AP BIO NOTES
Unit 1
Key Concepts and Definitions
● Matter consists of atoms, the fundamental building blocks of all substances
● Elements are pure substances that cannot be broken down into simpler
substances by chemical means and are composed of only one type of atom
● Compounds are substances made up of two or more elements that are
chemically combined in a specific ratio
● Molecules are groups of atoms held together by chemical bonds and can be
composed of the same or different elements
● Ions are atoms or molecules that have gained or lost electrons, resulting in
a net positive or negative charge
● pH is a measure of the concentration of hydrogen ions in a solution, indicating
its acidity or alkalinity on a scale from 0 to 14
● Buffers are substances that help maintain a relatively stable pH in a solution
by absorbing excess hydrogen or hydroxide ions
● Metabolism refers to the sum of all chemical reactions that occur within an
organism, including both catabolic and anabolic processes
Atomic Structure and Chemical Bonds
● Atoms consist of protons, neutrons, and electrons
○ Protons have a positive charge and are located in the nucleus
○ Neutrons have no charge and are also located in the nucleus
○ Electrons have a negative charge and orbit the nucleus in shells
● The atomic number of an element is equal to the number of protons in its
nucleus, which determines its identity
● Isotopes are atoms of the same element that have different numbers of
neutrons, resulting in different atomic masses
● Chemical bonds form when atoms share or transfer electrons to achieve a
more stable electronic configuration
● Covalent bonds involve the sharing of electrons between atoms, resulting in
the formation of molecules
○ Single, double, and triple covalent bonds involve the sharing of one,
two, or three pairs of electrons, respectively
● Ionic bonds involve the transfer of electrons from one atom to another,
resulting in the formation of positively and negatively charged ions that attract
each other
● Hydrogen bonds are weak electrostatic attractions between a hydrogen atom
bonded to a highly electronegative atom and another electronegative atom,
such as oxygen or nitrogen
Water and Its Properties
● Water is a polar molecule due to the uneven distribution of electrons between
the oxygen and hydrogen atoms, resulting in a slightly positive charge on
the hydrogen atoms and a slightly negative charge on the oxygen atom
● Hydrogen bonding between water molecules gives rise to many of water's
unique properties, such as high surface tension, cohesion, and adhesion
● Water has a high specific heat capacity, meaning it can absorb or release a
large amount of heat energy without significantly changing its temperature,
which helps regulate the temperature of living organisms
● Water's high heat of vaporization allows it to absorb a large amount of heat
energy during evaporation, which helps cool surfaces and regulate body
temperature through sweating
● As a universal solvent, water can dissolve a wide variety of polar and ionic
substances, facilitating chemical reactions and the transport of nutrients and
waste products in living organisms
● The density of water is highest at 4°C, which allows ice to float on the surface
of bodies of water, insulating the liquid water below and enabling aquatic life
to survive in cold environments
Carbon and Organic Molecules
● Carbon is the basis for all organic molecules due to its ability to form four
stable covalent bonds and create a wide variety of complex structures
● Hydrocarbons are organic molecules composed entirely of carbon and
hydrogen atoms, such as methane (CH4) and benzene (C6H6)
● Functional groups are specific arrangements of atoms within organic
molecules that give them distinct chemical properties
○ Examples of functional groups include hydroxyl (-OH), carboxyl
(-COOH), amino (-NH2), and phosphate (-PO4)
● Isomers are compounds that have the same molecular formula but different
structural arrangements, resulting in different properties
○ Structural isomers have the same atoms arranged in different bonding
patterns (butane and isobutane)
○ Stereoisomers have the same bonding patterns but different spatial
arrangements (cis and trans isomers)
● Polymers are large molecules composed of repeating subunits called
monomers, which are covalently bonded together
○ Examples of natural polymers include cellulose, starch, and proteins
○ Synthetic polymers include plastics like polyethylene and nylon
