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Topic 1.1 – Structure of Water and Hydrogen Bonding
 The subcomponents of biological molecules determine the properties of that molecule
o Water is composed of 2 main elements, oxygen and hydrogen, in a 1:2 ratio
respectively
o Covalent bonding is the term used to describe the bond type in which atoms
share electrons
o Oxygen is more electronegative compared to hydrogen, resulting in an unequal
sharing of electrons between oxygen and hydrogen
o Covalent bonding can result in polarity when there are differences in atomic
electronegativities, a water molecule has polarity
o A hydrogen bond is a weak bond interaction between the negative and positive
regions of two separate molecules
o Water can form hydrogen bonds with other water molecules or with other
charged molecules
o When you have two of the SAME molecules form hydrogen bonds with each
other this is called cohesion (Ex. Water and water)
o When two DIFFERENT molecules form hydrogen bonds with each other this is
called adhesion (Ex. water and amino acid)
 Living systems depend upon properties of water
o The hydrogen bonds between water molecules can result in surface tension
o Cohesion, adhesion, and surface tension allow for water to demonstrate
additional chemical behaviors known as emergent properties
o Life depends on properties of water
 Example: surface tension is a result of increased hydrogen bonding forces
between water molecules at the surface.
 Example 2: Water’s adhesive property gives water a high solvency ability
in its liquid state
 Example 3: Water’s cohesive property allows for unique hydrogen bond
interactions to occur when water is in a solid state, making ice (solid
water) less dense than liquid water.
 Aquatic organisms can still live in surface frozen aquatic
environments
 Example 4: Water’s cohesive property allows it to absorb a lot of thermal
energy before changing chemical states, resisting sudden changes in
temperature
 Example 5: Capillary action is a result of both the adhesive and cohesive
properties of water
 Key Takeaways
o (1) Water contains 1 oxygen atom covalently bonded to 2 hydrogen atoms
o (2) Oxygen has a higher electronegativity compared to hydrogen resulting in a
water molecule having polarity
o (3) Polarity allows molecules to form hydrogen bonds when oppositely charged
regions of two molecules interact
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o (4) The term cohesion refers to molecules of the same type forming hydrogen
bonds with one another, and adhesion refers to different types of molecules
forming hydrogen bonds with one another
o (5) Living systems depend upon water’s properties, like surface tension
Topic 1.2 – Elements of Life
 Living systems require a constant input of energy
o The law of the conservation of energy states that energy cannot be created or
destroyed only transformed
o Living systems follow the laws of energy
o Living systems need a constant input of energy to grow, reproduce, and maintain
organization
o Living systems mainly use the energy stored in chemical bonds
 Living systems require an exchange of matter
o Atoms and molecules from the environment are necessary to build new
molecules
o Carbon is used to build biological molecules such as carbohydrates, proteins,
nucleic acids and lipids
o Nitrogen is used to build proteins and nucleic acids
o Phosphorous is used to build nucleic acids and certain lipids
 Carbon is used to build macromolecules
o Carbon can bond to other carbon atoms creating carbon skeletons to which
other atoms attach
o Carbon skeletons allow for the creation of very large and complex molecules
o Carbon containing molecules can be used to store energy
o Carbon containing molecules can be used to form basic cell structures
 Key Takeaways
o (1) Living systems need a constant input of energy to grow, reproduce, and
maintain organization
o (2) Atoms and molecules from the environment are necessary to build new
molecules
o (3) Carbon is used to build all macromolecules, store energy and form cells
o (4) Nitrogen is used to build proteins and nucleic acids
o (5) Phosphorous is used to build nucleic acids and certain lipids
Topic 1.3 – Introduction to Biological Macromolecules
 Monomers have important properties
o Monomers are chemical subunits used to create polymers
o Polymers are macromolecules made of many monomers
o A covalent bond is formed between two interacting monomers
o Monomers have specific chemical properties that allow them to interact with
one another
o Polymers are specific to the monomers they consist of
 (Monomer: Polymer)
 (Monosaccharide: Polysaccharide)
 (Amino Acid: Protein)
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 (Nucleotide: Nucleic Acid)
 (Fatty Acid*: Lipids)
 *Lipids don’t have true monomers
Dehydration synthesis reactions form covalent bonds
o Dehydration synthesis reactions are used to create macromolecules
o The subcomponents of a water molecule (H and OH) are removed from
interacting monomers and a covalent bond forms between them
o The H and OH join together to form a molecule of water, water is a byproduct of
this reaction
Hydrolysis
o Polymers are hydrolyzed (broken down) into monomers during a hydrolysis
reaction
o Covalent bonds between the monomers are cleaved (broken) during a hydrolysis
reaction
o A water molecule is hydrolyzed into subcomponents (H and OH) and each
subcomponent is added to a different monomer
Example: A dehydration synthesis creates carbohydrates
o Carbohydrate monomers have hydroxides (OH) and hydrogen atoms (H)
attached
o One monomer will lose an entire hydroxide while the other monomer will only
lose the hydrogen from a hydroxide
o A covalent bond will form where the hydroxide and hydrogen atom were
removed
o The hydroxide (OH) and hydrogen (H) join forming a water molecule (H2O)
Example 2: A dehydration synthesis creates proteins
o Protein monomers are called amino acids
o Each amino acid has an amino group (NH2) terminus and a carboxyl group
(COOH) terminus
o A hydroxide (OH) is lost from the carboxyl group of one amino acid and a
hydrogen atom (H) is lost from the amino group of another amino acid
o A covalent bond will form between the monomers in the location where the
hydroxide and hydrogen atom were removed
o The hydroxide (OH) and hydrogen atom (H) will join forming a water molecule
(H2O)
Example 3: Proteins can undergo hydrolysis reactions
o Covalent bonds between amino acid can be cleaved (broken)
o A water molecule is hydrolyzed and each subcomponent of water (H and OH) will
be bonded to different amino acids
o The result is separate amino acid monomers
Key Takeaways
o (1) All monomers contain carbon and are used to build biological
macromolecules
o (2) Covalent bonds are used to connect monomers together
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o (3) Dehydration synthesis reactions are used to create biological macromolecules
and water is an additional product
o (4) Hydrolysis reactions use water to break down biological macromolecules
Topic 1.4 – Properties of Biological Macromolecules
 Function is related to structure
o Living systems are organized in a hierarchy of structural levels
o At every level of organization function is related to structure
o A change in structure generally results in a change in function
o In living systems the properties of biological molecules are determined by the
structure and function of the molecules
 The structure of nucleic acids determine function
o Nucleic acids are polymers comprised of monomers called nucleotides
o Nucleotides have a basic structure that contains 3 main subcomponents: a 5carbon sugar, a phosphate group, and a nitrogenous base
o All nucleic acids store biological information in the sequence of nucleotide
monomers
 There are differences in nucleic acid structure
o DNA and RNA are examples of nucleic acids
o DNA and RNA nucleotides differ in the type of sugar contained (deoxyribose vs.
