teichoic acids (polysaccharide 
connecting peptidoglycan layer and plasma 
membrane for rigidity and structure). 
 
Gram Negative Bacteria: 
● Stain pink (due to counterstain). 
● Thin peptidoglycan layer in cell wall. 
● Contains periplasm between inner and outer 
membranes. 
● Outer membrane present. 
  ● LPS present (in outer membrane). 
Mnemonic:   ● Secrete exotoxins. 
King Phillip Came Over For Great Soup.  ● No teichoic acids. 
The 6 kingdoms are: Archaea, Eubacteria,   
Protista, Fungi, Plantae, Animalia.  Eubacteria vs. Archaea 
  Similarities:  
Domains  ● Contain cell walls. 
  ● 70S ribosomes. 
A domain is the largest classification of life; the  ● DNA is organized in circular plasmids 
three domains are Archaea, Bacteria (Eubacteria)  (horizontal gene transfer via pilli). 
and Eukarya. Archaea are single-celled and tend  ● Flagellum for movement. 
to be extremophiles; they are prokaryotic.  ● Reproduce via binary fission. 
Bacteria are also single-celled and prokaryotic.  Differences: 
Eukarya are classified as having organelles and   

membrane-bound nuclei.   Eubacteria  Archaea 

 
Prokaryotes  Cell wall contains  Cell wall lacks 
  peptidoglycan; lipids  peptidoglycan; lipids 
bound via  bound via 
Prokaryotes: organisms that do not have 
ester-linkage.  ether-linkage. 
membrane bound nuclei and tend to not have 
membrane bound organelles. E.g. Eubacteria and  Ribosome has unique  Ribosome has unique 
Archaea.  structure.  structure. 
Eubacteria: Gram Positive vs. Gram Negative 
  DNA lacks introns and  Contain introns, some 
Gram positive bacteria have a thick peptidoglycan  histones.  have histones. 
layer in their cell wall, whereas gram negative   

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Eukaryotes  Fungi 
   
Eukaryotes: organisms whose cells contain  Fungi are heterotrophic saprophytes. 
membrane-bound nuclei and organelles. E.g.   
Protista, Fungi, Plantae, and Animalia.  1. Nonfilamentous fungi (e.g. yeast) are 
  unicellular, reproduce asexually by budding, and 
Protista  are facultative anaerobes. 
  2. Filamentous fungi (e.g. molds) are 
Protists: kingdom of (mostly unicellular)  multicellular, multinucleate (form hyphae), 
eukaryotic organisms.  reproduce sexually, and are aerobic. 
   
  Hyphae are long, branching filaments that extend 
1. Fungus-like protists: unlike fungi, no cell wall  out to form a network of fungi (mycelium). 
made of chitin. Can move via cilia or flagella  Mycelium can either grow with septate hyphae 
(e.g. slime molds). Are saprophytic and feed  (have septa dividing hyphae into different 
via phagocytosis. Reproduce via asexual  sections) or with coenocytic hyphae (one long 
reproduction and sporulation (resist  continuous multinucleated cell; cytokinesis does 
environmental conditions).  not occur during cell division). 
2. Plant-like (algae-like) protists: among the   
most important primary producers.    
● Diatoms, and euglenoids are unicellular,   
photosynthetic autotrophs that reproduce   
asexually and are found in aquatic   
environments.   
● Dinoflagellates: responsible for red tide   
(toxins build up, O2 in water is depleted),   
have two flagella (find food in absence of   
light), and are heterotrophic (parasitic).   
3. Animal-like protists: known as protozoa,   
have food vacuoles. Include amoeba and  Under favorable environments, fungi reproduce 
paramecium. Heterotrophic (move via flagella  asexually by producing a haploid spore-producing 
and cilia) and are often parasitic pathogens.  structure which produces haploid spores that grow 
  via mitosis. In unfavorable environments, fungi 
reproduce sexually-producing genetically different 
offspring with greater chance of survival. Two 
hyphae fuse their cytoplasm (plasmogamy) to 
create a single fused cell with 2 haploid pronuclei 
which fuse (karyogamy) to produce a single diploid 
cell. The diploid cell produces a spore-producing 
structure that produces spores via meiosis. 
 
Lichens are symbiotic autotrophs where a 
fungus is paired with either algae or cyanobacteria. 
The fungus protects the cyanobacteria/algae and 
  provides it with water and nutrients while 
https://commons.wikimedia.org/w/index.php?curid=38204234 
algae/cyanobacteria photosynthesize, to produce 
 
food for the fungi.  
   
 
   

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Animalia    
   
Animals are eukaryotic, diploid, multicellular   
heterotrophic aerobes.   
   
Animals can be distinguished based on the  Porifera: 
presence of a coelom (cavity). In coelomates 
mesoderm surrounds the coelom on all sides 
whereas in acoelomates it does not, and in 
pseudocoelomates the coelom is partially 
surrounded. The pseudocoelom is a 
hydroskeleton (fluid pressure providing structural 
support) that helps with motility. 

 
https://commons.wikimedia.org/wiki/File:Aplysina_archeri_(Stove-pipe_Sponge-pink_
variation).jpg 
 

 
Porifera: 
● E.g. Sponge 
● Body symmetry: Asymmetrical 
● Tissue organization: Parazoa (no true tissues) 
● Circulatory system: None (diffusion) 
● Nervous system: None 
● Respiratory system: None (diffusion) 
● Digestive system: Intracellular digestion via 
amoebocytes (totipotent cells contribute to 
structure, digestion, regeneration, move via 
pseudopodia) 
 
General characteristics: sessile (non-motile), 
suspension feeders, aquatic habitats, earliest 
animals, reproduce asexually (budding) or sexually 
(hermaphrodites - has male and female sex   
organs).  https://commons.wikimedia.org/wiki/File:Porifera_body_structures_01.png 
 
   
   

     
 
 

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Cnidaria:  Cnidaria: 
● E.g: hydra, jellyfish, sea anemone, coral. 
● Body symmetry: Radial (around central axis). 
● Tissue organization: Diploblasts (two cellular 
layers: endo- and ectoderm), true tissues 
(eumetazoa). 
● Circulatory system: None (diffusion). 
● Nervous system: Nerve net (neurons spread 
apart), no brain. 
● Respiratory system: None (diffusion). 
● Digestive system: gastrovascular cavity (one 
opening, two way digestion, acts as hydrostatic 
skeleton to aid movement). 
 
General Characteristics: Aquatic habitats, some   
have nematocysts (cells shooting poisonous  https://commons.wikimedia.org/wiki/File:Moon_jellyfish_at_Gota_Sagher.JPG 

barbs), some have life cycles that switch from   

polyp (non-motile, reproduce asexually) to medusa   
 
(motile, reproduce sexually) forms.   
   
Platyhelminthes:  Platyhelminthes: 
● E.g. Flatworms, trematoda, flukes, tapeworm, 
planaria. 
● Body symmetry: Bilateral (right and left 
halves, axis at sagittal plane) with 
cephalization (central nervous system - brain). 
● Tissue organization: Triploblasts (three germ 
layers), eumetazoa. 
● Circulatory system: None (diffusion). 
● Nervous system: Two nerve cords (dense 
nerve bundle running along length of 
invertebrates), anterior centralized ganglia 
(brain), some planarians have eyespots. 
● Respiratory system: None (diffusion). 
● Digestive system: Gastrovascular cavity   
(except tapeworms - absorb food).  https://commons.wikimedia.org/wiki/File:Platyhelminthes,_Tricladida,_Terricola,_Atla
ntic_forest,_northern_littoral_of_Bahia,_Brazil_(14617707721).jpg 
● Excretory system: Protonephridia (bundles     
of flame cells - involved in osmoregulation). 
 
General Characteristics: reproduce sexually 
(hermaphrodites) or asexually (regeneration), mainly 
aquatic habitats, parasitic lifestyles, most primitive 
of triploblasts, has organs.  
 
 
 
 
 
 
 
 

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Nematoda:   
● E.g. Round worm, hook worm, trichinella, C.   
elegans, ascaris.  Nematoda: 
● Body symmetry: Bilateral. 
● Tissue organization: Triploblasts, eumetazoa. 
● Circulatory system: None (diffusion). 
● Nervous system: Nerve cord and ring 
(surrounds esophagus). 
● Respiratory system: None (diffusion). 
● Digestive system: Alimentary canal (passage 
between mouth and anus). 
 
General Characteristics: Some have cuticle 
(prevents degradation by host digestive system), 
longitudinal muscles (no circular muscles), 
parasitic, not segmented. Primarily reproduce 
sexually, but some reproduce asexually through   
parthenogenesis.  https://commons.wikimedia.org/w/index.php?curid=646062 

   
Rotifera:  Rotifera: 
● Key names: Rotifers. 
● Body symmetry: Bilateral. 
● Tissue organization: Triploblasts, eumetazoa. 
● Circulatory system: None (diffusion). 
● Nervous system: Cerebral ganglia (brain) with 
nerves extending through the body. 
● Respiratory system: None (diffusion). 
● Digestive system: Alimentary canal, mouth 
and anus. 
● Excretory system: Protonephridia and flame 
cells. 
 
General Characteristics: Not truly segmented, 
can reproduce sexually or parthenogenetically, 
mostly freshwater environments. Draw food and 
water into mouth by beating cilia. 
 
     
 
 
 
 
 
 
 
 
 
 
 
 
 

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Annelida:  Annelida: 
● E.g. Earthworm, leech. 
● Body symmetry: Bilateral. 
● Tissue organization: Triploblasts, eumetazoa. 
● Circulatory system: Closed circulatory 
system (blood pumped through vessels by 
heart), multiple pairs of aortic arches, distinct 
arteries and veins. 
● Nervous system: Ventral nerve cord, anterior 
ganglia (brain). 
● Respiratory system: None (diffusion). 
● Digestive system: Alimentary canal, mouth 
and anus.   
● Excretory system: Most have metanephridia  https://commons.wikimedia.org/w/index.php?curid=105569 

(excretory glands for osmoregulation. Tubes of   

cilia move fluid emptying into coelom, ducts   
bring fluid to the exterior).   
● Embryonic development: Protostome   
(blastopore forms mouth).   
 
 
 
 
 
 
 
 
Adapted from: https://commons.wikimedia.org/w/index.php?curid=8062105   
   
General Characteristics: Segmented bodies,   
coelom is divided by septa, sexual (hermaphrodites)   
and asexual (regeneration) reproduction,   
longitudinal and circular muscles.   
   
Mollusca:   Mollusca: 
● E.g. Clam, snail, slug, squid, octopus, 
cephalopod, gastropod. 
● Body symmetry: Bilateral. 
● Tissue organization: Triploblasts, eumetazoa. 
● Circulatory system: Mainly open; hemocoel 
(spaces inside an organism where blood freely 
flows around organs).  
● Nervous system: Ventral nerve cords and 
brain. 
● Respiratory system: Gills. 
● Digestive system: Complete (alimentary 
 
canal and accessory glands), mouth and anus,  https://commons.wikimedia.org/wiki/File:Ab_mollusca_29.jpg 
radula (tongues covered in tiny teeth - unique     
to mollusks). 
● Excretory system: Nephridia (pairs of 
osmoregulatory ‘kidneys’ in invertebrates). 
● Embryonic development: Protostome 

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Arthropoda (all):   
● Body symmetry: Bilateral.   
● Tissue organization: Triploblasts, eumetazoa.   
● Circulatory system: open, hemolymph   
(equivalent to blood).   
● Nervous system: Fused ganglia (masses of   
nerve tissue), ventral nerve cord.   
● Digestive system: one-way digestion, some   
have salivary glands.   
● Embryonic development: Protostome.   
   
1. Arthropoda (Insecta):  Arthropoda (Insecta): 
● E.g. ant, grasshopper. 
● Respiratory system: Spiracles (small 
openings on exoskeleton where air enters) 
branch into tracheal tubes (site of gas 
exchange). 
● Excretory system: Malpighian tubules 
(small tubes on abdomen, help with uric 
acid excretion). 
 
General Characteristics: Exoskeleton of chitin, 
jointed appendages, three pairs of legs, more   
species than any other phylum combined,  https://commons.wikimedia.org/wiki/File:Grasshopper_2.JPG 

metamorphosis (distinct stages, altered   

 
appearance as insect matures).  Arthropoda (Arachnida): 
 
2. Arthropoda (Arachnida): 
● E.g. spider, scorpion. 
● Respiratory system: trachea or book 
lungs (sheets of vascularized tissue on 
either side to increase surface area). 
● Excretory system: Malpighian tubules and 
/ or coxal glands. 
 
General Characteristics: Exoskeleton, jointed 
 
appendages, four pairs of legs, terrestrial habitats.  https://commons.wikimedia.org/wiki/File:Class_Arachnida.png 
   
3. Arthropoda (Crustacea):  Arthropoda (Crustacea): 
● E.g. lobster, crayfish, crab. 
● Respiratory system: some have gills. 
● Excretory system: Green glands (aquatic), 
malpighian tubules (terrestrial). 
 
General Characteristics: Exoskeleton, jointed 
appendages, aquatic and terrestrial habitats.   
  https://commons.wikimedia.org/wiki/File:Arthropods_crab.jpg 

   
   
     
 

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Echinodermata:  Chordates (Most important for DAT): 

● E.g. Starfish, sea urchin, sea cucumber.  ● E.g. Vertebrates. 
● Body symmetry: Bilateral (larvae), five fold  ● Body Symmetry: Bilateral. 
radial (adult).  ● Tissue Organization: Triploblasts, eumetazoa. 
● Tissue Organization: Triploblasts, eumetazoa.  ● Embryonic Development: Deuterostome. 
● Circulatory system: open, no heart.   
● Nervous System: Nerve ring and radial 
nerves. 
● Respiratory system: None (diffusion). 
● Digestive system: Complete, mouth and anus. 
● Excretory system: None (diffusion). 
● Embryonic Development: Deuterostome 
(blastopore forms anus). 
 
General Characteristics: Spiny, central disk 
(central portion from which arms radiate, contains 
mouth, anus and opening for water to enter for 
water vascular system), tube feet (suction cups for 
walking and obtaining food), sexual or asexual   
reproduction, closest related major phyla to   
Adapted from: https://commons.wikimedia.org/wiki/File:Figure_29_01_04.jpg
chordates.   
  Shared Traits of all Chordates: 
Echinodermata:   
1. Notochord: cartilaginous rod derived from 
mesoderm. Forms the primitive axis and 
supports the body during embryonic 
development. Lost in most chordates, and 
replaced by bone. 
2. Dorsal Hollow Nerve Cord: forms spinal cord - 
basis of nervous system and brain. 
3. Pharyngeal Gill Slits: forms pharynx, gills, 
other feeding structures. Provide channels 
from pharynx to other structures. In humans 
forms Eustachian tubes and other head and 
neck structures. 
4. Muscular post-anal tail: lost during 
  embryonic development in humans and many 
https://commons.wikimedia.org/wiki/File:Fromia_monilis_(Seastar).jpg 
other chordates. 
 
 
 
   
   

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Types of Chordates:  5. Fish (Bony): 

  ● E.g. Salmon, halibut. 
1. Lancelets (also known as Amphioxus):  ● Subphylum: Vertebrata. 
● Subphylum: Cephalochordata.  ● Circulatory system: Two-chambered 
● Circulatory system: Closed circulatory  heart. 
system, lacks heart, contains contractile  ● Respiratory system: Gills. 
blood vessels.  ● General characteristics: scales, bony 
● Respiratory system: Gills.  skeleton. 
● General characteristics: Keep all the   
same developmental characteristics as  6. Amphibia: 
other chordates, but lack vertebrae.  ● E.g. Frog, toad, salamander, newt 
Commonly used to study the origin of  ● Subphylum: Vertebrata 
vertebrates.   ● Circulatory system: Three-chambered 
  heart. 
2. Tunicates (also known as Urochordata):  ● Respiratory system: Gills (juvenile), Lungs 
● Subphylum: Tunicata.  (adult). 
● Circulatory system: Both closed and open  ● General characteristics: No scales. 
circulatory systems.  Undergo metamorphosis. Tadpoles 
● Respiratory system: Gills.  (aquatic) have tails, no legs. Adults 
● General characteristics: Sessile, filter  (terrestrial) two pairs of legs, no tail. 
feeders, hermaphroditic, sexual and   
asexual (budding) reproduction. Benthic  7. Mammalia (Monotremes): 
habitats (bottom of a body of water),  ● E.g. Duckbill platypus, spiny anteater. 
notochord in larvae.  ● Subphylum: Vertebrata. 
  ● Circulatory system: Four-chambered 
3. Fish (Jawless):  heart. 
● E.g. Agnatha, lamprey, hagfish.  ● Respiratory system: Lungs. 
● Subphylum: Vertebrata.  ● General characteristics: Warm blooded 
● Circulatory system: Two-chambered  (homeothermic), feed young with milk, 
heart.  leathery eggs, mammary glands with many 
● Respiratory system: Gills, countercurrent  openings (no nipples). 
exchange.   
● General characteristics: Notochord in  8. Mammalia (Marsupials): 
larvae and adult, cartilaginous skeleton.  ● E.g. Kangaroo, opossum. 
  ● Subphylum: Vertebrata. 
4. Fish (Cartilaginous):  ● Circulatory system: Four-chambered 
● E.g. Shark.  heart. 
● Subphylum: Vertebrata.  ● Respiratory system: Lungs. 
● Circulatory system: Two-chambered  ● General characteristics: Homeotherms, 
heart.  feed young with milk. 
● Respiratory system: Gills.   
● General characteristics: Jaws and teeth,  9. Mammalia (Placental): 
reduced notochord with cartilaginous  ● E.g. Bat, whale, mouse, human. 
vertebrae.  ● Subphylum: Vertebrata. 
  ● Circulatory system: Four-chambered 
  heart. 
    ● Respiratory system: Lungs. 
● General characteristics: homeotherms, 
placenta supports fetus. 
 
   

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10. Reptilia:  11. Birds: 

● E.g. Turtle, snake, crocodile, alligator.  ● E.g. Eagle, blue jay. 
● Subphylum: Vertebrata.  ● Subphylum: Vertebrata. 
● Circulatory system: Three-chambered  ● Circulatory system: Four-chambered 
heart (exception: crocodiles and alligators  heart. 
= four-chambered heart).  ● Respiratory system: Lungs. 
● Respiratory system: Lungs.  ● General characteristics: homeotherms, 
● General characteristics: Mainly  eggs in shells. 
terrestrial, leathery eggs, internal     
fertilization, cold blooded 
(poikilothermic). 
 
 
Prokaryotes vs. Eukaryotes   

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Chapter 10: Plants  Primary vs. Secondary Growth 

   
Table of Contents:  Plant growth takes place via mitosis at meristems.  
● The Seed and Germination   
● Primary vs. Secondary Growth  Primary growth is vertical growth occurring at 
● Plant Tissues  apical meristems (located at tips of roots and 
● Leaf Structures  shoots). Occurs before secondary growth. 
● Movement of Water  Root Growth: root cap covers roots protecting the 
● Movement of Food  apical meristem. The root tip has three zones: 
● Plant Hormones  ● Zone of division: where apical meristem cells 
● Alternation of Generations  are located and divide. 
● Homosporous vs. Heterosporous Plants  ● Zone of elongation: above apical meristem, 
● Bryophytes  cells absorb water and elongate. 
● Tracheophytes  ● Zone of maturation: cells differentiate to 
● Flower Structures  specific plant tissues. 
● Angiosperms: Monocots vs. Dicots   
● Nitrogen Fixation  Secondary growth is horizontal growth occurring 
  at lateral meristems (vascular cambium and 
The Seed and Germination  cork cambium). Only occurs in woody plants. 
   