Macromolecules: Structure and Function
Carbohydrates
Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen
atoms, typically in a 1:2:1 ratio
○ Monosaccharides are simple sugars that serve as the building blocks
of more complex carbohydrates (glucose, fructose)
○ Disaccharides are formed when two monosaccharides are joined
together by a glycosidic bond (sucrose, lactose)
○ Polysaccharides are long chains of monosaccharides that serve as
energy storage or structural components (starch, cellulose)
Lipids
Lipids are a diverse group of hydrophobic organic molecules that include fats, oils,
waxes, and steroids
○ Triglycerides are the main form of energy storage in animals and
consist of three fatty acid molecules bonded to a glycerol molecule
○ Phospholipids are the primary components of cell membranes and
have a hydrophilic head and two hydrophobic tails
Proteins
Proteins are large, complex molecules composed of amino acids linked together by
peptide bonds
○ The sequence of amino acids in a protein determines its unique
three-dimensional structure and function
○ Enzymes are specialized proteins that catalyze biochemical reactions
by lowering the activation energy
Nucleic acids
Nucleic acids are organic molecules that store and transmit genetic information in
living organisms
○ DNA (deoxyribonucleic acid) is a double-stranded molecule that carries
the genetic instructions for an organism's development and function
○ RNA (ribonucleic acid) is a single-stranded molecule that plays various
roles in gene expression, including serving as a template for protein
synthesis
Enzymes and Biochemical Reactions
● Enzymes are biological catalysts that speed up chemical reactions in living
organisms without being consumed in the process
● The active site of an enzyme is a specific region where the substrate binds
and the reaction takes place
○ The shape and chemical properties of the active site determine the
enzyme's specificity for its substrate
● Enzymes lower the activation energy of a reaction by stabilizing the transition
state, allowing the reaction to proceed more quickly
● Factors that affect enzyme activity include temperature, pH, substrate
concentration, and the presence of inhibitors or activators
○ Enzymes typically have an optimal temperature and pH range at which
they function most efficiently
● Competitive inhibitors are molecules that bind to the active site of an enzyme,
preventing the substrate from binding and slowing down the reaction
● Non-competitive inhibitors bind to a site other than the active site, causing a
conformational change that reduces the enzyme's activity
● Allosteric regulation involves the binding of a molecule at a site other than the
active site, which can either enhance (allosteric activator) or inhibit (allosteric
inhibitor) the enzyme's activity
Energy in Living Systems
● Energy is the capacity to do work or cause change and is required for all life
processes
● The first law of thermodynamics states that energy cannot be created or
destroyed, only converted from one form to another
● The second law of thermodynamics states that every energy transfer or
transformation increases the entropy (disorder) of the universe
● Adenosine triphosphate (ATP) is the primary energy currency in living
organisms, used to power cellular processes such as metabolism, transport,
and movement
○ ATP consists of an adenosine molecule bonded to three phosphate
groups, with high-energy bonds between the phosphates
○ The hydrolysis of ATP to ADP (adenosine diphosphate) and inorganic
phosphate releases energy that can be used to drive cellular processes
● Photosynthesis is the process by which plants and other autotrophs convert
light energy into chemical energy stored in glucose
○ The light-dependent reactions occur in the thylakoid membranes of
chloroplasts and involve the absorption of light energy by chlorophyll to
generate ATP and NADPH
○ The light-independent reactions (Calvin cycle) occur in the stroma of
chloroplasts and use the ATP and NADPH from the light-dependent
reactions to fix carbon dioxide into glucose
● Cellular respiration is the process by which cells break down glucose to
release energy in the form of ATP
○ Glycolysis occurs in the cytoplasm and involves the breakdown of
glucose into two pyruvate molecules, generating a small amount of
ATP and NADH
○ The Krebs cycle (citric acid cycle) occurs in the mitochondrial matrix
and involves the oxidation of acetyl-CoA derived from pyruvate,
generating CO2, ATP, NADH, and FADH2