ribose)
o DNA and RNA nucleotides can differ in the nitrogen base contained
o Although both DNA and RNA store biological information, the structural
differences between them result in specific functional differences
 Proteins have different structures and proteins
o Amino acids are the monomers that make up proteins
o Amino acids have directionality with an amino (NH2) terminus and a carboxyl
(COOH) terminus
o A polypeptide, the primary structure of a protein, consists of a specific order of
amino acids and determines the overall shape the protein can achieve
 The chemical properties of R groups vary
o Amino acids differ in the R group, the atom(s) attached to the central carbon
o The R group can be hydrophobic, hydrophilic, or ionic
o A protein can have different amino acids in the polypeptide allowing the protein
to have regional differences in structure and function
 Carbohydrates and lipids vary in structure and function
o Complex carbohydrates can have monomers whose structures determine the
properties and functions of the carbohydrate
o Lipids are nonpolar macromolecules that do not have true monomers but are
comprised of subunits such as fatty acids and glycerol
o Lipids have fatty acid components that determine structure and function based
on saturation
o Specialized lipids, called phospholipids, contain hydrophilic and hydrophobic
regions that determine their interactions with other molecules
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Example: Membranes contain lipids and proteins
o Phospholipids and proteins are two main molecules that make up biological
membranes
o Phospholipids and some membrane proteins have hydrophobic and hydrophilic
regions
o The hydrophilic regions of phospholipids and proteins can interact with each
other and the water environments
o The hydrophobic regions of phospholipids and membrane proteins can interact
with each other but cannot interact with water environments
 Key Takeaways
o (1) Nucleotides can vary in the sugar and base components resulting in nucleic
acids with different structure and function
o (2) The amino terminus and carboxyl terminus give amino acids directionality
and determine how amino acids assemble into protein polymers
o (3) R group properties determine how amino acids interact within the
polypeptide and determine the structure and function of the protein
o (4) Differences in the components of carbohydrate monomers determine how
the monomers assemble into complex carbohydrates and determine function
o (5) Lipids are nonpolar macromolecules and differences in saturation determine
the structure and function of lipids
o (6) Phospholipids contain polar region that interact with other polar molecules
and nonpolar regions.
Topic 1.5 – Structure and Function of Biological Macromolecules
 Directionality of the subcomponents influences structure of nucleic acid polymers
o The linear sequence of all nucleic acids is characterized by 3’ hydroxyl and 5’
phosphate of the sugar in the nucleotide
o DNA is a nucleic acid polymer containing two strands, each strand in an
antiparallel 5’-3’ direction
o Adenine-Thymine base pairs are held together by 2 hydrogen bonds and
Guanine-Cytosine base pairs are held together by 3 hydrogen bonds
o Hydrogen bonds between base pairs in a DNA molecule stabilize the molecule’s
structure
o The linear sequence of nucleotides encodes biological information
o Any change to the sequence of the nucleotides may lead to a change in the
encoded information
o During the synthesis of nucleic acid polymers, nucleotides can only be added to
the 3’ end
o Covalent bonds are used to connect free nucleotides to the strand
 Key Takeaways
o (1) The linear sequences of all nucleic acids is defined by the 3’ hydroxyl and 5’
phosphate of the sugar in the nucleotide
o (2) DNA is structured as an antiparallel double helix with two strands running in
opposite 5’-3’ directions. This allows for the two strands of DNA to be held
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together by hydrogen bonds between the base pairs. A-T held together by 2
hydrogen bonds; G-C held together by 3 hydrogen bonds
o (3) During DNA and RNA synthesis, nucleotides can only be covalently added to
the 3’ end of a growing nucleotide strands
o (4) Changes in the linear sequences of the nucleotide bases may lead to
differences in the encoded biological information or the structural stability of the
molecule
Directionality of the subcomponents influences structure of proteins
o Proteins comprise linear chains of amino acids that have directionality with an
amino terminus and a carboxyl terminus
Four Elements of Protein Structure
o Primary structure is determined by the sequence of amino acids held together by
covalent bonds, called peptide bonds.
o Secondary structure arises through local folding of the amino acid chain into
elements such as alpha-helices and beta-sheets
o Tertiary structure is the overall 3D shape of the protein and often minimizes free
energy; Various types of bonds and interactions stabilize the protein at this level
o Quaternary structure arises from the interactions between multiple polypeptide
units
 Ex. Hemoglobin
Key Takeaways
o (1) Amino acids have directionality with an amino terminus (NH2) and a carboxyl
terminus (COOH) on the other. Amino acids are added to the carboxyl terminus
of a growing peptide chain by the formation of covalent bonds
o (2) There are 4 elements of protein structure; primary, secondary (alpha helices
& beta sheets), tertiary, and quaternary. Levels of structure beyond the primary
linear sequence of amino acids arise through local folding and other chemical
interactions among amino acids. The resulting 3D shape gives rise to the
protein’s specific function.
o (3) A change in an amino acid subunit at the primary level of structure may lead
to a change in the structure and function of the protein at subsequent levels.