1. Seed coat: hard outer layer that covers and  Vascular cambium is a ring of meristematic tissue 
protects the seed.  located between primary xylem (closer to center) 
2. Endosperm: storage material, provides the  and primary phloem (closer to outer edge). Cells 
embryo with nutrients.  produced inside the ring of vascular cambium 
3. Embryo: consists of 4 parts:   become secondary xylem (forms wood along with 
● Radicle: first to emerge, develops into root,  pith) and cells outside become secondary phloem 
anchors the plant into soil.  (forms bark with cork and cork cambium). New 
● Hypocotyl: bottom region of young shoot.  xylem is produced every year (forming growth 
● Plumule: develops into leaves.  rings) whereas new phloem replaces old phloem. 
● Epicotyl: top region (shoot tip).   
  Cork cambium is a ring of meristematic tissue 
located outside the phloem. Produces cork, the 
outermost protective layer. 
 
 
 
   

 
 
Germination: the sprouting of a seedling from a 
previously dormant state when environmental 
conditions are favorable. Water is the most 
important condition. The seed absorbs water 
(imbibition) which breaks the seed coat and 
initiates growth. 
   

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Plant Tissues  Leaf Structures 

   
1. Ground tissue: provides structural support,  Leaves are covered by an epidermal layer, 
makes up most of the plant's mass.  covered by a waxy cuticle. Stomata in the lower 
● Parenchyma: filler tissue, makes up the  epidermis open and close, allowing for gas 
bulk of plant, thin cell walls.  exchange. Water influx to the guard cells makes 
● Collenchyma: extra support (e.g. in areas  them turgid, opening the stomata. Stomata are 
of active growth), irregular cell walls.  open when CO2 concentration is low (allows for CO2 
● Sclerenchyma: provides main structural  intake and photosynthesis) and closed when CO2 
support, thick cell walls.  concentrations are high and when temperatures 
2. Vascular tissue: transports materials from a  are high (prevents water loss via transpiration). A 
source to a sink (source to sink theory). The  balance must exist between opening stomata for 
stele is formed by xylem, phloem, and the  food production via photosynthesis and closing 
pith (made of parenchyma) in the center of the  stomata to prevent water loss (desiccation). 
plant for transport.   
● Phloem: transports sugars from leaves  Between the upper and lower epidermis is the 
(source) to roots and other areas (sink).  mesophyll. 
Made of sieve cells (long cells, lacking  ● Palisade mesophyll: closer to upper 
organelles, connected to form a tunnel for  epidermis, tightly packed cells that carry out 
transport) and companion cells  photosynthesis. 
(connected to sieve cells, contain organelles  ● Spongy mesophyll: closer to lower epidermis, 
for metabolic functions).  loosely-packed allowing for gas exchange. 
● Xylem: transports water from roots   
(source) to leaves (sink) and provides  Bundle sheath cells surround and protect the 
structural support. Made up of tracheids  vascular bundle. 
(long and thin, water travels through pits in   
their tapered ends) and vessel elements 
(short and stout, water travels via 
perforations in cell walls). 
3. Dermal tissue: outer layer of the plant. 
Provides protection and regulation. 
● Epidermis: covered by cuticle (waxy layer) 
which limits water evaporation. 
● Root hairs: increase surface area of roots 
for greater nutrient and water uptake.    
  Adapted from: 
Water uptake in the roots occurs via the  https://commons.wikimedia.org/w/index.php?curid=521358 

symplastic pathway (inside the cell’s cytoplasm)   

or the apoplastic pathway (outside the cell   
through cell walls). The Casparian strip (made of     
fat and wax) is an impenetrable substance in the 
cell walls of the roots. It forces water coming from 
the cell walls into the cytoplasm for filtering before 
entering the rest of the plant. 
 
   

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Movement of Water  3. Cytokinins: regulate cell differentiation and 

  division with auxins. Can prevent aging. 
1. Cohesion-tension theory: transpiration, the  4. Gibberellins: responsible for stem and shoot 
driving force, causes water to evaporate from  elongation, elimination of dormancy of a seed, 
the stomata and leads to a transpirational  flowering, fruit production, leaf and fruit death. 
pull. This cohesive force (between similar  5. Abscisic Acid: functions during stress. 
substances, e.g. the water molecules) pulls the  Promotes dormant seeds, closes stomata 
water column upward.  (drought), inhibits growth. 
2. Capillary action: an adhesive force (between   
dissimilar substances) due to attraction  Alternation of Generations 
between water and xylem vessels that causes   
water to climb upwards.  Alternation between diploid and haploid. 
3. Root pressure: builds up in roots to produce 
an osmotic gradient which drives water from 
soil into the roots.  
 
Movement of Food 
 
Pressure flow hypothesis: source cells produce 
sugar and load it into phloem → increased sugar 
concentration creates a gradient that pulls water 
into phloem → turgor pressure in phloem increases, 
resulting in bulk flow movement of sugar from 
leaves down to roots. 
   
Plant Hormones   
  Two haploid gametes fuse producing diploid 
1. Ethylene: gas that increases fruit ripening.  zygote → zygote becomes sporophyte via mitosis 
2. Auxins: cause cell growth. Work with  → in their sporangia, sporophyte undergoes 
cytokinins. Responsible for plant tropisms  meiosis to produce haploid spores → spore 
(growth in certain directions). Auxin  becomes gametophyte via mitosis → 
concentrated on one side of a stem leads to  gametophyte produces gametes → cycle repeats. 
asymmetric growth.   
● Phototropism: growth towards light.   
● Gravitropism: growth away from pull of  Homosporous vs. Heterosporous Plants 
gravity.   
● Thigmotropism: growth in response to  Homosporous plants: bisexual gametophyte, 
contact (e.g. vine growing up a wall)  produces one type of spore. 
   
Heterosporous plants: produce two types of 
spores; microspores (male) and megaspores 
(female). 
 
   

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Bryophytes  not-flagellated and is dispersed in seeds 

  by wind. 
Nonvascular plants (e.g. mosses, hornworts,  ● Angiosperms: Most abundant plant. 
liverworts), therefore are small and short. Found in  Flower-bearing and fruit-producing (plant 
moist habitats, grow horizontally to remain close to  ovary, protects seeds). Sperm is 
water and nutrients. Contain rhizoids (hair-like  not-flagellated and is dispersed by wind 
projections) which aid in water absorption and  or animals often as pollen. Can exhibit 
minor anchorage.   double fertilization (female gamete 
  fertilized by two male sperm). 
Majority of their life cycle is spent in the   
gametophyte stage ; they have a reduced  Flower Structures 
sporophyte which depends on and is attached to   
the gametophyte.  1. Petals: attract animals to achieve pollination. 
2. Stamen: male plant sex organ. Composed of 
anther (site of microspore formation) and 
filament (supports anther). 
● Microspore undergoes mitosis to form 
generative cell (contains sperm) and tube 
cell which combine to form pollen. 
3. Pistil: female plant sex organ. Composed of 
stigma (top), style (tube leading to ovary), and 
ovary (contains ovule or egg). 
Fertilization 

 
 
Tracheophytes 
 
Tracheophytes are Vascular, grow vertically and 
 
tall, and have a root system for anchorage. Most of 
Pollen lands on stigma → tube cell elongates down 
the life cycle is spent in the sporophyte stage. 
style forming pollen tube → generative cell travels 
 
down pollen tube to ovary → splits forming two 
1. Seedless tracheophytes: (lycophytes and 
sperm cells (double fertilization) 
pterophytes, e.g. club moss, quillworts, fern, 
● One sperm cell meets ovule to form the 
horsetail). Mostly heterosporous with 
seed or embryo. Ovary develops into fruit, 
flagellated sperm. 
which is eaten by animals and deposited in 
2. Seed-bearing tracheophytes (all 
a new location (gene migration). 
heterosporous) 
● The other sperm cell combines with ovule’s 
● Gymnosperms: The first seeded plants. 
polar nuclei to form the endosperm. 
Seed not protected. E.g. conifers such as 
   
firs, spruce, pine, redwood. Sperm is 

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Angiosperms: Monocots vs. Dicots  Nitrogen Fixation 

   
Cotyledons: first leaves to appear on seedling.  Plants have a symbiotic relationship with 
Contain nutrients from seed to feed the growing  nitrogen-fixing bacteria. Bacteria fix atmospheric 
seedling.  nitrogen into a usable form for plants; in return, 
  plants produce food for bacteria via 
photosynthesis. 
Monocotyledons  Dicotyledons 
(Monocots)   (Dicots)   
1. Nitrogen fixing bacteria (in root nodules of 
Single cotyledon  Two cotyledon  legumes) fix atmospheric nitrogen (N2) to 
ammonia (NH3) and ammonium (NH4+). 
Long narrow leaf  Broad leaf  2. Nitrifying bacteria convert ammonia and 
    ammonium to nitrites (NO2-) and then to nitrates 
Parallel veins  Network of veins 
(NO3-). 
Vascular bundles  Vascular bundles in a  3. Nitrates are taken up by plants (assimilation of 
scattered  ring  nitrogen) and incorporated into amino acids 
and chlorophyll. Animals (consumers) acquire 
Floral parts in  Floral parts in  nitrogen by eating plants (producers). 
multiples of 3  multiples of 4 or 5  4. Detritus of dead decaying plants and animals 
  provides soil with nitrates. 
  5. Denitrifying bacteria: convert nitrates back to 
    atmospheric 
nitrogen 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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Chapter 11: Anatomy and Physiology
 
Chapter 11.1: Circulatory System…………………………………………..………………………….....66 

Chapter 11.2: Respiratory System………………………………………………………………………...71 

Chapter 11.3: Human Immune System………………………………………………………………...77 

Chapter 11.4: Nervous System……………………………………………………………………………..81 

Chapter 11.5: Muscular System…………………………………………………………………………....87 

Chapter 11.6: Skeletal System……………………………………………………………………………...90 

Chapter 11.7: Endocrine System…………………………………………………………………………..93 

Chapter 11.8: Digestive System…………………………………………………………………………….98 

Chapter 11.9: Excretory System…………………………………………………………………………….101 

Chapter 11.10: Integumentary System………………………………………………………………....103 

   

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Chapter 11.1: Circulatory System  Human Heart 

Table of Contents 

● Invertebrate Circulation 
● Vertebrate Circulation 
● Human Heart 
● Cardiac Cycle 
● Heart Function Measurements 
● Blood Vessels 
● Blood and Blood Types 
● Fetal Circulation 
● The Lymphatic System 

Invertebrate Circulation 

1. No circulatory system – use simple diffusion 

to distribute nutrients. Includes bacteria, 
protista, fungi, invertebrate animals.   

2. Open circulatory system – pumps fluid called  https://commons.wikimedia.org/wiki/File:Diagram_of_the_human_heart_(cropped).svg
 

hemolymph into sinuses or hemocoel. 

Flow of blood through heart 
Includes some mollusca, arthropoda, 
Echinodermata. 
1. Right atrium – Deoxygenated blood is returned 
here from the upper superior vena cava and 
3. Closed circulatory system – Use a pumping 
the lower inferior vena cava. Blood passes 
heart to move blood through vessels. Includes 
through the right atrioventricular valve (AV 
annelida (earthworms) 
valve, or tricuspid valve) to the right 
Vertebrate Circulation  ventricle. AV valve is attached to papillary 
muscles, which contract to close the AV valves 
Most chordates (eukaryotic vertebrates within  and prevent backflow of blood. 
kingdom Animalia) have a closed circulatory 
system.  2. Right ventricle – Pumps deoxygenated blood 
through the pulmonary semilunar valve to the 
● 2-chambered hearts (atrium and ventricle) – fish.  pulmonary artery. Blood enters pulmonary 
Deoxygenated blood fills the heart and is pumped  circulation. When the ventricle contracts, the 
to the gills for oxygen exchange.  AV valve is closed and the pulmonary 
● 3-chambered hearts (2 atriums and 1 ventricle) –  semilunar valve is open. When the ventricle 
amphibians and reptiles. Poikilothermic chordates.  relaxes, the AV valve is open to refill the 
Alligators and crocodiles are exceptions, they have  ventricle, and the pulmonary semilunar valve 
4-chambered hearts.  closes to prevent the backflow of blood. 
● 4-chambered hearts (2 atriums and 2 ventricles) – 
birds and humans. Homeothermic chordates.  3. Left atrium – Oxygenated blood is returned 
here from the lungs from the pulmonary vein. 
   Blood passes through the left AV valve (or 
bicuspid, or mitral valve) to the left ventricle. 
 
4. Left ventricle – Most muscular chamber of 
    the heart. Pumps oxygenated blood into the 
aorta and systemic circulation. 

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Pulmonary circulation moves deoxygenated 
blood from heart to the lungs and back in order 
for it to become oxygenated. Pathway: 

Right atrium → tricuspid valve → 

right ventricle → pulmonary semilunar valve → 
pulmonary arteries → lung → pulmonary veins → left 
atrium 
  
Systemic circulation moves oxygenated blood 
from the heart throughout the body. Pathway: 

Left atrium → bicuspid / mitral valve → left   

ventricle → aortic semilunar valve → aorta → body 
→ vena cava → right atrium  Systole occurs right after the ventricles eject their 
blood into the arteries they connect to. Therefore, 
Human Cardiac Cycle  it is the phase of the cardiac cycle where blood 
pressure is highest in the arteries. 
The heart needs to contract and relax rhythmically 
in order to pump blood throughout the body.  Diastole occurs right after the atria contract to fill 
Cardiomyocytes (heart muscle cells) have  the ventricles. The myocardium is completely 
automaticity, which means they are self-excitable  relaxed at this point. Diastole is the phase of the 
and able to initiate an action potential without an  cardiac cycle where blood pressure is lowest in the 
external nerve.  arteries. 

The cardiac cycle: 

1. The SA node (pacemaker) is located in the 

upper wall of the right atrium and usually 
initiates the cardiac cycle. It has the greatest 
automaticity and is most likely to reach 
threshold to stimulate a heartbeat. It sends a 
signal to contract both atria to send blood to 
the ventricles. It also sends a signal to the AV 
node to initiate contraction. 

2. The AV node is located in the lower wall of the 

right atrium. The function of the AV node is to 
add a brief delay between the contraction of 
the atria and the contraction of the ventricles. 
It also sends a signal to the bundle of His, 
located in the interventricular septum 
between the ventricles. The bundle of His 
 
carries the signal to the Purkinje fibers, which 
contract the ventricles.      

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Heart Sounds  Heart Function Measurements 

The heartbeat sound is described as a “lub-dub”.  Heart rate (HR) is how fast the heart beats. 
Tachycardia is greater than 100 beats per minute, 
1. Lub – The atria are relaxed, while the  bradycardia is less than 60 beats per minute. 
ventricles are contracting. The noise 
comes from the AV valves snapping shut  Stroke volume (SV) is the volume of blood 
as the ventricles contract.  pumped from the heart with each beat. Stroke 
volume is calculated by subtracting end-systolic 
2. Dub – The atria are contracting, while the  volume from end-diastolic volume. 
ventricles are relaxing. The noise comes 
from the semilunar valves snapping  Cardiac output (CO) is the stroke volume 
shut.  multiplied by the heart rate. This tells us the 
volume of blood being pumped by the heart in 1 
Systole happens between the lub-dub sounds.  minute. 
Diastole occurs between the dub and next lub 
sound.  CO = HR x SV 
 
Signal Transduction  Total peripheral resistance (TPR) is the total 
The heart has intercalated discs that connect  amount of resistance that blood faces when 
adjacent heart cells (cardiomyocytes). Intercalated  flowing through the vasculature of the body. 
discs are made of desmosomes and gap junctions  Vasoconstriction increases TPR, while vasodilation 
and function to transmit the signal to contract in a  decreases TPR. 
coordinated, rhythmic fashion. 
Systolic blood pressure is the highest pressure in 
Measuring the Cardiac Cycle  your arteries when your ventricles contract. This is 
the top number in a blood pressure reading. 

120/80 → 120 mmHg is the systolic 

pressure. 
 
Diastolic blood pressure is the pressure in your 
arteries while the heart is relaxing between beats. 
This is the bottom number in a blood pressure 
reading. 

120/80 → 80 mmHg is the diastolic 

pressure. 
 
Mean arterial pressure (MAP) is the average 
arterial pressure during one complete cardiac 
cycle. It is calculated by multiplying your cardiac 
output by your total peripheral resistance.  
 
MAP = CO x TPR 
MAP = (HR x SV) x TPR 
P wave – atrial depolarization 
 
Q wave – depolarization through interventricular 
septum 
 
R wave – ventricular depolarization 
S wave – completion of ventricular depolarization     

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Blood Vessels  Components of Blood 

1. Plasma contains water, proteins, nutrients, 

hormones, and makes up most of the blood 
volume. Makes up ~55% of blood volume.  

2. White blood cells (leukocytes) are our 

immune cells and defend against infection. 
The most common white blood cell is the 
neutrophil.  

3. Platelets (thrombocytes) are cell fragments 

that do not have a nucleus, they are 
responsible for clotting. Large bone marrow 
Vessels transport blood to and from the heart in a  cells called megakaryocytes are the precursor 
closed circulatory system. Arteries move blood  to platelets. Platelets release factors that help 
away from the heart, while veins move blood  convert fibrinogen into fibrin, which creates a 
toward the heart.  ‘net’ to stop bleeding. Many of the clotting 
factors are synthesized with Vitamin K, a 
Arteries are where blood pressure is the highest  deficiency in Vitamin K will lead to increased 
due to the hydrostatic pressure from the heart.  bleeding.  
They branch off into smaller arteries called   
arterioles. This is where we see the greatest drop  Leukocytes and thrombocytes make up <1% of 
of blood pressure. Arterioles branch further into  blood volume. 
capillaries, which are vessels that are 1 cell thick 
and diffuse gas and nutrients to the interstitial  4. Red blood cells (erythrocytes) are 
fluid. (Note: even though arterioles see the  responsible for transporting oxygen attached 
greatest drop in BP, they are not where BP is  to hemoglobin. Mature red blood cells are 
lowest. BP is lowest in the veins)  anucleate (they don’t have a nucleus) in order 
to maximize the amount of space they have to 
Capillaries also collect waste and CO2 and enter a  carry hemoglobin and oxygen. Makes up ~45% 
venule, which then connects to a vein, which  of blood volume.  
brings the blood back to the heart. Blood moves 
back to the heart by a series of valves within the 
veins that prevents backflow of blood. Skeletal 
muscles squeeze the veins to push the blood 
forward, it is not the pumping of the heart that 
moves blood through the veins. 

Veins contain more blood by volume than arteries 

and have the lowest blood pressure of all vessels. 