○ Oxidative phosphorylation occurs in the inner mitochondrial membrane
and involves the transfer of electrons from NADH and FADH2 through
the electron transport chain, creating a proton gradient that powers
ATP synthase to generate a large amount of ATP
Practical Applications and Lab Techniques
● Spectrophotometry is a technique used to measure the absorption of light by
a sample at different wavelengths, which can be used to determine the
concentration of a substance or monitor the progress of a reaction
● Chromatography is a method used to separate mixtures of compounds based
on their differential affinities for a stationary phase and a mobile phase
○ Paper chromatography and thin-layer chromatography (TLC) are
simple techniques that can be used to separate and identify pigments
or amino acids
○ Column chromatography and high-performance liquid chromatography
(HPLC) are more advanced techniques used for purifying proteins or
analyzing complex mixtures
● Electrophoresis is a technique used to separate charged molecules (such as
proteins or nucleic acids) based on their size and charge when subjected to
an electric field
○ Gel electrophoresis uses a porous gel matrix (such as agarose or
polyacrylamide) to separate molecules as they migrate through the gel
○ SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel
electrophoresis) is a common method for separating proteins based on
their molecular weight
● Enzyme assays are used to measure the activity of an enzyme by monitoring
the rate at which it catalyzes a specific reaction
○ Colorimetric assays involve the use of a substrate that changes color
when acted upon by the enzyme, allowing the reaction rate to be
measured using a spectrophotometer
○ Coupled assays involve linking the enzyme-catalyzed reaction to a
second reaction that produces a measurable product, such as NADH
or ATP
● Recombinant DNA technology involves the manipulation of DNA molecules to
create new genetic combinations or express foreign genes in host organisms
○ Restriction enzymes are used to cut DNA at specific sequences,
allowing DNA fragments to be isolated and combined with other DNA
molecules
○ Plasmids are small, circular DNA molecules that can be used as
vectors to introduce foreign DNA into bacterial cells for cloning or
expression purposes
Common Misconceptions and FAQs
● Misconception: Atoms are the smallest particles of matter.
○ Reality: Atoms are composed of even smaller subatomic particles,
such as protons, neutrons, and electrons. Quarks and leptons are
considered the smallest known particles.
● Misconception: All bonds involve the sharing of electrons.
○ Reality: While covalent bonds involve the sharing of electrons, ionic
bonds involve the transfer of electrons from one atom to another,
resulting in the formation of ions.
● Misconception: Water is a universal solvent because it can dissolve anything.
○ Reality: While water is an excellent solvent for many substances, it
cannot dissolve non-polar molecules like oils and fats. The term
"universal solvent" refers to its ability to dissolve more substances than
any other liquid.
● Misconception: All organic molecules contain carbon and hydrogen.
○ Reality: While most organic molecules contain carbon and hydrogen,
some (like carbon dioxide and carbon monoxide) do not contain
hydrogen. The defining characteristic of organic molecules is the
presence of carbon.
● Misconception: Enzymes are living organisms.
○ Reality: Enzymes are not living organisms; they are proteins that
catalyze chemical reactions. They are produced by living cells but are
not alive themselves.
● Misconception: Energy is lost during chemical reactions in living systems.
○ Reality: Energy is not lost but rather converted from one form to
another, in accordance with the first law of thermodynamics. However,
some energy is released as heat during these conversions, which
cannot be used to perform work (second law of thermodynamics).
● FAQ: What is the difference between an atom and a molecule?
○ An atom is the smallest unit of an element that retains its chemical
properties, while a molecule is a group of atoms held together by
chemical bonds. Molecules can be composed of the same or different
elements.
● FAQ: How do enzymes speed up chemical reactions?
○ Enzymes lower the activation energy of a reaction by providing an
alternative pathway for the reaction to occur. They do this by binding to
the substrate(s) and stabilizing the transition state, making it easier for
the reaction to proceed.