Directionality of the subcomponents influences structure and function of carbohydrates
o Carbohydrates comprise linear chains of sugar monomers connected by covalent
bonds
o Small direction change in the components of a molecule can result in functional
differences
 Ex. Starch vs. Cellulose
o Carbohydrate polymers may be linear or branched
o Starch and glycogen both function in energy storage (starch in plants and
glycogen in humans and other vertebrates)
o Cellulose functions as support and provides strength in plant cell walls
Key Takeaways
o (1) Carbohydrates comprise linear chains of sugar monomers connected by
covalent bonds. Sugar monomers may vary in the direction of some of their
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components, such as the bond orientation of -OH groups linked to the carbon
chain.
o (2) Depending on the type of sugar monomer used in its formation, a
carbohydrate polymer may have a linear or branched structure and can differ in
function
Topic 1.6 – Nucleic Acids
 Similarities between DNA and RNA
o Both are assembled from nucleotide subunits which are comprised of a
 5-carbon sugar
 Phosphate group
 Nitrogenous base
o Each nucleotide monomer is connected by covalent bonds forming the sugarphosphate backbone
o Each linear strand of nucleotides has a 5’ end and a 3’ end
o The nitrogenous bases are perpendicular to the sugar-phosphate backbone
 Differences between DNA and RNA
o DNA contains deoxyribose and RNA contains ribose
o DNA contains thymine and RNA contains uracil
o DNA is usually double stranded; RNA is usually single-stranded
o The two DNA strands in double-stranded DNA are antiparallel
 Key Takeaways
o (1) Both DNA and RNA are formed from nucleotide subunits connected by
covalent bonds to form linear molecule with 5’ and 3’ ends. Each nucleotide is
comprised of a sugar phosphate group and nitrogenous base.
o (2) Differences include the type of sugar, one of the nitrogenous bases (RNA
contains uracil whereas DNA contains thymine), and number of strands. DNA has
two nucleotide strands that are antiparallel.
Topic 2.1 – Cell Structure: Subcellular Components
 Subcellular components universal to all cells
o All living cells contain a genome and ribosomes, reflecting the common ancestry
of all known life
o Ribosomes synthesize protein according to mRNA sequence and the instructions
that are encoded in that mRNA sequence originate from the genome of the cell.
 Structure and Function: Ribosomes
o Ribosomes consist of two subunits that are NOT membrane-enclosed
o Ribosomes are made up of ribosomal RNA (rRNA) and proteins
o Ribosomes synthesize protein according to mRNA sequences
 Structure and Function: Endoplasmic Reticulum (ER)
o The endoplasmic reticulum is a network of membrane tubes within the
cytoplasm of eukaryotic cells
o Rough ER
 Has ribosomes attached to its membrane
 Compartmentalizes the cell
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Rough ER is associated with packaging the newly synthesized
protein made by attached ribosomes for possible export from the
cell
o Smooth ER
 Does NOT have ribosomes attached
 Functions include detoxification and lipid synthesis
o Structural differences between rough ER and smooth ER leads to functional
differences
 Structure and Function: Golgi Complex
o Series of flattened membrane-bound sacs found in eukaryotic cells
o Involved in the correct folding and chemical modification of newly synthesized
proteins and packaging for protein trafficking
 Structure and Function: Mitochondria
o Has a double membrane
o Outer membrane is smooth and inner membrane is highly convoluted, forming
folds called cristae
o Functions in production of ATP energy that eukaryotic cells can use for cell work
 Structure and Function: Lysosomes
o Membrane-enclosed sacs found in some eukaryotic cells that contain hydrolytic
enzymes
o Hydrolytic enzymes can be used to digest a variety of materials such as damaged
cell parts or macromolecules
 Structure and Function: Vacuoles
o Membrane-bound sacs found in eukaryotic cells
o Play variety of roles ranging from storage of water and other macromolecules to
the release of waste from a cell
 Structure and Function: Chloroplasts
o Found in eukaryotic cells such as photosynthetic algae and plants
o Double outer membrane
o Specialized for capturing energy from the sun and producing sugar for the
organism
 Key Takeaways
o (1) Ribosomes are not enclosed by a membrane and are subcellular components
found in ALL forms of life, reflecting the common ancestry of all known life.
Ribosomes function to synthesize proteins for cells.
o (2) Eukaryotic cells have additional membrane-enclosed organelles that perform
specialized functions for the cell. These include the rough ER, smooth ER, Golgi
complex, mitochondria, lysosomes, vacuoles, and chloroplasts.
Topic 2.2 – Cell Structure and Function
 Structure and Function: Chloroplasts
o Specialized for photosynthesis and capturing energy from the sun to produce
sugar
o Within chloroplasts are distinct compartments
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Thylakoid
 Highly folded membrane compartments that are organized in
stacks called grana
 Membranes contain chlorophyll pigments that comprise the
photosystems and electron transport proteins can be found
between the photosystems, embedded in the thylakoid
membrane
 Light-dependent reactions occur here
 Folding of these internal membranes increases the efficiency of
these reaction
 Stroma
 Fluid between the inner chloroplast membrane and outside
thylakoids
 The carbon fixation (Calvin-Benson cycle) reactions occur here
Structure and Function: Mitochondria
o Double membrane provides compartments for different metabolic reactions
o Mitochondria capture energy from macromolecules
o The Krebs cycle (Citric acid cycle) reactions occur in the matrix of the
mitochondria
o Electron transport and ATP synthesis occur in the inner mitochondrial membrane
o Folding of the inner membrane increases the surface area, which allows for more
ATP to be made
Structure and Function: Vacuoles
o Vacuoles play a variety of roles, including storage and release of water,
macromolecules, and cellular waste products
o In plants, vacuoles aid in retention of water for turgor pressure
o Turgor pressure is an internal cellular force, usually caused by water pushing up
against the plasma membrane and cell wall
Structure and Function: Lysosomes
o Contain hydrolytic enzymes and can contribute to cell function in the following
ways:
 Intracellular digestion
 Recycling of organic materials
 Programmed cell death (apoptosis)
Structure and Function: Endoplasmic Reticulum (ER)
o The ER performs the following functions for the cell
 Provides mechanical support
 Plays a role in intracellular transport
 Rough ER carries out protein synthesis on ribosomes that are bound to its
membrane
Key Takeaways
o (1) Subcellular components and organelles interact to support cell function. The
ER, mitochondria, lysosomes, and vacuoles, each have specialized functions that
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occur within their membrane-enclosed structures which increases the efficiency
of the cell to perform chemical reactions and store materials
o (2) Chloroplasts and mitochondria are structural features of eukaryotic cells that
allow organism to capture, store, and use energy. The folding of the inner
membrane in both these structures increases the surface area which allows for
more ATP to be synthesized.