   

 
Adapted from: https://commons.wikimedia.org/w/index.php?curid=3986752 
   

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Blood Types  The waste and carbon dioxide from the fetus is 
removed from the right ventricle to the umbilical 
Red blood cells (erythrocytes) have antigens on  cord. 
their surfaces. These antigens are little sugars and 
proteins that mark our blood as a certain type.  There is no mixing of the mother’s and fetus’ 
Blood types are described as follows.  blood in the placenta; the placenta provides an 
exchange of gas and nutrients across a barrier. 
1. Type A blood – has ‘A’ antigen 
Erythroblastosis Fetalis 
2. Type B blood – has ‘B’ antigen 
A concept that is occasionally tested is if the 
3. Type AB blood – has both ‘A’ and ‘B’ antigens.  mother has Rh (-) blood type and the fetus has Rh 
(+) blood. During labor, the fetal Rh (+) blood will 
4. Type O blood – has neither ‘A’ or ‘B’ antigens.  enter the mother’s system, and she will develop 
anti-Rh antibodies. This will not pose a problem 
In addition to blood type A and B, your body also  in the first pregnancy, but if the mother becomes 
has another surface protein called the Rhesus  pregnant again with another Rh (+) fetus, the 
factor (Rh). You either have the factor (Rh (+)) or  mother’s anti-Rh antibodies will attack the fetus, 
you do not (Rh (-)). If a donor is Rh(+) , they cannot  because antibodies are small enough to cross the 
donate to someone who is Rh(-), because the  placental barrier. 
donor has antigens on the surface of the blood 
cell.  Lymphatic System 

A universal donor (blood donor who can donate  Nutrient and gas exchange occur at the level of the 
to anyone) is O (-). O blood type has neither A nor  capillaries. Hydrostatic pressure pushes fluid out 
B surface antigens, and O (-) blood also does not  of the capillaries on the arterial end into interstitial 
have an Rh surface antigen. This means there are  space. Oncotic pressure, a type of osmotic 
no blood cell surface antigens that would stimulate  pressure, brings fluid back into the capillaries at 
immune clearance by someone receiving the O (-)  the venule end. However, not all the fluid is 
blood.  reabsorbed from the interstitial space into the 
venule. 
A universal acceptor is AB (+). Because an AB (+) 
person has both A and B cell surface antigens, as  Lymphatic capillaries collect the remaining fluid, 
well as an Rh surface antigen, they can receive any  called lymph, which consists of interstitial fluid, 
blood type and not mount an immune response.  bacteria, fats, and proteins. The lymphatic 
Any blood cell surface antigen they receive would  capillaries merge together to form larger vessels 
be something their blood cells already have.  that travel to the heart. Along the way, the lymph 
is filtered through lymph nodes, which are centers 
Fetal Circulation  for the immune response system to eliminate 
infections. Lymph vessels have no pressure (like 
A fetus gets the oxygen and nutrients it needs 
veins), and the fluid moves back towards the heart 
from the placenta through the umbilical cord, 
due to the constriction of skeletal muscle; 
which gets its oxygen from its mother. Because the 
backflow of fluid is prevented with a system of 
fetus gets its oxygen through the placenta, the 
valves, similar to veins.  
blood in its heart does not need to go to the 
pulmonary system – it is not exposed to air.     
Instead, the oxygenated blood in the right atrium 
goes directly to the left atrium through a hole in 
the heart called foramen ovale. 

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Chapter 11.2: Respiratory System  Respiration in Animalia Species 

   
Table of Contents  1. Cnidaria are small invertebrates that use 
  simple diffusion for respiration due to the lack 
● Respiration in Plants   of a circulatory system. Almost all cells must be 
● Respiration in Animalia Species   in direct contact with the environment. 
● Human Lungs   Environment must be moist for diffusion to 
● Gas Exchange   happen.  
● The Oxygen Dissociation Curve 
 
Respiration: the exchange of gases between the 
outside environment and the inside of an 
organism. 
 
Respiration in Plants 
 
Autotrophs produce their own food through 
photosynthesis, releasing oxygen and making 
carbohydrates. 
   
Cellular respiration is also performed by plants  2. Annelida includes earthworms that also use 
after photosynthesis, using up oxygen and  simple diffusion for respiration but have a 
carbohydrates to produce energy.  closed circulatory system. They use a slimy 
  mucus to facilitate the transport of oxygen 
Stomata (in leaves and green stems) and lenticels  into their closed circulatory system.   
(in woody stems) are pores found in plants that   
allow gas exchange to occur.   3. Arthropoda are invertebrates, such as 
insects and crustaceans, that have an open 
circulatory system with hemolymph, a fluid 
similar to blood. Gas exchange happens 
mainly through the tracheal system for 
insects and through book lungs for 
arachnids.  
 
4. Fish are a part of the phylum Chordata and 
have a closed circulatory system with blood 
to transport gas. Fish have gills with a large 
surface area for gas exchange and use 
countercurrent exchange to efficiently 
absorb oxygen and remove carbon dioxide 
from their blood.  
https://commons.wikimedia.org/wiki/File:Opening_and_Closing_of_Stoma.svg   
     
 
 
   

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Human Lungs  Lung Volumes 

   
Lungs are located in the thoracic cavity and are  Tidal volume is the volume of air that moves 
covered by the rib cage. The left lung has two lobes  through the lungs between a normal inhalation 
and is smaller than the right lung, which has three  and exhalation.  
lobes.    
  Inspiratory reserve volume is the maximum 
volume of air that can be inhaled further after a 
normal inhalation is already taken in.  
 
  Expiratory reserve volume is the maximum 
Adapted from: https://commons.wikimedia.org/w/index.php?curid=5140582 
volume of air that can be exhaled further after a 
 
normal exhalation is already released.  
The pleura covers the lungs and is a dual-layered 
 
membrane composed of the parietal layer (outer 
Residual volume is the minimum amount of air 
layer) and the visceral layer (inner layer).  
that needs to be present in the lungs to prevent 
 
collapse.  
The pleural space is a fluid-filled space in between 
 
the parietal and visceral layers. This space is at a 
Functional residual capacity is the entire volume 
lower pressure than the atmosphere, and creates 
of air still present in the lungs after a normal 
the intrapleural pressure.  
exhalation. It is also the sum of the expiratory 
 
reserve volume and the residual volume. 
1. Inspiration or inhalation involves the 
 
contraction of the diaphragm (pulls lungs 
Vital capacity is the maximum amount of air that 
downwards) and the external intercostal 
can be exhaled after a maximum inhalation. It is 
muscles (expands the rib cage). These 
the sum of the inspiratory reserve volume, tidal 
contractions cause the pressure of the 
volume, and expiratory reserve volume.  
intrapleural space to decrease and the volume 
 
of the lungs to increase, bringing air into the 
Total lung capacity is the sum of the vital 
lungs.  
capacity and the residual volume: it is the 
 
maximum volume the lungs could possibly hold at 
2. Expiration or exhalation involves the 
any given time.   
relaxation of the diaphragm and the external 
intercostal muscles, bringing 
the lungs back up and closing 
up the rib cage through 
elastic recoil. This causes the 
pressure of the intrapleural 
space to increase and the 
volume of the lungs to 
decrease, driving air out of the 
lungs. The internal 
intercostal muscles can also 
contract during a more 
forced expiration, closing the 
rib cage even more. 
 
 
 
   

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Pathways of Air   
  Oxygen: Air → Blood → Tissues 
1. The nasal cavity contains goblet cells   
(secrete mucus) and ciliated epithelial cells  Carbon Dioxide: Tissues → Blood → Air 
(move mucus and trapped debris) that work   
in tandem with each other.  Erythrocytes (red blood cells) contain 
2. The pharynx is at the beginning of the throat  hemoglobin. Hemoglobin is tetrameric and has 
after the nasal cavity. Under the control of the  a heme cofactor in each of its four subunits. 
epiglottis, it diverts air and food into the  Heme cofactors are organic molecules that 
larynx and the esophagus.  contain iron atoms, which bind oxygen. Thus, 
3. The larynx receives air and contains the  each hemoglobin can carry up to four oxygen 
voice box. The upper respiratory tract  molecules.  
refers to the nasal cavity, pharynx, and   
larynx. On the other hand, the esophagus  Oxyhemoglobin (HbO2) transports most of the 
receives food and connects to the stomach.  oxygen traveling in the blood.  
4. The trachea is below the larynx and has   
reinforced cartilage along with ciliated  Cooperativity describes the process by which 
epithelial cells to filter air.   the binding of one oxygen molecule to 
5. Next are the two main left and right bronchi,  hemoglobin makes it easier for others to bind 
which branch into smaller bronchioles and  due to changes in the shape of the hemoglobin 
eventually into alveoli. The lower  polypeptide. This also works in reverse, allowing 
respiratory tract refers to the trachea,  efficient unloading of oxygen in body tissues.  
bronchi, bronchioles, and alveoli. Alveoli   
contain type 1 epithelial cells (structural  Carboxyhemoglobin (HbCO) is produced when 
support) and type 2 epithelial cells (produce  carbon monoxide outcompetes oxygen for 
surfactant). Surfactant is a substance that  hemoglobin binding. Carbon monoxide poisoning 
prevents the lungs from collapsing by  occurs as a result, because oxygen can no longer 
reducing surface tension.  be transported efficiently. 
   
Carbaminohemoglobin (HbCO2) is a form of 
hemoglobin that transports carbon dioxide. 
However, carbon dioxide is much more soluble in 
blood than oxygen, so most of the carbon 
dioxide is dissolved in blood as bicarbonate 
anion (HCO3-). 
 
  Reduced hemoglobin (H+Hb) is produced by H+ 
 
Adapted from: https://commons.wikimedia.org/w/index.php?curid=10296586 ions binding to hemoglobin, outcompeting 
  oxygen and lowering oxygen binding affinity (less 
  HbO2). On the other hand, carbon dioxide 
Overall Pathway of Air  binding affinity is increased (more HbCO2).  
Nasal Cavity → Pharynx → Larynx → Trachea →   
Bronchi → Bronchioles → Alveoli  Myoglobin is a single peptide with one heme 
  cofactor. It has a much higher affinity for oxygen 
Differences in partial pressure allow gases to flow  than oxyhemoglobin and is found within cardiac 
from areas of high pressure to areas of low  and skeletal muscle cells to bring oxygen in. Also, 
pressure through simple diffusion. This is required  myoglobin has a hyperbolic oxygen dissociation 
for external respiration (gas exchange between  curve because it does not undergo cooperativity 
inspired air and lung alveolar capillaries) and  (hemoglobin’s curve is sigmoidal).  
internal respiration (gas exchange between 
blood and tissues).  

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  hemoglobin (H+Hb) has a lowered affinity for 

binding oxygen, resulting in less HbO2.  
● High partial pressure of carbon dioxide: 
more carbon dioxide is converted to 
bicarbonate anions (HCO3-) and protons (H+), 
which lower oxygen binding affinity through 
decreased pH. 
● 2,3-diphosphoglycerate (2,3-DPG) aka 
2,3-bisphosphoglycerate (2,3-BPG): 
accumulates in cells that undergo anaerobic 
respiration as a result of the loss of oxygen. 
This compound decreases oxygen binding 
affinity so more oxygen is released from 
  hemoglobin to fuel aerobic respiration. 
https://commons.wikimedia.org/w/index.php?curid=61796124   ● Increased body temperature: correlates to 
  more cellular respiration, which uses up 
Oxygen Dissociation Curve  oxygen and produces more carbon dioxide. 
  Thus, hemoglobin will need to unload more 
The oxygen dissociation curve reveals the  oxygen for tissues to use and have decreased 
relationship between the saturation of hemoglobin  oxygen binding affinity.  
with oxygen in the blood and the partial pressure  A left-shifted curve corresponds to an increased 
of oxygen. Certain conditions will shift this curve  affinity for oxygen in hemoglobin. Below are the 
either left or right.  main reasons for a left-shifted curve.  
  ● Increased pH (more basic): fewer protons (H+) 
  to produce reduced hemoglobin (H+Hb), so 
more oxyhemoglobin (HbO2) remains.  
● Low partial pressure of carbon dioxide: less 
carbon dioxide is converted to bicarbonate 
anions (HCO3-) and protons (H+), leading to 
increased oxygen binding affinity through 
increased pH. 
● Fetal hemoglobin: binds oxygen better than 
adult hemoglobin to help give oxygen to the 
fetus.  
● Decreased body temperature: less cellular 
respiration, so hemoglobin isn’t influenced to 
unload more oxygen and has an increased 
oxygen binding affinity.  
DAT Mnemonic: CADET, face Right! 
   
https://commons.wikimedia.org/wiki/File:Oxygen-Haemoglobin_dissociation_curves.s
vg  CADET = Carbon dioxide, Acid, 
 
2,3-Diphosphoglycerate, Exercise and 
 
Temperature.  
A right-shifted curve corresponds to a lowered 
 
affinity for oxygen in hemoglobin. Below are the 
CADET Increase → Right shifted curve 
main reasons for a right-shifted curve. 
   
 
● Decreased pH : a lower pH means there is a 
higher concentration of protons (H+), which 
produces reduced hemoglobin. Reduced 

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Changes in Hemoglobin Affinity  Gas Exchange in Lungs 

   
Bohr effect - hemoglobin has decreased oxygen  1. Blood travels to the lungs through bulk flow. 
affinity when carbon dioxide is high. Carbon  2. Since most of the carbon dioxide is present 
dioxide is converted to bicarbonate anions and  in the blood plasma as bicarbonate ions 
protons, which produce reduced hemoglobin  (HCO3-), the bicarbonate ions re-enter 
(H+Hb).  erythrocytes at the lungs and chloride ions 
  leave through the reverse chloride shift. 
Haldane effect - hemoglobin has increased  3. The bicarbonate buffer system equation 
carbon dioxide affinity when oxygen is low. As a  proceeds in the reverse direction, producing 
result of low oxygen, reduced hemoglobin  carbon dioxide and water. The carbon 
(H+Hb) levels are higher and have a greater  dioxide exits into the alveoli as gas while 
affinity for carbon dioxide.   oxygen enters the blood, forming 
  oxyhemoglobin.  
Gas Exchange in Tissues   
   
The bicarbonate buffering system can be     
described by the equation below and is catalyzed 
by carbonic anhydrase in both directions based 
on concentrations. Carbonic anhydrase is an 
enzyme present in red blood cells. 
 
CO2 + H2O ↔ H2CO3 ↔ HCO3- + H+ 
 
Carbonic acid (H2CO3) 
Bicarbonate anion (HCO3–) 
 
1. In erythrocytes (red blood cells) in the 
systemic circulation, the partial pressure of 
carbon dioxide is low. As a result, carbon 
dioxide continuously diffuses in from the 
tissues, and is converted into bicarbonate 
and protons. Bicarbonate is able to diffuse 
out of the cell, however, protons (H+) cannot 
leave. As some bicarbonate diffuses out, this 
creates a positive charge within the 
erythrocyte, and chloride ions (Cl-) must 
diffuse into the blood cell to cancel out the 
positive charge of the protons. This process 
is known as the chloride shift.  
2. Influx of protons causes the pH to decrease 
within the erythrocyte, resulting in the 
conversion of oxyhemoglobin into reduced 
hemoglobin. Reduced hemoglobin has lower 
affinity for O2, leading to release of oxygen 
which diffuses to the tissues.  
 
 
   

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Breathing Pace 
 
The medulla oblongata is located in the brain 
and controls the diaphragm to regulate 
respiratory rate. Central chemoreceptors and 
peripheral chemoreceptors signal to the medulla.  
 
Central chemoreceptors are located in the 
medulla oblongata and contained within the 
blood-brain barrier. Since carbonic anhydrase is 
present in the cerebrospinal fluid, carbon dioxide 
is converted into bicarbonate ions and protons 
here. However, protons cannot exit through the 
blood-brain barrier. As carbon dioxide 
accumulates, acidity increases and is directly 
sensed by central chemoreceptors, which signal 
to the medulla oblongata to increase breathing 
rate. 
 
Peripheral chemoreceptors surround the aortic   
arch and carotid arteries. These peripheral 
   
chemoreceptors directly sense oxygen, carbon 
dioxide, and proton levels to signal to the medulla 
oblongata. When carbon dioxide is high and 
oxygen is low, peripheral chemoreceptors signal to 
the medulla oblongata to increase breathing rate. 
 
Rate of Breathing 
 
Respiratory acidosis - lowered blood pH occurs 
due to inadequate breathing (hypoventilation)  
 
Respiratory alkalosis - increased blood pH 
occurs due to rapid breathing 
(hyperventilation) 
 
Metabolic acidosis (lowered blood pH) and 
metabolic alkalosis (increased blood pH) occur as 
a result of imbalances in carbon dioxide, oxygen, 
or proton levels.  
 
 
 
 
 
 
 
 
 
 
 

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Chapter 11.3: Human Immune System  Innate Immunity: Inflammatory Responses 

   
Table of Contents  Mast cells are a type of leukocyte responsible for 
  the first part of the inflammatory response, known 
● Innate Immunity: Overview  as rally signaling: 
● Innate Immunity: Inflammatory Responses   
● Innate Immunity: Immune Cells and  1. Mast cells sit in the tissue in preparation 
Molecules  for injury. 
● Innate Immunity: Complement System  2. If there is an injury, mast cells will release 
● Adaptive Immunity: Overview  histamine, which dilates blood vessels.  
● Adaptive Immunity: B cells  3. This increases blood flow and makes 
● Adaptive Immunity: T cells  vessels more permeable to let immune cells 
● Passive vs. Active Immunity  into the tissues. 
 
Pathogens: harmful microorganisms that cause 
disease. 
 
Leukocytes: white blood cells. 
 
Lymphocytes: white blood cells found mainly in 
the lymphatic organs (T cells, B cells, natural killer 
cells) that originate from the bone marrow. T cells 
mature in the thymus while B cells mature in the 
bone marrow. 
 
  Adapted from 
Innate Immunity: Overview  https://commons.wikimedia.org/wiki/File:2213_Inflammatory_Process.jpg 

   
The innate immune system is the first line of  Five signs of inflammation: 
defense and generates a nonspecific immune   
response (generalized).  DAT Mnemonic:  
  Inflammatory response → SLIPR 
The outer walls are the first layer of innate  Swelling  
immunity:  Loss of function  
  Increased heat  
● Skin - consists of a thick epidermis, dermis,  Pain  
and hypodermis. Also mucous membrane  Redness 
to trap pathogens and lysozyme to break  1. Swelling - permeable capillaries result in fluids 
down bacterial cell walls. Has sebaceous  leaking into tissues. 
glands to secrete oil (sebum) as a barrier.  2. Loss of function - body part with 
Sebum also has antimicrobial properties.   inflammation becomes less usable.  
● Cilia - hair-like projections in the respiratory  3. Increased heat - increased blood flow results 
tract that sweep away debris and pathogens.   in a higher temperature. 
● Stomach acid - gastric acid that kills microbes  4. Pain - throbbing pain caused by swelling, 
due to low pH.  which puts continuous pressure on nerve 
● Symbiotic bacteria - outcompete pathogenic  endings. 
bacteria and fungi.  5. Redness - increased blood flow causes 
  redness of skin. 
If these barriers are penetrated, the rest of the  A fever can also occur due to the inflammatory 
immune system will kick in.  response; this is controlled by the brain and 
  causes a systemic response to kill pathogens with 
  higher temperatures. 