UNIT 1 - BIOCHEMISTRY
Overview of Chemistry
● Ionic vs. covalent bonds
Ionic bonds = an atom donates electrons to another atom, creating
a bond
Covalent bonds = two atoms share electrons
● Bond polarity, molecular polarity, and electronegativity
EX: Water is very polar. Oxygen is a very electronegative element,
hogging electrons to itself
● Hydrogen bonds
EX: Water molecules form many hydrogen bonds with each other.
This is a cool simulation that shows how hydrogen bonds form. You
can actually move around the molecules
Hydrogen bonds will come up again and again throughout biology;
keep an eye out for it!
Properties of Water
● Emergent properties of water (which are all due to its ability to
hydrogen bond):
1.Cohesion, adhesion, surface tension
2.Keeps temperatures moderate through evaporative
cooling and a high specific heat
3.Ice floats on top of liquid water
4.Acts as a universal solvent
● Acids = increase the concentration of H+ ions in solution
EX: Ocean acidification. Carbon dioxide dissolves into
the ocean, creating carbonic acid
● Bases = decrease the concentration of H+ ions in solution
● Buffers = a substance that limits any significant changes
in H+ concentration. We have natural buffers inside our
bodies.
EX: carbonic acid in our blood, which regulates our blood
pH
Versatility of Carbon
● Organic compounds = compounds that contain carbon
● Organic chemistry is the study of how organic compounds
interact
● Shapes and types of organic molecules:
○ Carbons are usually the central atom in organic
molecules. They can form single, double, or triple bonds
with other atoms
○ Hydrocarbons = organic molecules that contain only
carbon and hydrogen
○ Organic molecules can be branched, straight chains
(such as hydrocarbons), or rings
○ Functional groups: be familiar with their general
structure and special properties. The key groups to
know are hydroxyl, carbonyl, carboxyl, amino,
sulfhydryl, phosphate, and methyl. You will see these
groups come up throughout the course
EX: The crucial molecule ATP (adenosine
triphosphate) has 3 phosphate groups. ATP is what our
cells use for energy
*Use this cheatsheet to study the functional group
chemical structures and properties
Diamonds are made of pure carbon and they are known as the hardest
substance on Earth becuse of the special crystal structure (called diamond
cubic) holding the carbon atoms together
Rice is full of starch. If you keep cooked rice in your mouth for a couple of
minutes, it will actually start tasting very sweet because enzymes in your
mouth are breaking down the starch into glucose molecules
Macromolecules
● Macromolecules synthesis and breakdown
○ Dehydration and hydrolysis reactions -- dehydration
synthesizes polymers, while hydrolysis breaks them
down
● Know the general structure and functions of each of the four
macromolecules listed below
● Types of macromolecules:
*Here is a study guide with the key points to know for each of
the macromolecules
● Carbohydrates
○ Glycosidic linkages = covalent bonds linking
monosaccharides together in a polysaccharide
○ Main polysaccharides to know (including the function of
each): starch, glycogen, cellulose, chitin,
peptidoglycan. Also know that glycogen and starch are
branched, while cellulose is linear in structure
○ Disaccharides to know: sucrose, maltose, lactose
○ Monosaccharides to know: glucose, fructose,
galactose
● Proteins (more details below)
● Nucleic acids (DNA, RNA)
○ DNA has the sugar deoxyribose, the nitrogenous
bases A, T, C, and G, and a sugar-phosphate backbone.
It is typically a double-stranded helix
○ RNA has the sugar riboseand the nitrogenous bases A,
U, C, and G. It also has a sugar-phosphate backbone
and is usually single-stranded
○ DNA and RNA store hereditary information that can be
passed on to offspring
● Lipids
○ Triacylglycerol = important source of energy in animals.