Topic 2.3 – Cell Size
 Cells are typically small
o Moving materials (such as nutrients and waste) in and out of cells gets more
difficult the larger a cell is
o Why? SA:V Ratio!
 Effect of SA to V Ratios on the Exchange of Materials
o The surface area of the plasma membrane must be large enough to adequately
exchange materials
o Smaller cells typically have a higher surface area-to-volume ration and more
efficient exchange of materials with the environment
o As cells increase in volume, the relative surface are decreases making it difficult
for larger cells to meet the demand for internal resources and remove waste
sufficiently
o These limitations can restrict cell size and shape
 Use of Specialized Structures and Strategies
o Membrane folding increases surface area
o Root hairs on the surface of plant roots increase the surface area of the root
allowing for increased absorption of water and nutrients
o Example: The Small Intestine
 The outer lining of the small intestine is highly folding containing fingerlike projections called villi
 The surface of each villi has additional microscopic projections called
microvilli which further increase the SA available for absorption of
nutrients
 If conditions arise that lead to the loss of this folding, these cells would
not be as efficient in absorbing nutrients for the organism
o As organisms increase in size, their SA to V ratio decreases, affecting properties
like rate of heat exchange with the environment
 Flattened shape of ear allows the elephant to dissipate more thermal
energy as blood flows closer to the surface
o Organisms have evolved highly efficient strategies to obtain nutrients and
eliminate wastes
 Cells and organisms use specialized exchange surfaces, such as stomatal
openings of leaves, to obtain molecules from and release molecules into
the surrounding environment
 When stomata are open, CO2 can enter the leaf and O2 and H2O can be
released into the atmosphere
 Key Takeaways
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o (1) As cell volume increases or a cell becomes specialized for transports across its
surface, structural modifications such as membrane folds are necessary to
adequately exchange molecules from or into the environment
o (2) As organisms increase in size, their SA to V ratio decreases making it harder
to release heat energy and adaptations may improve an organism’s efficiency in
doing so
o (3) Cells and organisms use specialized exchange surfaces (e.g., stomatal
openings on the surface of a leaf)
Topic 2.4 – Plasma Membranes
 Cells have membranes that allow them to establish an internal environment
o Cell membranes provide a boundary between the interior of the cell and the
outside environment
o Cell membranes control the transport of materials in and out of the cell
 Phospholipids have both hydrophilic and hydrophobic regions
o Phospholipids are amphipathic
 Hydrophilic phosphate head is polar
 Hydrophobic fatty acid tail is nonpolar
o Phospholipids spontaneously form a bilayer in an aqueous environment
 Tails are located inside the bilayer
 Heads are exposed to the aqueous outside and aqueous inside
environments
 Embedded proteins can be hydrophilic or hydrophobic
o Peripheral proteins
 Loosely bound to the surface of the membrane
 Hydrophilic with charged and polar side groups
o Integral proteins
 Span the membrane
 Hydrophilic with charged and polar side groups
 Hydrophobic with nonpolar side groups penetrate hydrophobic interior
of bilayer
 Example: transmembrane proteins
 Embedded proteins play various roles in maintaining the internal environment of the
cell
o Membrane protein functions
 Transport
 Cell-Cell recognition
 Enzymatic activity
 Signal transduction
 Intercellular joining
 Attachment for extracellular matrix or cytoskeleton
 The framework of the cell membranes is described as the Fluid Mosaic Model
o Structured as a mosaic of protein molecules in a fluid bilayer of phospholipids
o The structure is not static and is held together primarily by hydrophobic
interactions which are weaker than covalent bonds
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o Most lipids and some proteins can shift and flow along the surface of the
membrane or across the bilayer
 Fluid Mosaic Model components include steroids
o Cholesterol, a type of steroid, is randomly distributed and wedged between
phospholipids in the cell membrane of eukaryotic cells
o Cholesterol regulates bilayer fluidity under different environmental conditions
 Fluid Mosaic Model components include carbohydrates
o Diversity and location of the (molecules) carbohydrates and lipids enable them
to function as markers
 Glycoproteins – one or more carbohydrate attached to a membrane
protein
 Glycolipids – lipid with one or more carbohydrate attached
 Key Takeaways
o (1) Phospholipids spontaneously form a bilayer in an aqueous environment with
hydrophilic phosphate regions oriented toward the aqueous external or internal
environment and the hydrophobic fatty acid regions face each other within the
interior of the membrane
o (2) Embedded proteins can be hydrophilic, with charge and polar side groups,
and/or hydrophobic with nonpolar side groups
o (3) Embedded proteins have a variety of functions including transport, cell-to-cell
recognition, enzyme activity, signal transduction, intercellular joining, and
attachment to cytoskeleton and extracellular matrix
o (4) The Fluid Mosaic Model consists of a structural framework of phospholipid
molecules that are embedded with proteins, steroids (such as cholesterol in
eukaryotes), glycoproteins, and glycolipids that can flow around the surface of
the cell within the membrane
Topic 2.5 – Membrane Permeability
 The structure of the cell membrane
o Phospholipids are amphipathic
o Phospholipids spontaneously form a bilayer in an aqueous environment
o Fluid Mosaic Model
o Selective permeability is a direct consequence of membrane structure
 The cell membrane is selectively permeable
o Hydrophilic substances such as large polar molecules and ions can NOT freely
move across the membrane
o Hydrophilic substances move through transport proteins
 Channel proteins – A hydrophilic tunnel spanning the membrane that
allows specific target molecules to pass through
 Carrier proteins – Spans the membrane and change shape to move a
target molecule from one side of the membrane to the other
o Small polar molecules, like H2O, can pass directly through the membrane in
minimal amounts
 The cell wall is a structural boundary and permeable barrier
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o As a structural boundary:
 Protects and maintains the shape of the cell
 Prevents against cellular rupture when internal water pressure is high
 Helps plants stand up against the force of gravity
o As a permeable barrier:
 Plasmodesmata – small holes between plant cells that allows the transfer