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Innate Immunity: Immune Cells and Molecules  Dendritic cells are also part of innate immunity 
  and scan tissues using pinocytosis (cell drinking) 
Diapedesis is the process by which cells move  and phagocytosis (cell eating). They act as 
from the capillaries to the tissues in order to fight  antigen-presenting cells like macrophages, 
pathogens.   migrating to the lymph nodes to activate 
  adaptive immunity.  
Chemotaxis is the method by which cells move   
in response to a chemical signal. Immune cells  Interferons are secreted by virally-infected cells 
use chemotaxis to move to the tissues.  and bind to non-infected cells to prepare them for 
  a virus attack. Also, interferons help activate 
DAT Mnemonic:  dendritic cells. 
Five main types of leukocytes from highest to   
lowest in quantity → Never Let Monkeys Eat  Innate Immunity: Complement System 
Bananas   
  The complement system is a group of 
1. Neutrophils - phagocytes in innate immunity  approximately 30 proteins that aid immune cells 
that make up over half of all leukocytes.  in fighting pathogens. These proteins turn each 
2. Lymphocytes - B cells, T cells, and natural  other on through the complement cascade, 
killer cells. B and T cells are part of adaptive  which amplifies the complements effects by 
immunity and must be activated. Natural  releasing cytokines.  
killer (NK) cells are part of innate immunity   
and attack virally-infected cells + cancerous  Complement protein actions: 
cells. NK cells use perforin (create holes) and   
granzyme (stimulate apoptosis) to lyse cells.   ● Tags antigens for phagocytosis in a process 
3. Macrophages/Monocytes - phagocytes in  called opsonization 
innate immunity. Monocytes are the  ● Amplifies inflammatory response Eg. binds to 
immature form found in blood vessels and  mast cells for increased histamine release 
macrophages are the mature form after  ● Forms a membrane attack complex (MAC), 
diapedesis. Can also act as antigen-presenting  which pokes holes in pathogens and lyses 
cells to activate adaptive immunity.  them 
4. Eosinophils - part of innate immunity and   
have granules that can be released to kill   
pathogens, especially parasites.   
5. Basophils - least numerous leukocyte;   
contains granules with histamine     
(vasodilation) and heparin (an anticoagulant 
to prevent blood clotting). Very similar to 
mast cells, except basophils circulate as 
mature cells while mast cells circulate as 
immature cells.  
 
 
   

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Adaptive Immunity: Overview  Adaptive Immunity: B cells  

   
The adaptive immune system is a specific  B cells control antibody-mediated immunity 
immune response (targets specific antigens).   (humoral immunity) by managing the 
  production and release of antibodies. They can 
An antigen is an immunogenic foreign molecule  also act as antigen-presenting cells.  
and is the target of the immune response. The   
epitope is the important part of the antigen that  B cell receptors (BCRs) are located on B cells 
is recognized by the immune cell.  and bind to antigen epitopes either free-floating 
  or on APCs. Each B cell has a unique BCR.  
 
The clonal selection model describes the 
development of one type of BCR for every B cell. 
Through clonal expansion, these B cells divide 
into either plasma cells (antibody-secreting cells) 
or memory B cells (to be activated later in case 
of another attack).  
 
Antibodies (immunoglobulins) are structurally 
 
https://commons.wikimedia.org/wiki/File:Figure_42_02_03.png 
identical to BCRs but freely circulate in blood and 
  lymph. They can tag antigens for phagocytosis, 
The immune system recognizes self proteins from  neutralize the antigen by coating it, or activate the 
non-self proteins using the major  complement system. Antibodies contain light 
histocompatibility complex (MHC), which is  chains and heavy chains linked by disulphide 
found on the surface of cells. Thus, foreign  bonds. In addition, the variable region 
antigens and foreign MHC will be identified as  recognizes different antigens while the constant 
enemies by the immune system.  region is the same for antibodies within the 
  same class.  
MHC Class I is a surface molecule present on all   
nucleated cells, and each genetically different 
individual will have a different MHC I molecule. 
Organ transplants that have different MHC I may 
lead to failure and rejection, so 
immunosuppressants are given to transplant 
patients. Also, autoimmune diseases occur when 
the immune system attacks self MHC I.  
 
MHC Class II is a surface molecule present on 
antigen-presenting cells (dendritic cells, 
 
macrophages) and is used to present foreign  https://commons.wikimedia.org/wiki/File:Antibody_je2.png 
antigens to activate immune cells.    
     
 
   

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DAT Mnemonic:   Adaptive Immunity: T cells 

Classes of Antibodies → Me And Eve Don’t Go   
  T cells control cell-mediated immunity by 
1. IgM - present in a pentameric form and is the  directly acting on cells instead of sending 
largest antibody. The first antibody to be  antibodies out.  
produced; activates the complement system.   
2. IgA - present in a dimeric form and found  T cell receptors (TCRs) are unique just like BCRs, 
most abundantly in bodily secretions.  binding only to one type of antigen per T cell. 
Newborns receive passive immunity  Thus, T cells also undergo clonal selection just 
through breast milk containing IgA. Also, IgA  like B cells.  
mainly binds pathogens externally, outside   
of circulation.   T cells must bind to antigens presented on APCs 
3. IgE - monomer that is present on basophils  (antigen-presenting cells) to be activated. 
and mast cells as antigen receptors. When  There are two ways antigens may be presented 
bound to an allergen, triggers histamine  to T cells: 
release and an allergic reaction.   
4. IgD - monomer that we have very little  1. MHC I Presentation: T cells differentiate into 
information about. Only small amounts are  CD8 T cells (cytotoxic T cells), which directly 
produced.  kill infected cells through perforin (poke holes) 
5. IgG - monomer that is the most abundant  and granzymes (cause apoptosis). However, T 
antibody in circulation. Also the only  cells are different from natural killer cells 
antibody that can cross the placenta to give  because they are more specific and require 
fetus passive immunity. Helps the  antigen presentation.  
complement system to cause opsonization  2. MHC II Presentation: T cells differentiate into 
(tags antigens and subsequent phagocytosis).   CD4 T cells (helper T cells), which release 
  cytokines to boost both innate immunity and 
adaptive immunity. These cytokines help attract 
innate immune cells and increase proliferation 
of other T and B cells.  
 
Active vs. Passive Immunity 
 
Passive immunity refers to the immunity one 
organism gains from receiving the antibodies 
from another organism that already has that 
immunity. For example, a fetus gains passive 
immunity through the placenta (IgG) while a 
newborn gains passive immunity through breast 
milk (IgA). The fetus and newborn are referred 
  to as immuno-naive because they do not yet 
https://commons.wikimedia.org/wiki/File:Mono-und-Polymere.svg 
  have their own active immunity. 
Memory B cells survive for a long time and lay   
dormant until reactivated by the same antigen  Active immunity refers to the immunity an 
that triggered the original clonal expansion.  organism gains from being infected once already 
They are the key to vaccinations because  by a pathogen. A vaccination introduces the 
vaccines cause memory B cell production for  antigen or pathogen in a deactivated state to 
later reactivation. After reactivation, memory B  stimulate active immunity, which is referred to as 
cells cause massive antibody production.   artificial immunity in this case and induces 
  memory B and T cell formation.  
     

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Chapter 11.4: Nervous System  Action Potentials 

 
Table of Contents 
 
● The Neuron 
● Action Potentials 
● Synaptic Transmission 
● Neurotransmitters 
● Glial Cells 
● Central vs. Peripheral Nervous System 
● Central Nervous System 
● Peripheral Nervous System: Somatic vs. 
Autonomic Nervous System 
● Autonomic Nervous System: Sympathetic 
vs. Parasympathetic Nervous System 
● Special Senses   
  https://commons.wikimedia.org/wiki/File:Action_potential.svg 

The Neuron   
  Steps of an action potential: 
The neuron is the most basic unit of the nervous   
system. It has three parts: the soma (cell body),  1. At resting potential, the membrane potential 
dendrites (extensions that receive signals), and  of the neuron is around -70mV and is 
the axon (sends signals out).   maintained by Na+/K+ ATPases, which pump 
  three Na+ ions out and two K+ ions in, powered 
The Axon:  by hydrolysis of one ATP. K+ leak channels are 
  also present and help maintain resting 
● Axon hillock - area where the axon is  potential through passive K+ leakage. 
connected to the cell body. Responsible for the  2. When a stimulus causes threshold potential 
summation of graded potentials.  to be reached (around -55mV in neurons), 
● Myelin sheath - fatty insulation of the axon  voltage-gated Na+ channels open up, letting 
that speeds up action potential propagation by  Na+ in, resulting in depolarization of the 
stopping ion exchange. The myelin sheath is  neuron (reaches a peak of around +30mV to 
formed by oligodendrocytes (in the central  +40mV).  
nervous system) and Schwann cells (in the  3. Next is repolarization of the neuron due to 
peripheral nervous system).   the opening of voltage-gated K+ channels, 
● Nodes of Ranvier - gaps between myelin  letting K+ out. This causes the membrane 
sheaths where ion exchange occurs.  potential to become less positive since positive 
Propagation of the action potential occurs  ions are leaving. 
here, jumping from gap to gap (node to node)  4. When the membrane potential becomes even 
in a process called saltatory conduction.  more negative than the normal resting 
  potential, this is known as hyperpolarization. 
  This results in a refractory period being 
  established, during which another action 
  potential cannot be fired because the 
    membrane potential is very negative.  
5. The membrane potential returns to normal 
resting potential through the pumping of 
Na+/K+ ATPases and K+ leak channels. 
 
   

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The absolute refractory period refers to the  An inhibitory postsynaptic potential (IPSP) is a 
period after the initiation of the action potential  graded potential that hyperpolarizes the 
during which another action potential cannot be  membrane. Inhibitory neurotransmitters cause K+ 
fired no matter how powerful the stimulus is. It is  ion gates to open and let K+ ions flow out of the 
due to the inactivation of voltage-gated Na+  cell. Another IPSP type allows influx of Cl-, 
channels after they open.   allowing negative Cl- ions in.  
 
The relative refractory period refers to the 
period after the action potential fires during which 
a stronger than normal stimulus could cause 
another action potential to be fired. 
 
Synaptic Transmission 
 
The synapse is the space between two 
neurons. The presynaptic neuron sends the 
signal and releases neurotransmitters into the 
synapse, while the postsynaptic neuron 
receives the signal by interacting with the 
released neurotransmitters. 
 
Steps of synaptic transmission: 
 
1. Action potential reaches the end of the  https://commons.wikimedia.org/w/index.php?curid=30147934 
presynaptic axon, causing voltage gated   

calcium channels to open and letting Ca2+  Glial cells 

ions into the neuron.    
2. The Ca2+ ions cause synaptic vesicles to fuse  Glial cells are non-neuronal cells in the nervous 
and undergo exocytosis, releasing  system that help support and surround neurons. 
neurotransmitters into the synapse.  They are divided into microglial cells and 
3. The neurotransmitters (described in the table  macroglial cells.  
on the next page) bind to ligand-gated ion   
channels on the postsynaptic neuron,  Microglial cells are macrophages that protect the 
producing graded potentials (depolarizations  central nervous system (CNS). 
or hyperpolarizations of the membrane).    
4. These graded potentials summate at the axon  Macroglial cells have many subtypes: 
hillock and an action will fire if the summation   
of graded potentials is higher than the  ● Astrocytes are the most abundant glial cell 
threshold potential of neurons.   and form the blood-brain barrier. They also 
  help recycle neurotransmitters and provide 
An excitatory postsynaptic potential (EPSP) is a  blood supply to the CNS neurons. 
graded potential that depolarizes the membrane.  ● Schwann cells form the myelin sheath in the 
In an EPSP, excitatory neurotransmitters cause Na+  peripheral nervous system (PNS). 
ion gates to open and let Na+ ions flow into the cell.   ● Oligodendrocytes form the myelin sheath in 
  the central nervous system (CNS).  
  ● Satellite cells have the same functions as 
    astrocytes but instead help PNS neurons. 
● Ependymal cells produce cerebrospinal fluid 
(CSF), which cushions the CNS.   

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Neurotransmitters and their functions   

   
   
   
   
   
   
     
 
 
 
 
 
 
 

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Central vs. Peripheral Nervous System  The brainstem is composed of the midbrain 
  (relays senses to other parts of brain), pons (relays 
The central nervous system (CNS) is composed  messages from cerebellum to forebrain), and 
of the brain and spinal cord.  medulla oblongata (heart and breathing rate, 
  blood pressure, toxin sensing) and connects the 
The peripheral nervous system (PNS) is  cerebrum/cerebellum to the spinal cord.  
composed of nerves branching off the CNS.    
  The thalamus is known as the “relay center” of the 
Central Nervous System  brain and is located between the cerebrum and 
  the midbrain.  
In embryonic development, we consider the   
forebrain, midbrain, and hindbrain:  The limbic system is next to the thalamus and is 
  composed of the hypothalamus, hippocampus, 
and amygdala (details below). It is responsible for 
emotion, memory, learning, and motivation. 
 
Finally, the spinal cord is nervous tissue in part of 
the central nervous system; it connects the brain 
to the body. Sensory (afferent) neurons send 
signals to the spinal cord and subsequently the 
brain through dorsal roots. Motor (efferent) 
neurons send signals back out to the muscles 
through ventral roots.  
 
The meninges protect the CNS and have three 
  layers called the dura mater, arachnoid, and pia 
The developed brain cortex is divided into four  mater. 
main lobes.    
DAT Mnemonic for outermost to innermost 
meninges → DAP = dura → arachnoid → pia 
 
Somatic vs. Autonomic Nervous System 
 
The peripheral nervous system is divided into 
the somatic nervous system (voluntary motor 
action and sensory input) and the autonomic 
nervous system (involuntary).  
 
Different types of sensory (afferent) neurons in 
the peripheral nervous system are responsible for 
receiving input from stimuli, including 
mechanoreceptors (mechanical stimuli), 
  nociceptors (pain stimuli), thermoreceptors 
  (temperature-related stimuli), chemoreceptors 
The cerebellum is located underneath the  (chemical stimuli), and electromagnetic receptors 
occipital lobe and is responsible for the  (light, electricity, and magnetic stimuli).  
coordination of movement.   
   
     
   

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Autonomic Nervous System: Sympathetic vs.  A ganglion is defined as a cluster of nerve bodies 
Parasympathetic Nervous System  in the peripheral nervous system. The autonomic 
  nervous system’s neurons are either 
The autonomic nervous system can be further  preganglionic or postganglionic. The 
divided into the sympathetic nervous system  preganglionic neuron comes from the central 
(fight or flight) and the parasympathetic nervous  nervous system and synapses with the 
system (rest and digest).  postganglionic neuron at the ganglion. 
   
Sympathetic nervous system effects:  Sympathetic nervous system → short 
  preganglionic nerves and long postganglionic 
● Release of sugar into blood for energy.  nerves (ganglia far from effector organs) 
● Increase in heart rate for oxygen delivery to   
brain and muscles.  Parasympathetic nervous system → long 
● Dilation of bronchi and bronchioles to allow  preganglionic nerves and short postganglionic 
more oxygen into lungs.  nerves (ganglia close to effector organs) 
● Dilation of the pupil to give the brain more   
visual information.  Sympathetic nervous system → uses 
  acetylcholine (Ach) for preganglionic nerves and 
Parasympathetic nervous system effects  norepinephrine (NE)/epinephrine (E) for 
(through vagus nerve):  postganglionic nerves. The sympathetic nervous 
  system also can stimulate the adrenal medulla to 
● Relaxation of muscles.  release NE/E into the blood.  
● Decrease in heart rate.   
● Maintenance of homeostasis.  Parasympathetic nervous system → uses 
● Increase in gastrointestinal activity.  acetylcholine (Ach) for both preganglionic and 
  postganglionic nerves.  
   
   
     
   

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Special Senses   
  Eye: 
Ear:   
  ● Cornea - transparent; focuses light and 
● The outer ear takes in sound waves, and the  protects the eye.  
tympanic membrane transfers the sound  ● Iris - controls the size of the pupil. 
from outer ear to middle ear.  ● Pupil - controls how much light enters the eye. 
● The middle ear is composed of three bony  ● Lens - focuses images on retina. 
ossicles → the malleus, incus, & stapes. The  ● Retina - back of the eye that has 
ossicles transfer vibrations through the middle  photoreceptors (rods + cones).  
ear and amplify the signal.   ● Fovea - highest concentration of 
● The stapes transfers the vibrations from the  photoreceptors in the retina and responsible 
middle to the inner ear via the oval window.  for high acuity vision.  
● The cochlea uses fluid and hairs to convert the  ● Amacrine and bipolar cells take information 
mechanical signal into a neuronal signal,  from rods and cones, transmitting the 
known as transduction.   information to ganglion cells of the optic 
● The round window is a membrane covered  nerve fibers. 
opening between the middle ear and the inner  ● Optic nerve - bundle of axons that transmits 
ear, similar to the oval window. It helps the  visual information to the brain. 
fluid expand and vibrate.   ● Optic disk - the blind spot of the eye, where 
● The semicircular canal has fluid and hairs just  the optic nerve passes through to reach the 
like the cochlea but gives information about  brain.  
the person’s movement. It is also the reason  ● Sclera - protective connective tissue that 
we get dizzy.   surrounds the eye, the “white part” of the eye.  
● Choroid - vascular connective tissue. 
 
Tongue: 
 
● Five taste receptor cells, sensing salty, 
sweet, bitter, sour, and umami.  
● Taste information is sent to the thalamus and 
subsequently the gustatory cortex.  
 
Nose: 
 
● Contains olfactory receptor cells that sense 
molecules and send signals to the olfactory 
cortex, which gives us the perception of smell. 
These signals also integrate in the thalamus 
and orbitofrontal cortex for smell sensation. 
 
 
   

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Chapter 11.5: Muscular System  Skeletal Muscle Anatomy 

   
Table of Contents   Skeletal muscle is composed of many bundles 
  within bundles. 
● Types of Muscle    
● Skeletal Muscle Anatomy  Muscle → Muscle fascicles → Muscle fibers 
● Sliding Filament Theory of Muscle  (muscle cells) → Myofibrils (contractile protein) 
Contraction    
● Motor Units   The sarcolemma is the muscle fiber’s cellular 
● Twitch Contractions  membrane, and it protects each muscle fiber.  
● Muscle Fiber Types   
● Degrees of Muscle Contraction  The sarcoplasm is the cytoplasm of the muscle 
● How Muscles Work Together to Create  fiber and holds the myofibrils.  
Movement    
 
Types of Muscle 
 
There are three types of muscles: smooth 
muscle, cardiac muscle, and skeletal muscle. 
 