Made of 1 glycerol and 3 fatty acid chains
○ Phospholipids = the building block of the cell
membrane lipid bilayer. The phosphate head is
hydrophilic, while the two fatty acid tails are
hydrophobic
○ Steroids = the structure consists of 4 fused carbon
rings. Examples include cholesterol and steroid
hormones, such as estrogen
○ Cholesterol = a type of steroid that is found in the cell
membrane; important for maintaining membrane fluidity
● More about proteins:
○ Amino acids = the building blocks of proteins. There
are 20 unique amino acids, and each has a unique side
chain (also known as an R group) which gives a unique
set of chemical properties
○ Proteins are extremely diverse and have a wide range of
structures and functions. The key functions include:
enzymes (biological catalysts that speed up reactions),
structural support, transport (like ion channels),
hormones, receptors, motor proteins, and defensive
proteins such as antibodies from the immune system
○ Four Stages of protein structure:
1.Primary structure = the sequence of amino acids in the
peptide chain. The primary structure indirectly
determines the ultimate 3D structure of a protein
2.Secondary structure = hydrogen bonds form between
the peptide chain backbone, creating either alpha
pleated sheets or a beta-helix
3.Tertiary structure = chemical interactions between side
chains create more of the 3D structure. Can include
disulfide bridges, hydrogen bonding, and Van der
Waals interactions. All of these occur between the side
chains of amino acids. Tertiary structure directly
determines the 3D structure of a protein
4.Quarternary structure = present in some, but not all
proteins. This is when multiple peptide chains join
together to form a whole protein. Hemoglobin is an
example of a protein with a quaternary structure
Subcellular and Organelle Components
Subcellular and organelle components are especially important to know because they pop
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up throughout the year. All organelles are essential, and students must understand all of
them. However, the most critical organelles are:
👨👩👧👦
Ribosomes: composed of ribosomal RNA and protein. They help to synthesize proteins. All
forms of life have ribosomes, which demonstrates common ancestry .
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Endoplasmic Reticulum (ER): provides mechanical support and plays a role in intracellular
transport. There are two kinds of ER, rough and smooth.
Rough ER: helps to compartmentalize the cell and helps to carry out protein synthesis in the
ribosomes.
Smooth ER: helps in detoxification and lipid production, maintaining cellular homeostasis.
Golgi Complex: a membrane-bound organelle that is composed of several flattened
membrane sacs called cisternae. The Golgi is vital in the final stages of preparing a protein.
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A newly made protein will get help in correctly folding and modifying as needed. The Golgi
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also helps in packaging proteins and sorting them before transport.
Mitochondria: helps with ATP production. It has a small set of its own DNA and is a
double membrane organelle. The outer membrane is a smooth phospholipid bilayer. The
inner membrane is highly convoluted, meaning it is highly folded, which increases the
surface area for a growing number of electron transport chains. The increase in surface area
facilitates the production of ATP.
The mitochondria is the site where cellular respiration occurs. Glycolysis is the first step in
cell respiration and occurs with or without oxygen present and shows common ancestry.
After the completion of glycolysis, the rest of cellular respiration occurs in the mitochondria,
given that oxygen is present. The Citric Acid/Kreb’s Cycle happens in the matrix of the
💨
mitochondria, and oxidative phosphorylation, with the help of the electron transport chain,
occurs in the inner membrane.
Image from Micromagnet
Lysosomes: membrane-enclosed sacs that contain hydrolytic enzymes. These enzymes are
🚮☠️
digestive enzymes that help to break down excess or worn-out cell parts. The lysosomes
also help with programmed cell death, known as apoptosis.
Vacuole: a membrane-bound sac that has many different roles, including storage and
release of macromolecules and waste . Plants have a specialized large central vacuole that
also serves many functions. The primary function of the large central vacuole is water
🌱
retention. Water retention is important in turgor pressure, which helps to maintain the rigidity
and function of plant cells.
⚡️
Chloroplasts: photosynthetic algae and plants contain these specialized organelles that can
photosynthesize (capture, store, and use solar energy ) and make simple sugars.
Chloroplasts have a double membrane and thylakoids that are flattened sacs with a
phospholipid bilayer.