of nutrients, waste, and ions
 Cell walls are composed of complex carbohydrates
o Plants – Cellulose
 Polysaccharide
o Fungi – Chitin
 Polysaccharide
o Prokaryotes – peptidoglycan
 Polymer consisting of sugar and amino acids
 Key Takeaways
o (1) The structure of cell membranes results in selective permeability
o (2) Cell membranes separate the internal environment of the cell from the
external environment
o (3) Selective permeability is a direct consequence of membrane structure, as
described by the fluid mosaic model
o (4) Small, nonpolar molecules, including N2, O2, and CO2, freely pass across the
membrane
o (5) Hydrophilic substances, such as large polar molecules and ions, move across
the membrane through embedded channel and transport proteins
o (6) Polar uncharged molecules, including H20 pass through the membrane in
small amounts
o (7) Cell walls provide a structural boundary, as well as a permeability barrier for
some substances to the internal environments
o (8) Cell walls of plants, prokaryotes, and fungi are composed of complex
carbohydrates
Topic 2.6 – Membrane Transport
 Selectively permeable membranes allow for the formation of concentration gradients
o Concentration gradient
 A concentration gradient is when a solute is more concentrated in one
area than another
 A membrane separates two different concentrations of molecules
 Passive transport is the net movement of molecules from high to low concentration
o Net movement of molecules from high concentration to low without metabolic
energy, such as ATP, needed
o Plays a primary role in the import of materials and the export of wastes
o Diffusion – movement of molecules from high to low concentration
 Small nonpolar molecules pass freely (N2, O2, CO2)
o Facilitated Diffusion – movement of molecules from high concentration to low
concentration through transport proteins
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 Allows for hydrophilic molecules and ions to pass through membranes
 Endocytosis requires energy to move large molecules into the cell
o In endocytosis, the cell uses energy to take in macromolecules and particulate
matter by forming new vesicles derived from the plasma membrane
 Phagocytosis – cell takes in large particles
 Pinocytosis – cell takes in extracellular fluid containing dissolved
substances
 Receptor-Mediated endocytosis – receptor proteins on the cell
membrane are used to capture specific target molecules
 Exocytosis requires energy to move large molecules out of the cell
o In exocytosis, internal vesicles use energy to fuse with the plasma membrane
and secrete large macromolecules out of the cell
 Proteins such as signaling proteins
 Hormones
 Waste
 Key Takeaways
o (1) Passive transport is the net movement of molecules form high concentration
to low concentration without the direct input of metabolic energy
o (2) Active transport requires the direct input of energy to move molecules from
regions of low concentration to regions of high concentration
o (3) The selective permeability of membranes allows for the formation of
concentration gradients of solutes across the membrane
o (4) In exocytosis, internal vesicles use energy to fuse with the plasma membrane
and secrete large macromolecules out of the cell
o (5) In endocytosis, the cell uses energy to take in macromolecules and
particulate matter by forming new vesicles derived from the plasma membrane.
Topic 2.7 – Facilitated Diffusion
 Membrane proteins are necessary for facilitated diffusion
o Facilitated Diffusion – movement of molecules from high concentration to low
concentration through transport proteins
 Large and small polar molecules
 Large quantities of water can pass through aquaporins
 Charged ions, including Na+ and K+, require channel proteins
 Active transport establishes and maintains concentration gradients
o Active transport moves molecules and/or ions against their concentration
gradient from low to high concentration
 Carrier proteins called pumps
 Requires metabolic energy (such as ATP)
 Establishes and maintains concentration gradients
 Membrane proteins are necessary for active transport
o Cotransport – secondary active transport that uses energy from an
electrochemical gradient to transport two different ions across the membrane
through a protein
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 Symport – two different ions are transported in the same direction
 Membranes may become polarized by movement of ions
o The cell membrane allows for the formation of gradients
 Electrochemical gradient
 Type of concentration gradient
 Membrane potential – electrical potential difference (voltage)
across a membrane
o Membranes may become polarized by movement of ions across the membrane
 Key Takeaways
o (1) Membrane proteins are required for facilitated diffusion of charged and large
polar molecules through a membrane
o (2) Large quantities of water pass through aquaporins
o (3) Membranes becomes polarized by movement of ions across the membrane
o (4) Membrane proteins are necessary for active transport
o (5) Metabolic energy (such as from ATP) is required for active transport of
molecules and/or ions across the membrane and to establish and maintain
concentration gradients
o (6) The Na+/K+ ATPase contributes to the maintenance of membrane potential
Topic 2.8 – Tonicity and Osmoregulation
 Water moves by osmosis
o Osmosis is the diffusion of free water across a selectively permeable membrane
 Large quantities of water move via aquaporins
o Osmolarity is the total solute concentration in a solution
 Water has high solvency abilities
 Solute is the substance being dissolved
 Solvent is a substance that dissolves a solute
 Solution is a uniformed mixture of one or more solutes dissolved in a
solvent
 (solvent + solute = solution)
 Tonicity effects a cell’s physiology
o Tonicity is the measurement of the relative concentrations of solute between
two solutions (inside and outside of the cell)
o Internal cellular environments can be hypotonic, hypertonic, or isotonic to
external environments
 Hypertonic
 More solute and less solvent
 Isotonic
 Equal concentrations of solute and solvent
 Hypotonic
 Less solute and more solvent
o Water moves by osmosis into the area with a higher solute concentration
 Water concentration and solute concentration are inversely related
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Water would diffuse out of a hypotonic environment to a hypertonic
environment
 Solutes diffuse along their own concentration gradients, from the
hypertonic environment into the hypotonic environment
o When a cell is in an isotonic environment, a dynamic equilibrium exists with
equal amounts of water moving in and out of the cell at equal rates
 No net movement of water takes place
Osmoregulatory mechanisms contribute to survival