 
  Adapted from: https://commons.wikimedia.org/w/index.php?curid=30015037 
   
Striated means the muscle contains sarcomeres.  Sliding Filament Theory of Muscle Contraction 
Smooth muscle therefore lacks sarcomeres,   
whereas cardiac and skeletal muscle contain them.   All muscles always contract (pull) across a joint 
  to move body parts, they never push. 
Cardiac muscle contains intercalated discs,   
which are made of desmosomes (hold cells  Sarcomeres inside of myofibrils are the functional 
together) and gap junctions that connect the  unit of muscle fibers and shorten to cause muscle 
cytoplasm of cells together to allow ion exchange  contraction. 
and electrical impulse propagation.   Myofilaments are contained within sarcomeres, 
  divided into thin actin filaments and thick 
    myosin filaments. These filaments slide past 
each other to shorten sarcomeres through the 
sliding filament model of muscle contraction. 
 

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Stimulation of a muscle contraction:  Cross bridge cycling: 

   
1. Action potential propagation reaches the end  1. Initiation: Calcium ions expose the 
of a motor neuron’s axon.  myosin-binding-sites on actin. 
2. Acetylcholine is released as a  2. A cocked back, high energy myosin head 
neurotransmitter between the presynaptic  (containing ADP and Pi) forms a cross bridge 
motor neuron and postsynaptic skeletal muscle  with the actin.  
fiber at the neuromuscular junction.   3. The myosin head contracts and the power 
3. Acetylcholine binds to ligand - gated  stroke occurs, bringing the myosin head back 
sodium channels, causing sodium to enter  to a low energy state and releasing ADP and 
the cell, which creates graded potentials  Pi. As a result, the sarcomere shortens.  
on the muscle fibers.  4. A new ATP molecule binds to myosin, causing 
4. The graded potentials trigger opening of  detachment of the myosin head from the 
voltage-gated sodium channels, which may  actin filament. 
produce action potentials on the muscle if the  5. The myosin head is an ATPase, and it 
stimulus is large enough.  hydrolyzes the ATP into ADP and Pi. This 
  causes the myosin head to re-enter a cocked 
back, high energy state. (Return to Step 2 if 
calcium ions present).  
6. Termination: Neuronal signaling from motor 
neurons ends. The sarcoplasmic reticulum 
pumps calcium back into itself, and troponin 
brings tropomyosin back to cover 
myosin-binding sites on actin. 
 
Rigor mortis occurs in dead animals when there is 
no ATP available to release myosin from the actin.  
 
The Sarcomere 
   
Adapted from: 
https://commons.wikimedia.org/wiki/File:1009_Motor_End_Plate_and_Innervation.jpg  The Z lines are the ends of the sarcomeres. Thin 
  actin filaments branch from the Z lines towards 
The sarcolemma is the cell membrane of striated  the middle of the sarcomere.  
muscle and contains T-tubules, invaginations that   
quicken action potential propagation on the  The M lines are the midpoints of the sarcomeres. 
muscle.   Thick myosin filaments branch from the M lines 
  towards the ends of the sarcomere.  
The sarcoplasmic reticulum is the   
endoplasmic reticulum of muscle fibers that  The I band is the area in the sarcomere where 
releases stored calcium ions into the  only actin filaments are present. (Mnemonic: “I” is 
sarcoplasm through voltage-gated calcium  a thin letter, representing thin actin filaments) 
channels when triggered by the depolarization   
of the muscle cell.   The A band is the area in the sarcomere where 
  actin and myosin overlap. 
The calcium ions then bind to troponin, which   
removes tropomyosin from the  The H zone is the area in the sarcomere where 
myosin-binding-sites on actin, allowing myosin  only myosin is present. (Mnemonic: “H” is a thick 
to interact with actin and cause sarcomere  letter, representing thick myosin filaments) 
shortening, via sliding filaments. 
 
 

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Degrees of Muscle Contraction 

 
Summation is the process by which twitches add 
up to create a larger overall contraction.  
 
There are two types of summation: 
 
1. Wave summation (temporal summation) - 
depolarizing a motor unit again during the 
relaxation phase. May cause tetanus, which 
  is when the muscle fibers cannot be further 
Adapted from: https://commons.wikimedia.org/w/index.php?curid=7921353 
  stimulated due to a lack of relaxation. 
Motor Units  Twitches blend together during tetany, 
  eventually causing fatigue (loss of muscle 
Motor units make up muscles; a motor unit refers  contraction).  
to all the muscle fibers innervated by a single 
neuron.  
 
Small motor units include only a few muscle 
fibers and are used in precision movement. 
Large motor units include many muscle fibers 
that are innervated by a single neuron and are 
used in powerful movements.  
 
Twitch Contractions 
Adapted from: https://commons.wikimedia.org/w/index.php?curid=30015045 
 
 
A twitch contraction is the contraction of a 
2. Motor unit summation - different motor 
muscle fiber through motor unit stimulation. 
units are stimulated at different times to 
Each twitch has the same size and duration. 
produce the intended amount of muscle 
Twitch contractions also follow the all-or-none 
contraction. This is also known as the size 
principle, which states that a depolarization will 
principle of motor unit recruitment 
cause all the muscle fibers to twitch if it is above 
because smaller motor units are stimulated 
threshold potential but will not cause any 
first before larger motor units come in to 
twitching if the depolarization is below threshold 
help. 
potential.  
 
 
Weak and involuntary twitches in small motor 
Three phases of a twitch: 
unit groups contribute to maintaining muscle 
 
tone (muscle tonus). Fatigue is never reached 
1. Latent: action potential spreads over 
because different motor units are stimulated at 
sarcolemma and T-tubules, signaling to 
different times.    
sarcoplasmic reticulum to release calcium. 
2. Contraction: formation of cross bridges as 
a result of calcium ions binding to troponin. H 
zones shrink and muscle tension increases. 
3. Relaxation: calcium is pumped back into the 
sarcoplasmic reticulum, ending cross bridge 
cycling and decreasing muscle tension. 
 
 
   

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Chapter 11.6: Skeletal System 

 
Table of Contents  
 
● Types of Skeletons 
● Types of Bones and their Structure 
● Bone Remodeling  
● Embryonic Ossification 
● Connective Tissues and Joints 
 
Types of Skeletons 
 
An exoskeleton is an external skeleton. Many 
invertebrates and all arthropods possess 
exoskeletons.  
 
Vertebrates contain an endoskeleton on the 
inside. An endoskeleton can be divided into the 
axial skeleton (core bones) and the 
appendicular skeleton (appendages).  
   
Adapted from: https://commons.wikimedia.org/w/index.php?curid=27796930 
Types of Bones and their Structure 
 
 
2. Short bones - as wide as they are long and 
Types of bones in the endoskeleton: 
mainly provide support (eg. parts of the 
 
wrist).  
1. Long bones - made of cortical bone 
3. Flat bones - mainly provide protection (eg. 
(compact) and pockets of cancellous bone 
skull).  
(spongy). Important features include the 
4. Sesamoid bones - found within tendons to 
epiphysis, diaphysis, medullary cavity, 
help muscles pull (eg. kneecap). 
metaphysis, and epiphyseal plate. 
5. Irregular bones - irregularly shaped (eg. 
● Epiphysis - end of a long bone that forms 
pelvis).  
joints with other bones and contains red 
 
bone marrow for hematopoiesis (blood 
Cortical bone is the dense outer layer of bone that 
cell synthesis). 
supports the weight of our bodies. It is composed 
● Diaphysis - long hollow shaft in center of 
of many microstructures: 
bone. 
 
● Medullary cavity - located within the 
● Osteons - cortical bone’s functional unit, 
diaphysis and contains red and yellow 
composed of tiny multi-layered cylinders. 
bone marrow (area of fat storage). 
Also known as haversian systems because 
● Metaphysis - similar to epiphyses and 
they contain a haversian canal in their center. 
found between the medullary cavity and 
● Haversian canals - ‘tubes’ that contain blood 
epiphyseal plates. 
vessels for nutrient supply. 
● Epiphyseal plate - “growth plate” located 
● Lamellae - layers of the osteon.  
between epiphysis and metaphysis. Made 
● Lacunae - small spaces between lamellae that 
out of hyaline cartilage and works to 
hold bone cells and interconnect through 
lengthen the diaphysis through growth and 
canaliculi. 
ossification. 
● Canaliculi - small channels that connect 
 
lacunae and the haversian canal.  
● Volkmann’s canals - connect Haversian canals 
to the periosteum, which provides nutrients.  

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Cancellous bone is the spongy inner layer of bone  Mechanisms involved in bone remodeling: 
that soaks up red bone marrow via a web of   
trabeculae (connective tissue that supports  ● Parathyroid hormone - increases blood 
cancellous bone).   calcium levels by stimulating osteoclasts and 
depressing osteoblasts. Secreted by the 
parathyroid gland. 
● Vitamin D - increases blood calcium levels by 
raising intestinal calcium absorption. Activated 
by parathyroid hormone, but provides 
negative feedback on PTH production. 
● Calcitonin - decreases blood calcium levels by 
depressing osteoclasts, allowing osteoblasts to 
build bone without competition. Secreted by 
the thyroid gland. 
 
Osteoid is the organic component of bone 
https://commons.wikimedia.org/w/index.php?curid=378948 
  containing many proteins such as collagen (gives 
Bone Remodeling  bone tensile strength).  
   
Bone remodeling is the process of going back and  Hydroxyapatite is the inorganic mineral 
forth between the processes of ossification (bone  component of bone that gives the bone density 
formation) and resorption (bone loss).  and strength. 
   
Types of cells involved in bone remodeling:     
 
● Osteoprogenitors - immature precursor cells 
that differentiate into osteoblasts. 
● Osteoblasts - build bone by secreting 
proteins and utilizing blood calcium. They 
mature into osteocytes after getting trapped 
inside the bone matrix they create. 
● Osteocytes - live in lacunae in osteons to 
maintain bone.  
● Osteoclasts - eat and resorb bone, bringing 
calcium back into the blood. Derived from 
monocytes. 
 
 
 
   

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Embryonic Ossification  Connective Tissue and Joints 

   
Two types of embryonic ossification:  Types of connective tissue: 
   
1. Intramembranous ossification - bone is  1. Fibrous connective tissue has a matrix made 
created directly within fibrous membranes,  up of fibers.  
mainly for flat bones. Osteoblasts start by  ● Tendons - connect muscle to bone. 
secreting osteoid, which hardens and houses  ● Ligaments - connect bone to bone. 
osteocytes. Eventually, cortical bone is  ● Periosteum - membrane that covers 
created.   cortical bone with an outer fibrous layer 
2. Endochondral ossification - bone is created  (vascularized) and an inner/cambium 
indirectly through a cartilage model, mainly  layer (collagen for attachment to cortical 
for long bones. The cartilage model calcifies  bone) 
during fetal development, creating  ● Endosteum - membrane located between 
ossification centers that help form the  cortical and cancellous bone. 
features of long bones.  2. Cartilage is avascular (lacks blood vessels) 
and is not innervated (as opposed to bone 
which is highly vascular and innervated).  
 
Chondroblasts build cartilage by secreting 
collagen and elastin.  
● Hyaline cartilage - slightly flexible and 
important in providing support and 
stability to joints.  
● Fibrous cartilage - high rigidity and resists 
tension, found in intervertebral discs and 
knee meniscus.  
● Elastic cartilage - highly flexible and 
found in ears and epiglottis.  
3. Joints are vascularized and innervated. They 
  are found between bones. Below are types of 
https://commons.wikimedia.org/w/index.php?curid=4353671 
  joints. 
  ● Synarthroses - dense, fibrous joints that do 
  not move. 
  ● Amphiarthroses - cartilaginous joints that 
  partially move. 
  ● Diarthroses - synovial joints that fully 
    move. Typically contain hyaline cartilage. 
 
 

   

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Chapter 11.7: Endocrine System  There are three types of hormones: peptide 
  hormones, steroid hormones, and amino-acid 
Table of Contents   derived hormones. 
   
● Hormones  1. Peptide hormones (protein hormones): 
● Hypothalamus and Pituitary   
● Thyroid and Parathyroid   Synthesis - produced in the rough ER and made 
● Pancreas  of amino acids connected by peptide bonds.  
● Adrenal Gland   
● Testes and Ovaries  Action - binds to cell surface receptors because 
● Feedback Loops  they cannot pass freely through the cell 
  membrane as a result of being water-soluble 
Hormones  (and not lipid-soluble). The process of hormone 
  function is an indirect stimulation. The two 
Hormones can be secreted in the following ways:  ways the signal can be received is through 
  intracellular secondary messengers or 
● Endocrine - through the bloodstream.   ligand-gated ion channels.  
● Exocrine - through ducts.   
● Paracrine - to neighboring cells.  G protein coupled receptors (GPCRs) are cell 
● Autocrine - onto the same cell that is secreting  surface receptors that can initiate a secondary 
the hormone.  messenger response after binding to a peptide 
  hormone extracellularly. A G protein is coupled 
to the receptor and dissociates into subunits 
(alpha (α), beta (β) and gamma (γ)) after 
activation. These subunits then act upon 
intracellular second messengers to propagate 
the signal. 

 
Receptor tyrosine kinases (RTKs) are another 
cell surface receptor that dimerizes and initiates 
second messenger responses upon binding to a 
peptide hormone (eg. insulin). The intracellular 
domains of RTKs cross-phosphorylate each 
other and initiate second messenger signaling 
within the cell. 
 
The second messenger system of peptide 
hormone signaling allows for quick and 
immediate physiological changes. 
   
  Ligand-gated ion channels change shape upon 
    binding to peptide hormones, allowing ions to flow 
across the cell membrane. No second messengers 
are involved.  
   

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2. Steroid hormones:  3. Amino-acid derived hormones: 

   
Synthesis - produced in the smooth ER and  Can have properties that are similar to both 
made up of a fused 4-ring structure.   peptide hormones and steroid hormones.  
   
Synthesis - produced in rough ER and cytosol. 
Mainly derived from the amino acid tyrosine. 
 
Examples - all hormones produced by the 
adrenal medulla (epinephrine and 
norepinephrine, which are water-soluble). Also 
includes T3 and T4 (lipid-soluble). 
 
 
Examples - all hormones produced by the adrenal     
cortex (glucocorticoids, mineralocorticoids, 
androgenic steroids) and reproductive organs 
(progesterone, testosterone, estrogen).  

Action - requires a protein carrier to travel 

through the bloodstream due to being lipophilic. 
Freely crosses the cell membrane, and binds to 
receptors either in the cytoplasm or the nucleus to 
form molecule-receptor complexes that bind to 
DNA, and influence gene transcription. This 
process is known as direct stimulation.  

 
 
Steroid hormones cause slow and gradual 
physiological changes. 
 
 
   

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Hypothalamus and Pituitary   

  Hypothalamic-inhibiting hormones are released 
The hypothalamus coordinates the body’s  by the hypothalamus to inhibit the release of other 
internal environment and maintains homeostasis.  hormones by the anterior pituitary. 
   
The pituitary gland (hypophysis) is under the  The anterior pituitary then produces its own 
hypothalamus and is composed of two lobes -  hormones, classified as tropic hormones and 
the anterior pituitary and posterior pituitary.  direct hormones. 
   
1. Posterior pituitary:  Tropic hormones target other endocrine glands 
  for further hormone release. Important 
Known as the neurohypophysis because it is  examples released from the anterior pituitary: 
made of neuronal tissue. It is a direct neuronal   
extension of the hypothalamus.   ● FSH (follicle stimulating hormone) - follicle 
  growth (females) and sperm maturation 
Two hormones are stored and released by the  (males) in the gonads. 
posterior pituitary (and are produced by the  ● LH (luteinizing hormone) - stimulates 
hypothalamus):  ovulation, corpus luteum formation (females), 
  and testosterone production (males) in the 
1. Anti-diuretic hormone (ADH aka  gonads. 
vasopressin) - decreases urination by  ● ACTH (adrenocorticotropic hormone) - 
increasing water retention. Targets nephrons,  stimulates release of glucocorticoids from the 
increasing the number of aquaporins for  adrenal gland to fight stress. 
water reuptake.   ● TSH (thyroid stimulating hormone) - stimulates 
2. Oxytocin - causes uterine contractions during  T3 and T4 production by the thyroid gland to 
child labor and the release of milk during  increase metabolism.  
breastfeeding (mammary gland).    
  Direct hormones target organs directly for effects. 
2. Anterior pituitary:  Important examples released from the anterior 
  pituitary: 
Known as the adenohypophysis, it is made of   
glandular tissue, and produces its own hormones.  ● Prolactin - stimulates mammary gland 
It is connected to the hypothalamus through a  development and increases milk production 
hypophyseal portal system, which allows for  after childbirth.  
quick diffusion of hormones through a portal  ● Growth Hormone (somatotropin) - stimulates 
vein. Hypothalamic-releasing hormones are  body cells to grow and divide. 
released by the hypothalamus to stimulate the   
anterior pituitary to release other hormones.   Finally, the pineal gland in the brain produces 
  melatonin, which regulates circadian rhythm.  
● GnRH (gonadotropin-releasing hormone)   
- causes release of luteinizing hormone     
(LH) and follicle stimulating hormone 
(FSH).  
● TRH (thyrotropin-releasing hormone) - 
causes release of thyroid stimulating 
hormone (TSH). 
● CRH (corticotropin-releasing hormone) - 
causes release of adrenocorticotropic 
hormone (ACTH). 
● GRH (growth hormone-releasing hormone) 
- causes release of growth hormone (GH). 

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Thyroid and Parathyroid  Pancreas 

   
The thyroid gland is the largest endocrine organ  The pancreas is a gland that contains exocrine 
and is located in front of the trachea.  and endocrine tissue. 
   
Three main hormones of the thyroid:  The exocrine tissue secretes digestive enzymes 
  through the pancreatic duct into the small 
1. Triiodothyronine (T3) - released in response  intestine.   
to TSH and increases metabolism in the  The endocrine tissue (the islets of Langerhans) 
body. Has a negative feedback effect on  secretes glucagon, insulin and somatostatin. 
TSH secretion.  These three hormones are each secreted by a 
2. Thyroxine (T4) - performs the same actions  different cell type as listed below: 
as T3 above. However, T4 has one more   
iodine and gets converted into T3 upon cell  1. Alpha (α) cells - secrete glucagon in response 
uptake. It is much less potent than T3 but is  to low blood glucose levels. Glucagon raises 
more stable in the blood.  glucose levels by stimulating the liver and fat 
3. Calcitonin - secreted by the parafollicular  tissue to release their glucose storages.  
cells to decrease blood calcium levels.  2. Beta (β) cells - secrete insulin in response to 
Stimulates osteoblasts to use up blood  high blood glucose levels. Insulin lowers 
calcium to build bone and inhibits  glucose levels by stimulating the liver, 
osteoclasts. Also decreases calcium uptake in  muscle, and fat tissue to store glucose.  
intestines and kidneys.  3. Delta (δ) cells - secrete somatostatin, which 
  inhibits growth hormone. It also inhibits the 
Hypothyroidism describes the under-secretion  secretion of glucagon and insulin.  
 
of T3 and T4, resulting in reduced levels of 
metabolism in the body.      
 
Hyperthyroidism describes the over-secretion of 
T3 and T4, resulting in increased levels of 
metabolism in the body.  
 
Both hypothyroidism and hyperthyroidism can 
lead to goiter (physical enlargement of the 
thyroid gland). Hypothyroidism causes 
over-secretion of TRH to compensate for low T3 
and T4, enlarging the thyroid gland, while 
hyperthyroidism itself results from a 
hyperactive thyroid gland.  
 