☀️
Chloroplasts are the site where photosynthesis occurs. The two stages of photosynthesis
are the light-dependent reaction and the light-independent reaction. The light-dependent
reaction occurs in the grana and produces the ATP and NADPH necessary for the
🌓
light-independent reaction. The light-independent reaction is where the Calvin-Benson cycle
takes place and carbon is fixed to make simple sugars.
Image from biologydictionary.
Cell Size
Cell size is a concern because surface area-to-volume ratios affect the ability of a biological
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system to obtain necessary resources, eliminate wastes, pull in or remove heat energy, and
exchange materials with the environment.
Plasma Membrane
The plasma membrane is made of a phospholipid bilayer, composed of two layers of
phospholipid molecules, with the hydrophobic tails facing inward and the hydrophilic heads
facing outward. The arrangement of the phospholipids in the bilayer creates a
semi-permeable barrier that selectively allows certain molecules to pass through while
preventing others from entering or leaving the cell.
The plasma membrane is not a static structure and is constantly undergoing changes in
response to various signals and stimuli. Many proteins are embedded in the membrane, and
these proteins play a number of important roles in the cell. Some proteins are involved in cell
recognition, helping the cell to communicate and interact with other cells. Others act as
channels or pumps, allowing specific molecules to pass through the membrane. Others help
to maintain the structural integrity of the membrane, providing rigidity and support.
The movement of molecules across the plasma membrane is regulated by the hydrophobic
and hydrophilic properties of the phospholipids. Small, nonpolar molecules like nitrogen,
oxygen, and carbon dioxide can freely pass through the membrane, while larger, polar
molecules and ions need the help of proteins to cross the membrane. Water is a small, polar
molecule that can move across the membrane in small quantities, but it needs the help of
aquaporins and other proteins to cross the membrane in larger amounts.
Image from Biology Dictionary.
Membrane Transport
In order for a cell to function properly, it's important for the internal environment to be
maintained in a way that is conducive to the life and function of the cell. To do this, materials
must be able to move in and out of the cell as needed, and this movement is facilitated by
the plasma membrane. The movement of molecules across the plasma membrane occurs
through a process called membrane transport.
Depending on the type of molecule being transported, the cell may need the help of a
transport protein to facilitate its movement across the membrane. Transport proteins are
specialized proteins that are embedded in the plasma membrane and are responsible for the
movement of specific molecules across the membrane. There are different types of transport
proteins, including channels, pumps, and carriers, which work to transport molecules in
different ways. There are several different types of membrane transport:
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Passive Transport means that the molecules are moving from an area of high concentration
to an area of low concentration. Energy is not required in passive transport.
Active Transport means that the molecules are moving from an area of low concentration to
an area of high concentration and will require energy use.
Endocytosis is the process of taking bulk material into the cell.
Exocytosis is the process of removing bulk material out of the cell.
Image from Wikibooks
Tonicity and Osmoregulation
Water moves by osmosis from high water potential (low osmolarity, low solute
concentrations) to low water potential (high osmolarity, high solute concentrations.)
Osmoregulation maintains water balance and allows organisms to control the internal
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environment. Remember, the movement of water in osmosis will always occur in a way that
brings the concentration of solute to equilibrium! More on this below.
Image from wikipedia.
Image from LibreTexts/02%3A_Cell_Biology/2.01%3A_Osmosis).
Image from apcentral.
Water potential is the tendency for water to move in one direction or another. In this case,
osmoregulation allows cells to maintain their internal solute balance. These two equations
are used to find the solute concentration inside a cell and the tendency that water will leave
the cell. As evolution has occurred, cells have changed and have been altered. One thing
that helps cells to be able to take care of different processes inside the cell is the membrane
and organelles that have membranes as well. The endosymbiotic theory is where organelles
that were once free-living prokaryotic cells became engulfed and serve a purpose now inside
the cell. The endosymbiotic theory is summarized below. (Click on the image to see a larger
version)