o In plant cells, osmoregulation maintains water balance and allows control of
internal solute composition/ water potential
 Environmental Hypertonicity
 Less cellular solute and more cellular water
 Plasmolysis
 Isotonic Solution
 Equal solute and water
 Flaccid
 Environmental Hypotonicity
 More cellular solute and less cellular water
 Turgid
o The cell wall helps maintain homeostasis for the plant in environmental
hypotonicity
 Osmotic pressure is high outside of the plant cell due to environmental
hypotonicity
 Water flows into the plant vacuoles via osmosis causing the vacuoles to
expand and press against the cell wall
 The cell wall expands until it begins to exert pressure back on the cell,
this pressure is called turgor pressure
 Turgidity is the optimum state for plant cells
o In animal cells, osmoregulation maintains water balance and allows control of
internal solute composition/ water potential
 Environmental Hypertonicity
 Less cellular solute and more cellular water
 Shriveled
 Isotonic Solution
 Equal Solute and Water
 Normal
 Environmental Hypotonicity
 More cellular solute and less cellular water
 Lysed
Key Takeaways
o (1) External environments can be hypotonic, hypertonic, or isotonic to the
internal environment of the cells
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o (2) Water moves by osmosis from areas of low osmolarity/ solute concentration
to area of high osmolarity/ solute concentration
o (3) Growth and homeostasis are maintained by the constant movement of
molecules across membranes
o (4) Osmoregulation maintains water balance and allows organisms to control
their internal solute composition
 Water moves by osmosis
o Water potential measures the tendency of water to move by osmosis
 Calculated from pressure potential and solute potential
o Water moves from an area of high water potential to an area of low water
potential
o The values of water potential can be positive, zero, or negative
o The more negative the water potential, the more likely water will move into the
area
 Water potential of pure water has a value of zero (0) in an open container
 Osmoregulation allows organisms to control their internal solute composition and water
potential
o Increasing the amount of solute in water will cause
 An increase in solute potential
 A decrease in water potential
o Increasing water potential will cause
 An increase in pressure potential
o Decreasing pressure potential will cause
 A decrease in water potential
 Solute potential of a solute
o In an open system, the pressure potential is zero, so water potential is equal to
the solute potential
 Solute potential = -iCRT
 i= ionization constant
 C=Molar concentration
 Molarity (M) = moles of solute/ volume of a solution
 R = pressure constant
 0.0831 L Bars/mol K
 T = Temperature in Kelvin
 Temperature in Celsius + 273 = K
 Key Takeaways
o (1) Water moves by osmosis from areas of high water potential to areas of lower
water potential
o (2) Water moves by osmosis from areas of low solute potential to areas of high
solute potential
o (3) Osmoregulation maintains water balance and allows organisms to control
their internal solute composition/ water potential
Topic 2.9 – Mechanisms of Transport
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Passive transport is the net movement of molecules down their concentration gradient
o Diffusion – movement of molecules from high concentration to low
concentration
 Small nonpolar molecules pass freely (N2, O2, CO2) across a cell
membrane
 Small amounts of very small polar molecules, like water, can diffuse
across a cell membrane
 Facilitated Diffusion – movement of molecules from high to low concentration through
transport proteins
o Large and small polar molecules
o Charged ions, including Na+ and K+, require channel proteins
 Osmosis is the diffusion of water across a selectively permeable membrane
o Large quantities of water move via aquaporins
o Differences in relative solute concentrations can facilitate osmosis
 Active transport is the movement of molecules against their concentration gradient,
from low concentration to high concentration
o Protein pumps are carrier proteins used in active transport
o Requires metabolic energy (such as ATP)
o Establishes and maintains concentration gradients
 Movement of large molecules into and out of cells requires energy
o In endocytosis, the cell uses energy to take in macromolecules and particulate
matter by forming new vesicles derived from the plasma membrane
 The types of endocytosis are phagocytosis, pinocytosis, and receptormediated endocytosis
o In exocytosis, internal vesicles use energy to fuse with the plasma membrane
and secrete large macromolecules out of the cell
 Key Takeaways
o (1) Passive transport is the net movement of molecules from high concentration
to low concentration without direct input of metabolic energy
o (2) Water is transported in small amounts across the membrane by simple
diffusion and in large amounts via facilitated diffusion through aquaporins
embedded in the membrane
o (3) Active transport requires the direct input of energy to move molecules from
regions of low concentration to regions of high concentration
o (4) Large molecules and large amounts of molecules are moved into the cell by
endocytosis and out of the cell by exocytosis
Topic 2.10 – Compartmentalization
 Compartmentalization in Eukaryotic Cells
o Cells have a plasma membrane that allow them to establish and maintain
internal environments that are different from their external environments
o Eukaryotic cells have additional internal membranes and membrane-bound
organelles that compartmentalize the cell
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o Cellular compartments allow for various metabolic process and specific
enzymatic reactions to occur simultaneously, increasing the efficiency of the cell
 Cellular compartments: lysosomes
o Membrane minimizes competing interactions
o The hydrolytic enzymes of the lysosome function at an acidic environment
o By having this compartmentalization, the inside of the lysosome can maintain a
more acidic pH and allow for efficient hydrolysis to occur, while the rest of the
cytoplasm can remain a more neutral environment
 Cellular compartments: mitochondria
o Membrane folding maximizes SA for metabolic reactions to occur
o Electron transport and ATP synthesis occur in the inner mitochondrial
membrane.
o Folding of the inner membrane increases the SA, which allows for more ATP to
be made
 Cellular compartments: chloroplasts
o Membrane folding maximizes SA for metabolic reactions to occur
o The thylakoids are highly folded membrane compartments that increase the
efficiency of the light dependent reactions
 Key Takeaways
o (1) Eukaryotic cells contain various membrane-bound organelles including, but
no limited to; the ER, Golgi Complex, lysosomes, mitochondria, and chloroplasts.