The parathyroid gland secretes parathyroid 
hormone (PTH) which performs in the opposite 
way as calcitonin. It stimulates osteoclasts and 
decreases calcium uptake by bones. Parathyroid 
hormone increases blood calcium levels.  
 
 
   

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Adrenal Gland  Testes and Ovaries 

   
Our body has two adrenal glands. Each adrenal  After stimulation by LH and FSH from the anterior 
gland has an outer cortex and an inner medulla.  pituitary, the ovaries produce progesterone and 
They mainly help the body deal with stress.  estrogen, while the testes produce androgens 
  such as testosterone. 
 
Females: 
 
● LH - during menstrual cycle, the LH surge 
causes ovulation. This results in the 
formation of a corpus luteum, which 
produces progesterone and estrogen. 
● FSH - stimulates follicle growth in ovaries, 
  which results in the increased production of 
progesterone and estrogen. 
Adrenal cortex:   
  Males: 
● Deals with longer term stress.   
● Stimulated by secretion of ACTH from the  ● LH - triggers testosterone production by 
anterior pituitary.  Leydig cells. 
● Releases steroid hormones.   ● FSH - stimulates sperm maturation.  
● Produces glucocorticoids (i.e. cortisol) to   
raise blood glucose levels for immediate fuel  Feedback Loops 
during periods of long-term stress. However,   
this also lowers our immune response.  Hormonal control relies on feedback systems, 
● Produces mineralocorticoids (i.e.  which fall under positive and negative feedback 
aldosterone) to increase blood volume and  loops.  
blood pressure by raising reabsorption of   
Na+. Water passively gets reabsorbed with  1. Positive feedback - the change causes the 
Na+ due to osmosis.   amplification of itself, forming a loop that 
● Produces a small amount of male sex  continues to intensify. You can think of it as 
hormones (androgens).  promoting exponential growth. 
  2. Negative feedback - the change causes the 
Adrenal medulla:  inhibition of itself, forming a loop that 
  prevents hormone overproduction. You can 
● Deals with short-term stress.  think of it as promoting stability in the body. 
● Stimulated by sympathetic nervous system. 
● Releases amino-acid derived hormones. 
● Produces catecholamines (epinephrine and 
norepinephrine) to initiate “fight or flight” 
response by increasing heart rate and the 
breakdown of glucose. Also increases blood 
flow to brain/muscles and air flow to lungs. 
 
 
   

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Chapter 11.8: Digestive System   

Mouth, Pharynx, Esophagus 
Table of Contents: 
 
● Digestion in Humans 
Mechanical (chewing) and chemical (salivary 
● Mouth, Pharynx, Esophagus 
amylase) digestion begin in the mouth. Salivary 
● Stomach  
amylase in saliva breaks down starch into 
● Small Intestine 
maltose (glucose + glucose). Saliva also lubricates 
● Liver 
the food, creating a bolus.  
● Large Intestine 
 
● Summary: Digestive Hormones & Enzymes 
Upon swallowing, food enters the pharynx 
 
(common to digestive and respiratory systems) which 
Digestion is the process of breaking down large 
separates to form the trachea and the esophagus. 
food into smaller substances for absorption by 
The epiglottis blocks the opening to the trachea, 
the body.  
preventing choking. 
● Intracellular digestion = within cells (eg: 
 
amoeba pseudopods bring food inside 
Food continues to the esophagus (tubular 
its single cell for digestion) 
structure guiding food to stomach). The bolus is 
● Extracellular digestion = outside of cells 
pushed down via peristalsis (rhythmic waves of 
(eg: humans digest food then brings 
contraction). The upper third of the esophagus 
nutrients into its cell for further 
consists of skeletal muscle, the lower third 
processing) 
consists of smooth muscle, and the middle third 
 
is a mixture of the two. 
Digestion in Humans 
 
 
Stomach 
The digestive tract has two openings: mouth and 
 
anus 
Food enters the stomach via the cardiac 
sphincter (ring of muscles) where mechanical 
(churning of food) and chemical (enzymatic 
breakdown of protein and fat) digestion occur.  
 
The stomach lining is filled with gastric pits 
leading to gastric glands (multiple cell types). 
Mucous cells produce mucus, which lubricates 
and protects the stomach lining from the acid. 
 
Food entry causes the stomach to distend, 
signaling G cells to release gastrin, a hormone 
with two functions: 
 
1. Stimulates parietal cells to release 
extremely acidic gastric juice (pH= 2; high 
HCl concentration). 
2. Stimulates chief cells to secrete gastric 
lipase (breaks down fats to fatty acids + 
  glycerol) and pepsinogen (a zymogen - 
Adapted from:  an inactive enzyme precursor) which is 
 
https://commons.wikimedia.org/wiki/File:Digestive-system-for-kids.png
activated to pepsin in acid. Pepsin cleaves 
1. Mechanical Digestion = physical breakdown 
peptide bonds (proteins → amino acids). 
of food 
 
2. Chemical Digestion = chemical breakdown 
Chyme (acidic, semi-digested food) exits to the 
of food, using enzymes. 
small intestine via the pyloric sphincter. 

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Small Intestine  Inside the villus, nutrients (glucose and amino 

  acids) are absorbed into blood capillaries and fats 
Responsible for 90% of digestion and nutrient  (fatty acids and glycerol) into lacteals.
absorption. Consists of 3 parts: duodenum 
(digestion), jejunum, and ileum (absorption) - 
remember DJ Eye (D > J > I). 
 
Goblet cells secrete mucus to protect the 
epithelial lining from acidic chyme. Chyme also 
triggers the release of secretin (a hormone), 
which stimulates the pancreas to release basic 
bicarbonate ions (HCO3-) into the duodenum via 
the pancreatic duct. 
 
Cholecystokinin (CCK) released by the small   
intestine slows gastric emptying, stimulates  Adapted from: 
pancreas to release digestive enzymes, and tells   
https://commons.wikimedia.org/wiki/File:Villi_%26_microvilli_of_small_intestine.svg
 
gallbladder to release bile into the duodenum. 
Liver 
 
 
Accessory organs in the digestive system include 
In addition to bile production, the liver is 
the pancreas, liver, and gallbladder.  
involved in many processes. 
 
 
Bile (emulsifies fats) is produced by the liver and 
1. Blood Maintenance  
stored and concentrated by the gallbladder.  
● Stores blood. 
 
● Filters and detoxifies blood coming 
The pancreas secretes HCO3- (neutralization), 
from the digestive system via the hepatic 
pancreatic amylase (starch → maltose) and 
portal system. 
proteases (proteins → amino acids). The 
● Destroys erythrocytes and bacteria. 
pancreatic proteases are trypsin and 
Kupffer cells (phagocytes) eat bacteria 
chymotrypsin, which are initially released as 
and break down hemoglobin in red 
zymogens (trypsinogen and chymotrypsinogen). 
blood cells (red) to bilirubin (yellow) for 
Enteropeptidase in the duodenum converts 
secretion in the bile.  
trypsinogen to trypsin, which then converts 
 
chymotrypsinogen to chymotrypsin. 
2. Glucose Metabolism  
 
● Glycogenesis - converts excess glucose 
Food is moved via peristalsis to the jejunum 
into glycogen for storage in the liver 
and ileum for absorption. Villi (finger-like 
(after meals). 
projections which increase surface area) are 
● Glycogenolysis - breaks down glycogen to 
made of enterocytes that are lined with 
glucose for bodily use (between meals). 
microvilli. Villi and microvilli increase surface 
● Gluconeogenesis - converts glycerol and 
area and absorption efficiency. Crypts 
amino acids into glucose when glycogen 
(invaginations in the intestinal wall) contain cells 
stores are depleted. 
that secrete enzymes and produce new epithelial 
 
cells for the lining. 
  3. Protein Metabolism 
  ● Synthesizes plasma proteins from amino 
    acids (albumin and blood clotting 
factors). 
● Converts ammonia (dangerous byproduct 
of protein metabolism) into urea (safer) for 
excretion. 

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Large Intestine  Summary: Digestive Hormones & Enzymes 

   
Water and mineral absorption occur at the   
cecum (small pouch). The appendix (projection   
in the cecum) is a vestigial structure with   
negligible immune function that can become 
inflamed (appendicitis). In the colon water 
absorption is completed, hardening feces. The 
feces is stored in the rectum and expelled 
through the anus. Many species of bacteria 
coexist in the large intestine; these bacteria serve 
a critical function in aiding digestion. These 
bacteria, as well as all the other bacteria that are 
present in or on the body, are collectively known 
as a microbiome. 
 
The large intestine has 3 functions: 
1. Water absorption. 
2. Mineral absorption (salts). 
3. Vitamin production and absorption: in a 
mutualistic relationship, bacteria produce 
vitamins B and K (absorbed), metabolize 
bile acid, and ferment fiber. 
 

 
https://commons.wikimedia.org/wiki/File:Stomach_colon_rectum_diagram-en.svg 
 

 
   

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Chapter 11.9: Excretory System 

Table of Contents: 
● The Kidney 
● The Nephron 
● Filtration 
● Reabsorption 
● Secretion 
● Excretion 
● Hormones in Excretory System 
● General Pathway 
 
Excretion is the filtering out of metabolic wastes 
from the body’s fluids and eliminating them as 
urine. 
 
The Kidney  Filtration 
   
Humans have two kidneys. Each kidney consists  Filtration occurs in the cortex at the renal 
of a cortex (outer portion where blood enters  corpuscle, which consists of the glomerulus and 
the kidney), a medulla (middle portion), and a  the Bowman’s capsule. Blood enters from the 
pelvis (inner portion where filtrate exits the  afferent arteriole into the glomerulus, which acts 
kidney).  as a sieve. Podocytes from the Bowman’s 
capsule surround the glomerulus to form 
fenestrations that allow small substances (water 
and solutes) to be filtered into the Bowman’s 
capsule while larger substances (proteins and 
blood cells) remain in the blood. The glomerulus 
exits the Bowman’s capsule via the efferent 
arteriole, which goes on to form the peritubular 
capillaries. 
 
Reabsorption 
 
Throughout the nephron, water and solutes that 
the body needs are reabsorbed from the filtrate 
 
back into the blood.  
Adapted from: https://commons.wikimedia.org/wiki/File:Kidney_Cross_Section.png 
The loop of Henle descends into the medulla 
 
and has selective permeability. It is surrounded 
The Nephron 
by the vasa recta (capillaries running parallel to 
 
the loop of Henle). Water is reabsorbed into the 
A nephron is a single, functional unit of a kidney. 
blood as the filtrate travels down the 
There are four main processes that occur in the 
descending limb (filtrate becomes more 
nephron: 
concentrated), and solutes are reabsorbed as the 
1. Filtration 
filtrate travels up the ascending limb (filtrate 
2. Reabsorption 
becomes less concentrated).  
3. Secretion 
   
4. Excretion 

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Secretion  Angiotensin II has many effects in the 

  body. The most important are: 
Secretion is the transfer of solutions from the   
blood vasculature directly into the nephron tubule 
● It stimulates additional aldosterone 
filtrate. This occurs at the distal convoluted 
release from the adrenal gland cortex 
tubule and the proximal convoluted tubule.  
(so aldosterone levels increase). 
 
Excretion  ● It increases Na+ reabsorption from 
  the proximal tubule (and water will 
The filtrate (now urine) travels from the  follow the salt). 
nephrons to the collecting duct, which leads to  ● It is a potent systemic 
the renal pelvis and then to the ureter.  vasoconstrictor, causing vessels to 
The ureter connects the kidney to the bladder,  constrict and thereby increasing total 
where urine is stored. When the signal is received,  peripheral resistance (TPR). 
urine is excreted from the bladder and the body 
● It makes the individual more thirsty: 
via the urethra. 
so they drink more and increase their 
 
blood liquid volume (increasing TPR). 
Hormones 
 
 
1. Parathyroid Hormone (PTH) = more  4. Aldosterone: is a mineralocorticoid 
blood calcium. Stimulates calcium  produced by the adrenal cortex. It 
reabsorption in the tubules, and indirect  increases salt and water reabsorption and 
stimulation of osteoclasts (more bone  potassium secretion in the distal tubules 
breakdown)  and collecting ducts 
  5. Antidiuretic Hormone (aka ADH or 
2. Calcitonin = less blood calcium (calcitonin  vasopressin). Released from the posterior 
tones down calcium). Inhibits calcium  pituitary upon stimulation from the 
reabsorption in the tubules, inhibits  hypothalamus. Causes aquaporins to 
osteoclasts (less bone breakdown)   insert into the collecting duct of the 
  nephron and increases water reabsorption 
3. Renin Angiotensin Aldosterone 
System:   6. Atrial natriuretic peptide (ANP) is 
  produced by atrial cells in response to atria 
Juxtaglomerular cells can detect  distension by increased blood volume and 
changes in blood pressure and sodium  pressure. ANP will reduce the blood 
levels. When blood pressure or blood  volume and blood pressure. It 
sodium is low, these cells release renin.   accomplishes this by: Increasing the 
  glomerular filtration rate (GFR); decreasing 
Renin is an enzyme which acts on  sodium reabsorption and increasing 
angiotensinogen to activate it to the  sodium excretion; inhibiting renin and the 
form angiotensin I. Another enzyme  renin-angiotensin-aldosterone system 
called Angiotensin Converting Enzyme  (RAAS).   
(ACE) acts on angiotensin I to convert it to 
angiotensin II. Angiotensin II is the active 
hormone. 
 
 
   

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Chapter 11.10: Integumentary System  Dermis 

 
Table of Contents: 
Located just below the epidermis, the dermis 
● Epidermis 
supports the epidermis and cushions against 
● Dermis 
injury. It contains 2 layers: the papillary dermis 
● Hair 
(more superficial and thin, high surface area) and 
● Glands 
the reticular dermis (deeper and thick, made of 
● Hypodermis 
dense irregular connective tissue). 
 
 
The integumentary system has 3 layers: 
Hair: made of keratin, generated from hair 
epidermis, dermis, and hypodermis. It has a 
follicles, stands up via erector pili muscles, and 
role in homeostasis, vitamin D production, and 
offers sun and hypothermia protection.  
protection from pathogens.  
 
 
Glands 
Epidermis 
 
 
1. Sudoriferous (Sweat) glands consist of: 
The epidermis is the most superficial layer of 
a. Eccrine glands (sweat glands) 
the skin and contains keratinocytes. It protects 
located on the entire body surface 
against dehydration, UV radiation, and 
and are important in 
pathogens. The layers of the epidermis from 
thermoregulation. 
superficial to deep are: 
b. Apocrine glands are located at 
 
specific sites and secrete into a 
Stratum  Corneocytes (dead  hair follicle. They produce earwax 
Corneum   keratinocytes) form the  (ceruminous) or milk 
outermost, protective layer.  (mammary), depending on their 
Stratum  Dead keratinocytes that are not  location. 
Lucidum*  yet fully differentiated into  2. Sebaceous glands are located over the 
corneocytes. *It’s present in  entire body except at the palms of hands 
palms and soles.  and soles of feet. They secrete sebum 
Stratum  Keratinocytes secrete lamellar  (oils + wax) into a hair follicle  
Granulosu bodies to form a water-barrier.   
m  Hypodermis 
Stratum  Important for strength   
Spinosum  (desmosomes) and immunity  The hypodermis is the deepest layer and contains 
(Langerhans cells).  larger nerves and blood vessels. Made of loose 
Stratum  Precursor keratinocyte stem  connective tissue and adipose (fat) tissue, its 
Basale (or  cells proliferate here. This is also  main function is fat storage. 
stratum  where light touch sensation 
germinativu (Merkel cells) and melanin 
m)  synthesis (melanocytes) occurs. 
Mnemonic:  
Come Let’s Get Some Beers 
Corneum Lucidum Granulosum Spinosum Basale 
 
 
   

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Chapter 12: Reproduction and Developmental  Human Reproduction 

Biology   

  Sexual reproduction: joining of two gametes 

Table of Contents  (male sperm and female egg) to create offspring. 
● Asexual Reproduction  Germ cells (male spermatogonia, female oogonia) 
● Human Reproduction  produce gametes via meiosis. 
 
● Male Anatomy and Spermatogenesis 
Male Anatomy and Spermatogenesis 
● Hormones in Males 
● Female Anatomy and Oogenesis 
● Hormones in Females 
● Menstrual Cycle 
● Hormone Feedback Loops 
● Fertilization 
● Cleavage, Morula, Blastula 
● Gastrulation 
● Organogenesis 
● Extraembryonic Development 
● Important Animal Embryonic Models   
 
● Factors Influencing Development 
  Spermatogenesis: 
Asexual Reproduction  Spermatogonia undergo two meiotic divisions 
  to become spermatids and differentiate into 
1. Binary Fission: Done by Unicellular organisms  sperm. 
(prokaryotes and the mitochondria and  1. Seminiferous tubules of testes = site of 
chloroplasts of eukaryotes). DNA is replicated,  spermatogenesis (sperm production) and 
migrates to opposite ends of the cell. Septum  contain: 
forms in the middle and separates, creating  ● Sertoli cells: activated by follicle 
two separate cells.  stimulating hormone (FSH). Surround and 
2. Budding: bud (outgrowth) forms on the  nourish sperm. Produce inhibin (inhibits 
organism. DNA is replicated and deposited into  FSH - negative feedback). 
bud, which buds off, eg. hydra, yeast.  ● Spermatogenic cells: produce 
spermatozoa. 
2. Sperm (not yet mature) transported via 
peristalsis to epididymis (duct around testes) 
for maturation and storage. 
3. Regeneration or fragmentation: piece of 
3. Sperm moves through vas deferens (group 
organism breaks off. Can regenerate broken 
of tubules) to ejaculatory duct (where vas 
piece or sometimes a new organism can 
deferens meets seminal vesicles) which 
grow from a fragment, eg. hydra, flatworms. 
propels sperm into urethra and leads to 
4. Parthenogenesis: unfertilized egg develops 
ejaculation out of penis as semen (sperm + 
to a viable organism, eg. Honeybees exhibit 
accessory gland secretions). 
haplodiploidy (males haploid, females 
 
diploid). 
Mnemonic (SEVEn UP): Seminiferous tubules → 
 
Epididymis → Vas Deferens → Ejaculatory Duct → 
 
Urethra → Penis. 
   