These structures compartmentalize intracellular processes and enzymatic
reaction increasing the efficiency of cellular function
o (2) Internal membranes facilitate cellular processes by minimizing competing
interactions and by increasing surface areas where reactions can occur.
o (3) Loss of these intracellular compartments or changes to the unique internal
surfaces and environments within membrane-bound organelles may hinder
proper cell function
Topic 2.11 – Origins of Cell Compartmentalization
 Comparison of compartmentalization in prokaryotic and eukaryotic cells
o Both cell types have a plasma membrane that separates their internal
environment from their surrounding environment
o Prokaryotic cells have an internal region, nucleoid region, that contains its
genetic material
o Eukaryotic cells have additional internal membrane and membrane-bound
organelles that compartmentalize the cell
 Genetic material is contained with a membrane-bound nucleus
 The evolution of membrane-bound organelles
o The nucleus and other internal membranes (e.g. ER) are theorized to have
formed from the infoldings of the plasma membrane
o Mitochondria and chloroplasts evolved from previously free-living prokaryotic
cells via endosymbiosis
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A free-living aerobic prokaryote was engulfed by an anaerobic cell
through endocytosis
 The engulfed prokaryotic cell did not get digested by the engulfing cell;
this arrangement became mutually beneficial
 Overtime, the engulfed cell lost some of its independent functionality and
became the mitochondria/chloroplast of the eukaryotic cells
o Relationship between the functions of endosymbiotic organelles & their
ancestors
 Both mitochondria and chloroplasts have double membranes, which
function to regulate the passage of materials into and out of the cell and
to maintain a stable internal environment
 Like prokaryotic cells, mitochondria and chloroplasts
 Both have their own circular DNA encoding genetic information
and can reproduce by a similar process used by prokaryotes
 Both contain their own ribosomes that synthesize proteins
 Key Takeaways
o (1) Both prokaryotic and eukaryotic cells have external plasma membranes.
However, whereas prokaryotes only have internal regions where specialized
structures and functions can occur (e.g. nucleoid region containing DNA),
eukaryotic cells have additional internal membrane-bound organelles that
compartmentalize the cells.
o (2) According to the theory of endosymbiosis, previously free-living prokaryotes
(bacteria) was engulfed by another cell through endocytosis. After living
together symbiotically for some time, the once free-living prokaryote lost its
independent functionality and gave rise to either the mitochondria or the
chloroplasts
o (3) Evidence supporting the evolution of mitochondria and chloroplasts via
endosymbiosis includes the presence of double membranes, circular DNA, and
ribosomes in both these organelles
Topic 3.1 – Enzyme Structure
 Enzymes are macromolecules
o Enzymes are biological catalysts that speed up biochemical reactions
o Most enzymes are proteins
 Tertiary shape must be maintained for functionality
 The active site interacts with the substrate
o A molecule that can interact with an enzyme is called a substrate
o Enzymes have an active site, specifically interacts with substrates
 Has a unique shape and size
 Can have chemical change(s) or not
 Physical and chemical properties of the substrate must be compatible
 Slight changes can occur to align with substrate
o Enzyme names often indicate the substrate or chemical reaction involved
 Enzyme names often end in -ase
 Example: Sucrase is an enzyme that digests sucrose
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o Enzymes are reusable
 Not chemically changed by the reaction
 Cells typically maintain a specific enzyme concentration
o Enzymes can facilitate synthesis or digestion reactions
 Key Takeaways
o (1) Enzymes speed up biochemical reactions by lowering activation energy
requirements
o (2) The structural characteristics of an enzyme make the enzyme very reaction
specific
o (3) The shape and charge of the substrate must be compatible with the active
site of an enzyme for a reaction to occur
o (4) Enzymes are not consumed by the reaction. Enzymes are reused.
Topic 3.2 – Enzyme Catalysis
 Enzymes are biological catalysts
o Enzymes are biological catalysts, typically proteins, that speed up biochemical
reactions
o Enzyme structure is very specific resulting in each enzyme only facilitating one
type of reaction
o Enzymes can facilitate synthesis or digestion reaction
 Enzymes affect the rate of biological reactions
o All biochemical reactions require initial starting energy, called activation energy
o Some reactions result in a net release of energy and some reactions result in a
net absorption of energy
o Typically, reactions resulting in a net release of energy require less activation
energy compared to reactions resulting in net absorption of energy
o Enzymes lower the activation energy requirement of all enzyme-mediated
reactions, accelerating the rate of reactions
 Key Takeaways
o (1) Enzymes are biological catalysts that facilitate chemical reactions in cells by
lowering activation energy requirements
o (2) Activation energy is the initial energy required for a reaction to occur
Topic 3.3 – Environmental Impacts on Enzyme Function
 A change to the molecular structure of an enzyme may result in loss of enzyme function
o Enzymes have unique functional 3D shapes; known as the conformational shape
or tertiary structure
o Changes in the conformational shape of the enzyme = denaturation
 Changes in environmental temperature can lead to denaturation
 Changes in environmental pH can lead to denaturation
 Enzyme denaturation is typically irreversible, and the catalytic ability of
the enzyme is lost or severely decreased
 In some cases, enzyme denaturation is reversible, allowing the enzyme to
regain catalytic activity
 Environmental temperature can alter the efficiency of enzyme activity
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o Optimum Temperatures
 Range in which enzyme-mediated reactions occur the fastest
 Reaction rates change when optimum temperatures aren’t maintained
o Environmental increase in temperature
 Initially increases reaction rate
 Increased speed of molecular movement
 Increased frequency of enzyme-substrate collisions
 Temperature increases outside of optimum range result in enzyme
denaturation
o Environmental decrease in temperature
 Generally slows down reaction rate
 Decreased frequency of enzyme-substrate collisions
 Does not disrupt enzyme structure, no denaturation
Environmental pH can alter the efficiency of enzyme activity
o pH measures the concentration of hydrogen ions in solution
 Measured on a logarithmic scale
 Small changes in pH values equate to large shifts in hydrogen ion
concentration
 Example: pH 6 has 10x more hydrogen ions in solution compared to pH 7
o Optimum pH
 Range in which enzyme-mediated reactions occur the fastest
 Changing the pH outside of this range will slow or stop enzyme activity
 Enzyme denaturation can occur as result of increases and decreases
outside of optimum
 Changes in hydrogen ion concentration can disrupt hydrogen bond
interactions that help maintain enzyme structure
Concentrations of substrates and products affect reaction rate
o Initial increases in substrate concentration increase reaction rate
 More substrates mean more opportunity to collide with enzyme
o Substrate saturation will eventually occur
 Results in no further increase in rate
 Reaction rate will remain constant if saturation levels are maintained
o Increased concentration of products decrease opportunity for addition of
substrate
 Matter takes up space
 More product in an area means lower chance of enzyme-substrate
collisions
 Slows reaction rate
Enzyme concentration impacts reaction rate
o Changes in enzyme concentration can also impact reaction rate
o Less enzyme = slower reaction rate
 Less opportunity for substrates to collide with active sites
Competitive Inhibitors can bind to the active site
AP Biology
o Competitive Inhibitor molecules can bind reversibly or irreversibly to the active
site of the enzyme
 Competes with the normal substrate for the enzyme’s active site
 If inhibitor concentrations exceed substrate concentrations reactions are
slowed
 If inhibitor concentrations are considerably lower than substrate
concentrations, reactions can proceed normally
 If inhibitor binding is irreversible, enzyme function will be prevented
 If inhibitor binds reversibly, enzyme can regain function once inhibitor
detaches
 Noncompetitive inhibitors bind to enzymes and change enzyme activity
o Enzymes can have regions other than the active site to which molecules can
bind, called the allosteric site
o Noncompetitive inhibitors
 Do not bind to the active site
 Bind to the allosteric site
 Binding causes conformational shape change
 Binding prevents enzyme function because the active site is no longer
available
 Reaction rate decreases
o Increasing substrate cannot prevent effects of noncompetitive inhibitor binding
 Key Takeaways
o (1) Denaturation of an enzyme occurs when the conformation protein structure
is disrupted, eliminating the ability to catalyze reactions
o (2) Changes in pH outside of the optimum pH range, in either direction, will
result in decreased enzyme activity and eventually enzyme denaturation
o (3) Increasing temperature, outside of optimum temperature range, will initially
cause in increased reaction rates with continued increases resulting in
denaturation. Decreasing temperature outside optimum range will result in
slowed reaction rates but not the denaturing of the enzyme
o (4) Increased enzyme concentration increases reaction rate. Decreased enzyme
concentration will decrease reaction rate.