 
   

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Sperm Structure:  ● Uterus: muscular, vascular organ. Provides 

● Head: contains nucleus and acrosome  ideal environment for fertilized egg to 
● Midpiece: mitochondria (ATP production).  implant and develop. 3 layers: perimetrium 
● Tail: long flagellum (microtubules) to  (outer), myometrium (middle, smooth 
propel sperm.  muscle), endometrium (inner epithelial, lined 
  by mucous membranes). 
Accessory Glands:  ● Cervix: narrow opening of uterus leading to 
  vagina. 
1. Seminal Vesicles: secrete fructose (nutrients  ● Vagina: opens to external environment (where 
to produce ATP), viscous mucus (cleans and  sperm enters and birth occurs). 
lubricates urethra), and prostaglandins   
(causes urethral contractions which propels  Oogenesis: 
sperm).  1. Many oogonia produced, majority die via 
2. Prostate Gland: alkaline secretions (basic) to  apoptosis, small fraction remain and 
counteract uterine acidity.  differentiate to primary oocytes (begin 
3. Bulbourethral Glands: viscous mucus (cleans  meiosis but are arrested in prophase I until 
and lubricates urethra).   puberty). 
  2. At puberty: one egg per month ovulates, 
Hormones in Males  completing meiosis I, which produces a large 
  secondary oocyte (arrested in meiosis II 
1. Follicle Stimulating Hormone (FSH):  during metaphase II) and a polar body. 
stimulates sperm development in seminiferous  3. If fertilization occurs: meiosis II is completed. 
tubules.  4. At the end of meiosis II: 2-3 polar bodies 
2. Luteinizing Hormone (LH): stimulates Leydig  (non-viable) and 1 oocyte (viable, contains 
cells to produce testosterone.  majority of cytoplasm and nutrients for fetus) 
3. Testosterone: matures sperm, gives rise to  are produced. 
male secondary sex characteristics.   
  Hormones in Females 
   
Female Anatomy and Oogenesis  1. Follicle Stimulating Hormone (FSH): 
 
stimulates follicles in ovary to develop and 
production of estrogen and progesterone. 
2. Luteinizing Hormone (LH): stimulates 
ovulation of egg, corpus luteum formation, 
which produces estrogen and progesterone. 
3. Estrogen and Progesterone: menstrual cycle 
and reproduction, give rise to female secondary 
sex characteristics. 
 
   

 
Adapted from: 
https://commons.wikimedia.org/wiki/File:Scheme_female_reproductive_system-en.sv
g 
 
● Ovary: produces eggs (singular: ovum; plural: 
ova) which travel through the oviduct (or 
fallopian tube) to the uterus. 
   

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Menstrual Cycle   
   
1. Follicular Phase: hypothalamus releases  4. If No Implantation Occurs: LH and FSH 
Gonadotropin Releasing Hormone (GnRH)  levels drop (due to hypothalamus and 
→ anterior pituitary releases LH and FSH →  pituitary inhibition by increased progesterone 
FSH binds to the ovaries and induces follicles  and estrogen) → corpus luteum can no longer 
to develop → developing follicles release  be maintained → progesterone and 
estrogen → endometrium thickens → rapid  estrogen levels drop (hypothalamus and 
LH spike → ovulation.  pituitary are not inhibited anymore) → 
  endometrium sloughs off (menstruation) → 
2. Ovulation: Ovulation (egg is released from  cycle repeats. 
Graafian follicle) → fimbriae on oviduct   
catches egg, cilia sweep egg into oviduct →  5. If Implantation Occurs: outer layer of 
egg travels down oviduct (awaiting sperm  placenta produces Human Chorionic 
fertilization).  Gonadotropin (HCG) → maintains corpus 
  luteum → progesterone and estrogen levels 
3. Luteal Phase: follicle develops into the  maintained → endometrium remains (no 
corpus luteum (maintained by FSH and LH)  menstruation). 
→ corpus luteum produces progesterone     
and some estrogen → uterine lining thickens 
(prepares for implantation).  
 
   

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Hormone Feedback Loops  2. Acrosomal reaction: recognition process 

  between sperm and egg before fusion. 
Positive feedback loops stimulate a pathway to  Ensures same-species fertilization. Sperm 
increase production.   goes through the corona radiata to reach 
● Lactation: Infant suckling increases  zona pellucida. Actin from sperm binds to 
prolactin production which causes  ZP3 protein of egg’s zona pellucida (mutual 
lactation (milk production) and further  recognition). Membranes of sperm head and 
increases infant suckling. Oxytocin  acrosome fuse, releasing hydrolytic 
releases milk (milk let down reflex).  acrosomal enzymes to digest zona pellucida 
● Childbirth: Oxytocin induces  and allow sperm to fuse with plasma 
contractions which push the baby out of  membrane of egg (fertilization). 
the womb. The baby pushes against a 
nerve in the cervix that signals the 
hypothalamus and pituitary to release 
more oxytocin. 
 
Negative feedback loops inhibit a pathway to 
decrease production. 
● The hypothalamus releases GnRH   
causing the pituitary to release FSH and  Adapted from: 
https://commons.wikimedia.org/wiki/File:2901_Sperm_Fertilization.jpg 
LH which increase testosterone levels.   
High testosterone levels inhibit the  3. Polyspermy Block: prevents polyploidy by 
hypothalamus from releasing GnRH,  inhibiting polyspermy (multiple sperms 
lowering FSH and LH and testosterone.   penetrating egg). 
● The same occurs with estrogen and  ● Fast block occurs first when sodium ions 
progesterone in the menstrual cycle.   diffuse into the egg, depolarizing its 
  membrane and prevents sperm binding. 
Fertilization  ● Slow block: gradual, long-lasting occurs 
  second. Calcium ions released in egg 
Fertilization is the joining of a haploid sperm and  stimulate cortical reaction (exocytosis of 
a haploid egg to form a diploid zygote.  cortical granules). Cortical granules 
  make zona pellucida impenetrable and 
Sperm: head (with acrosome at its tip), midpiece  stimulate proteases to separate zona 
(contains mitochondria), tail.  pellucida from plasma membrane. 
   
Egg: Outermost layer, corona radiata (jelly coat,  4. Completion of Meiosis II for the Secondary 
made of follicular cells), nourishes developing egg.  Oocyte: During meiosis II, the egg is arrested 
Underneath is the vitelline layer (zona pellucida  in metaphase. After penetration, meiosis in 
in mammals), made of glycoproteins. Plasma  the secondary oocyte continues creating a 
membrane is under the zona pellucida.  haploid oocyte and producing a second 
  polar body. 
1. Capacitation: the final maturation step for   
sperm prior to fertilization. Triggered by  5. Zygote formation:  
secretions in uterine wall. Destabilizes sperm  ● Monozygotic twins: identical twins. One 
plasma membrane proteins and lipids  zygote splits. Two embryos with identical 
resulting in:  genetic material. 
● Preparation of sperm tip for acrosomal  ● Dizygotic twins: fraternal twins. Two 
reaction.  separate eggs fertilized by two separate 
● Increased calcium permeability causing a  sperms. Two zygotes with different 
hyperactive state (flagella beats harder,  genetic material. 
sperm swims faster).   

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Cleavage, Morula, Blastula  Embryogenesis in Mammals 

   
Cleavage is rapid cell division without changing  Morula (ball of blastomeres): forms at 12-16 cell 
the total mass of cells. The subsequently smaller  stage. 
cells resulting from cleavage are called   
blastomeres.  Blastula stage (hollow cavity): forms at 128 cell 
  stage. Blastocoel is hollow, fluid filled centre. 
1. Axis of Cleavage. 
● Radial Cleavage: cells aligned in vertical 
axis (eg. deuterostomes). 
● Spiral Cleavage: misaligned cells, deviate 
from axis (eg. protostomes). 
 

 
Blastocyst stage: cells of blastula divide and 
differentiate to form: 
1. Trophoblast (outer ring of cells) 
● Forms extraembryonic membranes 
(amnion, yolk sac, chorion, allantois) - 
support embryo. 
● Implants embryo in the uterus. 
● Produces HCG (maintains corpus luteum 
and endometrium). 
2. Inner Cell Mass (ICM) forms embryo. 
  Differentiates into two layers (bilaminar 
2. Fate of Cells.  stage). 
● Determinate Cleavage: blastomeres  ● Hypoblast: partially contributes to yolk 
have decided fate.  sac, remainder degenerates via apoptosis. 
● Indeterminate Cleavage: blastomeres  ● Epiblast: contributes to main embryo. 
do not have pre-set fate.  Cells thicken to form primitive streak 
3. Evenness of Embryo Division.  which defines left-right and top-bottom 
● Holoblastic Cleavage: throughout entire  axes and is crucial for gastrulation to 
embryo, evenly divides embryo, in  begin. 
animals with little yolk (eg. humans, sea   
urchins).  Fertilization occurs in the oviduct, cleavage 
○ Exception: Frogs have lots of yolk  occurs as fertilized egg travels to the uterus. At 
and also undergo holoblastic  the uterus, fertilized egg is at blastocyst stage. 
cleavage that is uneven (exhibit  To implant in uterine wall, blastocyst undergoes 
polarity).  zona hatching. Trophoblasts replace zona 
● Meroblastic Cleavage: partial cleavage,  pellucida and implantation can occur. 
embryo not evenly divided, in animals   
with lots of yolk (eg. birds, fish, reptiles).     
Exhibits polarity with animal pole 
(active cleavage) and vegetal pole 
(mainly yolk, negligible division). 
 
 
   

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Gastrulation  ● Epithelial lining of digestive, respiratory, 

  and excretory systems. 
Gastrulation is the formation of a trilaminar  ● PLTT (Pancreas, liver, Thyroid and 
embryo. Epiblast cells invaginate inwards through  parathyroid. Thymus). 
the primitive streak to form three germ layers:  Organogenesis 
endoderm, mesoderm, ectoderm. Embryo is   
now at the gastrula stage.  Organogenesis: formation of new organs. 
 
Neurulation is nervous system development: An 
embryo at this stage is known as a neurula. 
1. Notochord stimulates ectoderm to thicken, 
forming the neural plate. 
2. Neural plate folds onto itself forming the 
neural fold / neural groove. 
3. Neural fold continues to fold, forming a 
hollow tube (neural tube). 
● Some cells roll off to form neural crest 
  cells (migrate to form teeth, bones, skin 
pigmentation, etc.). 
 
As cells invaginate they create an opening called 
the blastopore, which forms the archenteron 
(center cavity - 
becomes 
digestive tract).  
 
 
 
 
 
 
 
1. Ectoderm (outer germ layer) forms: 
● CNS (brain and spinal cord) and PNS. 
● Sensory parts of ear, eye, and nose. 
● Epidermis layer of skin, hair, and nails.  4. Neural tube differentiates into CNS. 
● Mammary and sweat glands.  Mesoderm cells (somites) form two masses 
● Pigmentation cells.  alongside notochord. Becomes vertebrae and 
● Enamel of teeth..  skeletal muscles associated with axial skeleton. 
● Adrenal medulla.   
2. Mesoderm (middle germ layer) forms:  Stem cells are undifferentiated cells with 
● Bone and skeleton.  potential (potency) to become many types of 
● Muscles.  cells. 
● Cardiovascular system.  ● Totipotent stem cells can become any cell 
● Gonads.  (eg. zygote, blastomeres of morula). 
● Adrenal cortex.  ● Pluripotent stem cells can become any of of 
● Spleen.  the 3 germ layers (eg. ICM cells → embryonic 
● Notochord (induces spinal cord formation  stem cells). 
from ectoderm).  ● Multipotent stem cells can only differentiate 
3. Endoderm (inner germ layer) forms:  to a few cell types of a specific tissue type (eg. 
hematopoietic stem cell → many blood cells). 

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Extraembryonic Development 
 
Development of structures outside the embryo 
(derived from the trophoblast layer). Provide 
protection and nourishment to fetus. 
 
Placental mammals have internal pregnancies   
while egg-laying animals such as reptiles, birds,   
and monotremes (egg-laying mammals) lay eggs.  Important Animal Embryonic Models 
Marsupials are mammals that carry their babies   
in a pouch.  Frog Embryo 
   
1. Amnion: innermost layer, membrane around  Lots of yolk, Uneven holoblastic cleavage with 
embryo secretes amniotic fluid (water  animal pole (darker colour) and vegetal pole 
cushion, protecting embryo).  (paler). Gray crescent is opposite to the site of 
● Amniotes (reptiles, mammals, birds)  sperm entry. Forms due to cytoplasm rotation, 
have an amnion, anamniotes  causing mixing from the two poles. Any cell from 
(amphibians, fish) do not (surrounding  the first cleavage that receives a bit of the gray 
water serves as cushion).  crescent can become a full frog embryo. Frog 
2. Chorion: outermost layer.  embryos have no primitive streak. Instead, 
● Placental mammals: forms fetal half of  gastrulation begins at the dorsal lip of 
the placenta (platform for exchange of  blastopore (forms at site of gray crescent). 
gases, nutrients, and waste).   
● Egg-laying animals: membrane for gas  Chick Embryo 
exchange just underneath egg shell.   
3. Allantois: sac that buds off of the  Model for all egg-laying animals. Embryo has no 
archenteron. Stores waste for disposal.  direct connection to mother and needs large 
● Placental mammals: transports waste to  yolk for nutrients. Chalaza connects yolk to ends 
placenta, becomes the umbilical cord,  of shell (allows nutrient distribution to entire 
and in adults forms urinary bladder.  embryo). Chicks have a primitive streak. 
● Egg-laying animals: initially stores uric  Blastodisc (analogous to ICM in mammals) is 
acid, later fuses with chorion (helps with  flattened resulting in an elongated blastopore 
gas exchange).  upon gastrulation at primitive streak.  
4. Yolk Sac: contains yolk (intraembryonic,   
provides nutrients).  Factors Influencing Development 
● Placental mammals: transient function   
until placenta develops. First site of blood  1. Embryonic Induction: 
cell formation.  ● Organizers secrete chemicals that 
● Egg-laying animals: sole player in providing  influence what neighboring cells become 
nutrients.  in the future (eg. dorsal lip of blastopore 
  in frogs). 
2. Homeotic genes:  
● Master controller turns different gene 
expressions on / off. A Homeobox is a 
common sequence containing homeotic 
genes homologous across organisms 
(~180 nucleotides). Crucial in animal 
development. 
3. Egg Cytoplasm Determinant: 

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● If egg cytoplasm is unevenly distributed 

(creating animal and vegetal poles), an 
axis is created, influencing how the 
embryo divides during cleavage. 
4. Apoptosis: 
● Programmed cell death important for 
normal development of fetus (eg. 
removing webbing between fingers) and 
adults (preventing cancer).   

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Chapter 13: Evolution  Theory of Evolution 

   
Table of Contents:  1. Cuvier proposed catastrophism. 
● Evidence of Evolution  Catastrophes lead to mass extinctions of 
● Theory of Evolution  species in those areas. The different 
● Natural Selection  populations in different areas were shaped 
● Gene Equilibrium  by what catastrophes had occurred, and 
● Microevolution  what random organisms then survived and 
● Macroevolution  populated that area.  
● Origins of Life  2. Lamarck proposed: 
  ● Use and disuse: used body parts will 
Evolution is the gradual development and  develop and unused ones are weakened, 
change of heritable traits (allele frequencies) in  leading to evolution.  
populations over successive generations.  ● Inheritance of acquired traits: traits 
Evolution increases biodiversity.  acquired through use and disuse are 
  passed onto offspring (eg. giraffe 
Evidence of Evolution  stretching neck will cause its neck to 
  develop, and produce long necked 
1. Paleontology is the study of fossils through  offspring). This is incorrect - acquired 
actual remains of the animal or their traces  characteristics are generally not heritable. 
(ichnofossils). We can see the development  3. Darwin - Theory of Natural Selection. 
of species through time by comparing   
deepest (oldest) fossils to shallowest  Natural Selection 
(youngest).   
2. Looking at biogeographic evidence, we can  Natural selection is the gradual, non-random 
see the spread of different species around  process where allele frequencies change as a 
the world and analyze similarities and  result of environmental interaction. Survival of 
differences.  the fittest occurs as individuals with greatest 
3. Embryology allows us to see embryological  fitness (ability to survive and produce viable 
similarities and differences between early  and fertile offspring) have greatest success, and 
stages of related organisms. Eg. all chordates  pass on more DNA to future generations 
have a gill slit during development.  compared to less fit parents. Leads to the 
4. Comparative Anatomy compares different  evolution of the population (not individuals). 
body parts of different animals:   
● Homologous structures: may or may not  Requirements for Natural Selection 
perform the same function but have a  1. Demand for resources exceeds supply: 
common ancestor. eg. forearm of bird and  results in competition for survival (fittest 
forearm of human.  survive to pass on genes). 
● Analogous structures: same function, do  2. Difference in levels of fitness due to variation 
not have a common ancestor. eg. bird  in traits: differentiate ability to compete and 
wings and bat wings.  survive (eg. black peppered moths favored 
● Vestigial structures: serve no purpose  over white moths during Industrial 
but are homologous to functional  Revolution). 
structures in other organisms eg. human  3. Variation in traits must be genetically- 
appendix and cow cecum.  influenced (heritable) to be passed onto 
5. Biochemical methods allow for DNA  offspring. 
sequence comparisons. Can see conserved  4. Variation in traits must be significant for 
DNA sequences (higher similarity = higher  reproduction and/or survival: genes 
relatedness) and common conserved  improving reproductive success/survival are 
pathways (eg. Krebs cycle). .  favored and increase over generations and 
  vice versa. 

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Types of Natural Selection 

 

 
Adapted from: https://commons.wikimedia.org/wiki/File:Selection_Types_Chart.png 
 
1. Stabilizing Selection: mainstream (average)   
is favored (eg. birth weight). Diagram follows  The requirements for Hardy-Weinberg 
a standard bell curve.  equilibrium are:  
(Mnemonic: Large, Random, M&M) 
2. Directional Selection: one extreme favored 
● Large population: minimizes genetic drift. 
(eg. longest giraffe neck allows access to the 
● Random mating 
most leaves). 
● No mutation 
3. Disruptive Selection: rare traits favored, 
● No natural selection 
mainstream is not. (eg. snails living in low 
● No migration (gene flow): population must 
and high vegetation areas). 
be isolated. 
 
 
Other Types of Selection 
When conditions are not met, evolution occurs. 
 
 
Sexual Selection: non-random mating between 
Microevolution 
males and females. Females favor high quality 
 
partners, males prefer high quantity of partners 
Microevolution is the process when gene 
to increase their number of offspring.  
frequencies change within a population over 
Note: traits selected for may be favorable for 
generations (favorable genes increase, 
reproduction but not for survival. 
unfavorable decrease).  
 
 
Artificial Selection: carried out by humans to 
Factors Causing Microevolution 
selectively breed for specific traits (eg. dog 
 
breeding). 
1. Genetic Drift: allele frequencies change by 
 
chance. Larger effects on small populations. 
Gene Equilibrium (No Evolution) 
● Bottleneck effect: smaller gene pool, 
 
some alleles may be lost (eg. disaster 
The Hardy-Weinberg formula calculates genetic 
killing majority of population). 
frequency during genetic equilibrium (no 
● Founder effect: some individuals migrate 
change in gene frequencies). If both equations 
away from the population. 
hold true, the population is under 
2. Non-random Mating: sexual selection, 
Hardy-Weinberg equilibrium. 
  outbreeding, inbreeding. 
3. Mutations: can be dormant until 
environmental change allows it to flourish. 
4. Natural Selection: no luck involved 
5. Gene Flow: migration (non-random) moving 
alleles between populations, leading to 
variation through mixing.  
 

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Sources of Genetic Variation 

 
1. Mutation: must not be fatal. 
2. Sexual Reproduction: crossing over, 
independent assortment and random joining 
of gametes. 
3. Balanced Polymorphism: maintains a 
variety of phenotypes within a population. 
● Heterozygote advantage (eg. sickle Cell 
Anemia). 
● Minority Advantage: rare phenotypes 
offer higher fitness. Cycle between high 
and low frequency. (eg. advantageous 
against hunters’ search images). 
● Hybrid Advantage: Two strains of 
organisms produce more superior 
offspring.   
● Neutral Variations: may become   
beneficial if the environment changes.  2. Postzygotic Isolation: backup in case hybrid 
4. Polyploidy: plants have multiple copies of  zygote forms. 
alleles introducing more variety and  ● Hybrid Mortality: hybrid zygote 
preserving different alleles. Can also mask  not-viable (often due to different 
effects of a harmful recessive allele.  chromosome numbers). 
  ● Hybrid Sterility: hybrid zygote sterile. 
Macroevolution  ● Hybrid F2 Breakdown: offspring of 
  hybrids have decreased fitness. 
Macroevolution is long-term and occurs at a   
level at or higher than species. Species are 
reproductively isolated (via prezygotic and 
postzygotic isolating mechanisms) resulting in a 
lack of gene flow between species.  
 
1. Prezygotic Isolation prevents fertilization 
from occuring between species. 
● Habitat Isolation: occupying different 
habitats. 
● Temporal Isolation: reproducing at 
different times/seasons. 
● Behavioral Isolation: different courtship 
rituals. 
● Mechanical Isolation: male and female 
genitalia are not compatible. 
● Gamete Isolation: gametes do not 
recognize / fertilize each other (eg. zona 
pellucida on mammalian oocytes). 
 
 
 
 
 
 
 
   
 
 

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Speciation is how species form, starting with   

reproductive isolation, which leads to  Patterns of Evolution 
interruption of gene flow between populations   
that gradually develop into two species. 
 
1. Allopatric Speciation: occurs due to a 
geographical barrier. 
● Adaptive Radiation: occurs when many 
species arise from one ancestor as they   
adapt differently to their environments.   
During adaptive radiation, species can  1. Divergent Evolution: species diverge from 
specialize to fill different niches within  common ancestor.  
the same environment.  2. Convergent Evolution (Homoplasy): 
2. Sympatric Speciation: occurs without a  unrelated species adapt to similar 
geographical barrier.  environments becoming more alike 
● Balanced Polymorphism: different  (analogous structures).  
phenotypes are isolated within the same  3. Parallel Evolution: species diverge from a 
area.  common ancestor but undergo similar 
● Polyploidy: in plants results from  changes. 
nondisjunction during meiosis. (eg. Two  4. Coevolution: two species impart selective 
3n organisms - usually sterile - meet and  pressure on each other. 
are reproductively compatible).  ● Camouflage (cryptic coloration): match 
● Hybridization: some hybrids are more fit  appearance to environment to avoid 
than purebreds.  detection. 
● Aposematic Coloration (warning 
coloration): vibrant coloration in 
poisonous animals to warn predators. 
● Mimicry: evolving to resemble another 
species. In Batesian mimicry a 
non-harmful animal resembles a harmful 
one. In Mullerian mimicry, two 
poisonous animals resemble each other to 
warn their predator. 
 
Phylogenetic Trees 
 
A Phylogenetic tree is a branched diagram that 
shows inferred evolutionary relationships 
  between different taxa. A clade is a cluster with 
https://commons.wikimedia.org/wiki/File:Speciation_modes.svg 
  an ancestor and all its descendants. 
Theories of Macroevolution:   
  Parsimony means the simpler the evolutionary 
1. Phyletic gradualism: evolution happened  explanation, the better. Phylogenetic trees 
gradually via accumulation of small  minimizing evolutionary reversals, convergent 
intermediary changes. Not likely to be true (not  evolution and parallel evolution are preferred. 
supported by fossil evidence).   
2. Punctuated equilibrium: short spurts of     
evolutionary changes during periods of stasis 
(supported by fossil evidence). 
 

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Origins of LIfe  Organic “Soup” Theory: proposed by Oparin 

Timeline:  and Haldane. They believed that oxygen in the 
● Big Bang: ~ 14 billion years ago.  primordial atmosphere must have been too 
● Earth: ~ 4.5 billion years ago.  reactive for organic chemicals to be produced, 
● Prokaryotes: ~ 3.5 billion years ago.  and therefore oxygen must have been lacking in 
● Eukaryotes: ~ 2 billion years ago.  the primordial atmosphere. Strong energy (eg. 
  lightning, volcanic heat, UV radiation) drove 
Earth’s current atmosphere:  reactions that formed organic compounds. 
● Nitrogen gas (most common) = 78%.   
● Oxygen gas = 21%.  Miller-Urey Experiment: mimicked the reducing 
● Argon gas = 0.9%.  environment proposed by Oparin and Haldane. 
● Trace amounts of CO2, methane, ozone.  Set up a flask containing inorganic compounds 
  and simple organic compounds but no oxygen 
Primordial Earth:  (CH4, NH3, H2, H2O) connected it to another flask 
  with electrodes (simulates lightning) and heated it 
1. Earth’s primordial atmosphere consisted of  up (simulates high temperatures). Complex organic 
inorganic compounds and no oxygen - it was a  compounds (amino acids, organic acids, but no 
reducing environment.  complete nucleic acids) were formed. Supports 
2. Earth cooled down, gases condensed to  the Organic “Soup” Theory. 
form the primordial sea.   
3. Simple compounds became more complex, 
organic compounds formed. 
4. Organic monomers became polymers to 
form protenoids (behave like proteins). 
5. Protobionts arose: precursors to cells. Had 
microsomes (membrane-like) and proteinoids. 
6. Heterotrophic prokaryotes form. 
7. Autotrophic prokaryotes form (eg. 
cyanobacteria - can photosynthesize). 
● Important: The development of 
autotrophs led to the production of 
oxygen and its accumulation (oxidizing 
environment forms). 
8. Oxygen accumulates, reacts with UV light to 
form ozone layer, which blocks UV. This 
terminates abiotic chemical evolution. 
9. Primitive eukaryotes form   
Adapted from: 
● Endosymbiotic theory:  https://commons.wikimedia.org/wiki/File:Miller-Urey_experiment-en.svg 
membrane-bound organelles 
(mitochondria, chloroplasts), once 
free-living, were phagocytosed by other 
prokaryotes and lived in symbiosis with 
them as organelles.  
10. More complex eukaryotes and multicellular 
organisms begin to evolve. 
 
 
   

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Chapter 14: Ecology  Gause’s Law (competitive exclusion principle): 

  Two species cannot occupy the same niche and 
Table of Contents:  maintain population levels: one will outcompete 
● Ecological Niche  the other. Resource partitioning allows species 
● Speciation  to coexist. 
● Biological Interactions 
● Ecosystem Ecology 
● Population Ecology 
● Ecological Succession 
● Biomes 
 
Key Terms 
● Abiotic factors: nonliving elements of an 
ecosystem (eg. temperature, water, light). 
● Biotic factors: living elements of an   
Biological Interactions 
ecosystem (eg. plants, animals, etc.). 
 
● Species: a group that can interbreed and 
In competition (short-term interaction), 2 species 
have viable, fertile offspring. 
compete for the same resources. 
● Population: a specific species living in a 
 
specific location.  ● Intraspecific competition occurs between 
● Habitat: the type of place where a specific  members of the same species (eg. two rabbits 
organism lives. Includes other organisms  competing for carrots). 
(biotic) and physical aspects (abiotic).  ● Exploitation competition is indirect and 
● Ecological community: all populations in a  occurs when resources are depleted. (eg. 
given area.  cheetahs deplete gazelle population, 
● Ecosystem: all the organisms in an ecological  affecting lions). 
community (biotic), and the abiotic factors  ● Apparent competition occurs when one 
interacting within it.  predator preys on two species. 
● Biosphere: all ecosystems on Earth, their 
interactions with each other and the 
lithosphere, geosphere, hydrosphere, 
atmosphere. 
● Density-dependent factors depend on 
population density (eg. disease, resource 
competition). 
● Density-independent factors do not depend 
on population density (eg. climate, weather). 
 
Ecological Niche 
 
An organism’s niche is the biotic and abiotic 
resources it uses. Its realized niche is where it 
truly lives and its fundamental niche is the full 
range of environmental conditions where it could 
survive.  
 
 
   
   
   
 

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  level as energy transfer is inefficient between 

Symbiosis (living together) is a close, long-term  trophic levels.  
interaction between two organisms (symbionts).   
   
 
● Mutualism (+/+): both organisms benefit (eg.   
oxpecker bird eating ticks off rhino).   
● Commensalism (+/0): one organism benefits 
and the other is unaffected. (eg. jackal eating 
tiger’s leftovers). 
● Parasitism (+/-): one organism benefits at the 
other’s expense. (eg. tapeworm in human 
gastrointestinal tract). 
 
Ecosystem Ecology 
 
● Food chain: linear depiction of what eats 
what (eg. carrot → rabbit → fox → lion). 
● Food web: expanded food chain depicting 
interconnections between food chains. 
● Trophic level: an organism’s position within 
a food chain or food web.   
● Autotroph: produces organic compounds  Scavengers (carnivores or herbivores) 
from abiotic factors (sunlight, water, CO2,  decompose other dead animals (or plants). eg. 
etc.)  vultures, some beetles. Saprophytes (plants, 
● Heterotroph: must ingest organic  fungi, microorganisms) are decomposers that 
compounds to generate energy & survive.  consume dead or decaying organic material, and 
● Predation: relationship between predator  work with scavengers in organic recycling. Fungi 
(hunter) and prey (hunted - plant or animal).  (most important decomposers) and some 
● Herbivore: plant eater.   bacteria decompose organisms, forming 
● Carnivore: meat eater.  detritus (feces and decomposing matter). 
● Omnivore: plant and meat eater.  Detritivores (worms and slugs) consume 
● Invasive species: non-native species that  detritus, exposing more organic material for 
outcompetes native species and overtakes  decomposers. 
ecosystem.   
● Noninvasive species: non-native species   
that survives in but does not overrun an   
ecosystem.   
   
Primary producers, at the lowest trophic level,   
are autotrophs undergoing energy production     
(eg. photosynthesis) to generate the biomass of 
an ecosystem. Consumers (higher trophic levels) 
eat producers or other consumers.  
 
Primary consumers (often herbivores) are just 
above producers. Secondary consumers 
(carnivores) prey on primary consumers and 
tertiary consumers prey on secondary 
consumers. An apex predator is at the top of 
the chain (tertiary consumer or higher). 
 
Only ~10% of energy stored in a trophic level is 
converted to organic tissue in the next trophic 

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Population Ecology  Ecological Succession 

   
Population dynamics explores how populations  Ecological succession is the predictable process 
change in space and time and how they interact  where an ecological community develops and 
with their environment.   changes over time. Occurs in a new habitat or 
  after a disturbance.  
● Biotic potential: a species’ ability to undergo   
its highest population growth (highest births,  Primary succession occurs after a large 
lowest deaths) when conditions are ideal.   disturbance in an area that has never supported 
● Carrying capacity: the maximum population  life. Begins with a pioneer species (eg. lichen, 
size an ecosystem can sustain.  fungi, algae).  
   
r/K selection theory  The order of organisms colonizing is:  
  pioneer species → thin soil → vascular plants 
K-selected species: long gestation period, few,  (grasses, shrubs) → larger plants (trees) → 
large offspring, long time to mature, significant  animals 
parental investment, high survival to reproductive   
age (eg. humans, large mammals). Demonstrated  Eventually a climax community results. A steady 
by a type I survivorship curve.  state is reached and a balance of species is 
  achieved.  
R-selected species: abundant, small offspring,   
mature quickly, no parental investment, many do  Secondary succession occurs on terrain that has 
not survive to reproductive age (eg. bacteria,  supported life previously, and has had destruction 
insects, species with free swimming larvae).  following a disturbance (eg. flood, fire). Follows a 
Demonstrated by a type III survivorship curve.  similar pattern as primary succession but begins 
  with grasses & shrubs. 
In a type II survivorship curve, survival   
probability is constant regardless of age (eg.  A keystone species maintains ecological balance 
hydra, some birds & small mammals, lizards).  despite low abundance (eg. keystone predator 
  hunts other animals and prevents 
 
overabundance). 
 
Biomes 
 
Aquatic Biomes: 
 
Largest of Earth’s biomes (~75% of Earth’s 
surface). Photosynthetic algae contribute most of 
Earth’s atmospheric O2.  
 
Divided into freshwater biomes (~3%) and 
saltwater biomes (~97%). Estuaries are areas 
where freshwater meets saltwater. 
 
Layers of the ocean are divided based on the 
amount of sunlight received: 
 
● Euphotic zone: Strong irradiance allows for 
  plant survival and photosynthesis. Closest to 
  surface. The littoral zone is the area of the 
  euphotic zone where sunlight penetrates all 
    the way to the ocean floor. 

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● Disphotic zone: semi-irradiated with sun (not   

sufficient for plants). Bioluminescent  Terrestrial Biomes:  
species produce light here.   
● Aphotic zone: no light or photosynthetic  Land based (non-aquatic) biomes. Summarized in 
species. Some bioluminescent species. Select  the chart. 
fish can survive off of dead matter 
descending to the ocean floor. 
   

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Chapter 15: Animal Behavior  Learned Behaviors 

   
Table of Contents:  Learned behaviors increase an animal’s fitness, 
● Types of Animal Behaviors  allowing it to adapt to unexpected events. 
● Animal Movements   
● Communication  1. Classical conditioning: pairing a neutral 
● Social Behavior  stimulus (elicits no physiological response) to an 
● Mating  unconditioned stimulus (naturally elicits a 
  physiological response - unconditioned 
Ethology: the study of animal behaviors, which  response). This conditions the unconditioned 
are inherited (innate), or learned.  response to be mentally paired with a neutral 
  stimulus (becomes a conditioned stimulus) 
Types of Animal Behaviors  resulting in a conditioned response. 
   
Inherited Behaviors: 
 
1. Instincts: innate behaviors that occur without 
thought. eg: birds undergoing migration in 
response to seasonal changes. 
 
2. Reflexes are involuntary rapid responses to a 
stimulus. Reflex arcs are controlled by a neural 
circuit. There are 2 types: 
1. Simple reflexes are most rapid. An 
afferent sensory neuron travels from 
stimulus to central nervous system and 
synapses on efferent motor neurons,   
Adapted from: https://commons.wikimedia.org/w/index.php?curid=32037734 
which travel from central nervous system 
 
to muscle. 
● Stimulus generalization: a conditioned 
2. Complex reflexes are slower because 
animal responds to stimuli not identical to 
peripheral nerves are separated by an 
the original conditioned stimulus. The more a 
interneuron. 
stimulus differs from the original conditioned 
 
stimulus, the smaller the conditioned 
3. Fixed Action Patterns are hardwired actions 
response (stimulus generalization 
initiated by a specific stimulus (releaser or sign 
gradient). 
stimuli) and are considered the simplest form of 
● Stimulus discrimination: differentiation 
an instinct. Once initiated, they will continue to 
between a conditioned stimulus and other 
completion even if the stimulus is removed during 
similar, but different, non-conditioned stimuli. 
the behavior. Leads to predictable and 
 
appropriate behaviors that do not need to be 
   
learned. (ex: goose rolling egg back into nest, 
male insects attacking red bellied males). 
 
4. Imprinting: an innate way that animals learn 
behaviors that will never be forgotten. Occurs 
during the critical period or critical imprinting 
stage (eg: ducklings treating a moving object as 
their mother & following it). 
 
 
   

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Learned Behaviors (continued)  Communication 

2. Operant conditioning: learning to associate a   
behavior with a reward (increases behavior) or a  Allows coordination of social behaviors with 
punishment (decreases behavior).  other animals (finding shelter, food, mates, & 
  avoiding predation). 
B.F. Skinner: Skinner box for experiments   
  1. Visual: associated with aggressive (eg: wolves 
baring teeth) and submissive behaviors (eg: 
wolves lowering tail). Another example is 
courtship/mating rituals. 
 
2. Auditory: communication via sounds. 
Beneficial at night and over long distances. 
 
3. Tactile: communication via touch (eg: wolves 
  greeting by licking muzzles). 
3. Associative Learning: learning that two things   
are connected to each other. Increases stimulus  4. Chemical: communication via chemicals. 
response efficiency. Can be forgotten (extinction)  Releaser pheromones (immediate, reversible 
or remembered via re-association (recovery)  behaviors) and primer pheromones (long term 
● Spatial learning: associating a response with  behaviors). 
a specific location.   
● Sensitization: as stimulus occurs more often,  Social Behavior 
behavioral response increases.   
● Habituation: decreasing behavioral response  Allows interaction for companionship, finding 
in response to repetitive, meaningless  food, protection, and mating. 
stimulus. If stimulus is absent for some time,   
spontaneous recovery of the behavior can  Cooperation: grouping together to better 
occur.  achieve a goal (eg: coordinated hunting). 
● Observational learning: learning by   
watching another animal perform the same  Agonistic behaviors: competing for food, 
behavior.The animal learns without  territory, or mates. Include: threats, aggression 
reinforcement and increases efficiency.  (often detrimental to both parties), and 
● Insight: learning in a new situation. No  submission. Appeasement behavior (a threat 
reinforcement required.  by one animal causes another animal’s 
  submission) avoids aggression (prevents injuries). 
Animal Movements   
  Dominance Hierarchy = pecking order. Alpha 
1. Kinesis: changing speed in random directions -  male = top ranked male. 
no target (Favourable environment → reduce   
speed; Unfavourable environment → increase  Territoriality: behaviors used to protect an 
speed). eg: flatworm escaping when exposed to  animal’s territory or safe space (eg: employing 
light.  watchers and defenders and using pheromones 
  to scare off others). 
2. Taxis: movement with a specific direction,   
towards (positive taxis) or away (negative taxis)  Search images: abbreviating what food looks like 
from a stimulus. Light stimulus = phototaxis;  to quickly locate abundant and safe food without 
chemical stimulus = chemotaxis.  much thought. 
   
3. Migration: long-distance movement from one  Altruistic behaviors: sacrifices made for 
area to another due to instinct, often seasonal.  relatives.  

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● Inclusive fitness = sum of animal’s direct  ● Monogamy = one mating partner at once. 
(genes animal passes on) and indirect (genes  ● Polygamy = multiple partners at once. 
passed on by relatives) fitness. Increased by  ● Polygyny = one male multiple females. 
indirect fitness (kin selection).  ● Polyandry = one female multiple males. 
● Semelparity = mate once in lifetime (multiple 
offspring, low survival, harsh conditions, no 
parental care). 
● Iteroparity = mate many times in lifetime 
(one offspring, high survival, dependable 
environment, parental care). 
 

 
● Reciprocal altruism: sacrifices made for 
other organisms in anticipation of a future 
reward (‘I help your family, you later help 
mine’). 
 
Herds, flocks, schools, packs provide greater 
power and protection. 
 
Mating 
 
Sexual selection: how males and females differ 
in mating behavior to maximize fitness. 
● Females contribute a lot of energy in mating 
(maximize fitness with focus on high quality 
mates and offspring), while males contribute 
little energy (maximize fitness with focus on 
quantity of offspring).  
● Female choice increases attractive traits in 
males. 
● Male competition rewards strongest males 
with more mating opportunities. 
● Sexual dimorphism: males and females of 
same species look different (eg. males larger 
than females).  
   
   

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