o (5) Increasing substrate concentration will initially increase reaction rate.
Substrate saturation will not result in a continued increase in reaction rate.
Reaction rate will remain constant if substrate saturation levels are maintained.
o (6) Competitive inhibitors can bind reversibly/irreversibly to active sites,
potentially altering reaction rate
o (7) Noncompetitive inhibitors can bind to allosteric sites, decreasing the catalytic
capability of enzymes
Topic 3.4 – Cellular Energy
 All living systems require constant input of energy
o Sunlight is the main energy input for living systems
o Autotrophs capture energy from physical sources, like sunlight, or chemical
sources and transform that energy into energy sources usable by all cells
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o During every energy transformation process, some energy is unusable, often lost
as heat
 Life requires a highly ordered system and does not violate the second law of
thermodynamics
o Every energy transfer increases the disorder of the universe
o Living cells are not at equilibrium; there is a constant flow of materials in and out
of the cell
o Cells manage energy resources by energy coupling. Energy-releasing processes
drive energy-storing processes
 Pathways in biological systems are sequential
o Within a chemical pathway, the product of one reaction can serve as a reactant
in a subsequent reaction
o The sequential reactions allow for a more controlled and efficient transfer of
energy
 Key Takeaways
o (1) Living things use the chemical energy stored in molecular bonds of
macromolecules and ATP to perform necessary life functions
o (2) Pathways in biological systems are sequential to allow for a more controlled
and efficient transfer of energy.
Topic 3.5 – Photosynthesis
 Organisms capture and store energy for use in biological processes
o Photosynthesis is the biological process that captures energy from the Sun and
produces sugars
o Evidence supports the claim that prokaryotic photosynthesis by organisms, such
as cyanobacteria, was responsible for the production of oxygen in the
atmosphere
o Photosynthetic pathways are the foundation of eukaryotic photosynthesis
 Light-dependent reactions of photosynthesis in eukaryotes involve a series of pathways
o Light-dependent reactions capture light energy by using light-absorbing
molecules called pigments
o Pigments help transform light energy into chemical energy
o Chemical energy is temporarily stored in the chemical bonds of carrier
molecules, called NADPH
o Light-dependent reactions help facilitate ATP synthesis
o ATP and NADPH transfer stored chemical energy to power the production of
organic molecules in another pathway, called the Calvin cycle.
o Oxygen is produced as a result of water hydrolysis.
 Key Takeaways
o (1) Plants and other autotrophs use pigments to trap light energy to make
organic molecules
o (2) The pigments used in the light-dependent reactions help transform light
energy into chemical energy. The chemical energy is temporarily stored in the
chemical bonds of carrier molecules, called NADPH
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o (3) The products of the light-dependent reactions are ATP and NADPH
o (4) ATP and NADPH are products that will be used in the Calvin cycle to produce
carbohydrates
During photosynthesis, chlorophylls absorb energy from light
o What role do chlorophylls play in the process?
 Capture energy from sunlight and convert it to high-energy electrons
o What happens to chlorophyll electrons when light absorption occurs, and what is
the importance of this?
 Electrons will be energized. The energy from the electrons will be used to
establish a proton gradient and reduce NADP+ to NADPH
Photosystems I and II are embedded in the internal membranes of chloroplasts
o What is a photosystem?
 Light-capturing unit in a chloroplasts’ thylakoid membrane
o Why is the hydrolysis of water necessary as it relates to PSII and the lightdependent reactions?
 The hydrogen molecules from the splitting of the water are released into
the thylakoid space and use to create an electrochemical/ proton
gradient
When electrons are transferred between molecules in a reaction, they pass through the
electron transport chain.
o How are PSII and PSI functionally related to the electron transport chain (ETC)?
 PSII and PSI pass high-energy electrons to the ETC
o What is an electrochemical/proton gradient?
 It is a difference in concentration of protons (hydrogen ions) across a
membrane
The formation of the proton gradients is linked to the synthesis of ATP
o Photosynthesis uses a form of passive transport to generate ATP from ADP
o What is ATP synthase?
 ATP synthase is an enzyme that creates ATP when protons pass through
the enzyme
The energy captured in the light powers the production of carbohydrates in the Calvin
cycle
o The Calvin cycle uses ATP, NADPH, and CO2 and produces carbohydrates
o What is the ultimate goal of the Calvin cycle reactions?
 Make organic products that plants need using the products from the light
reactions of photosynthesis
o Where do plants and other organisms mainly get their carbon dioxide from?
 Plants and other organisms mainly get their carbon dioxide from the
environment
Key Takeaways
o (1) Chlorophyll captures energy from sunlight and excites electrons
AP Biology
o (2) As the electrons pass through the electron transport chain, protons are
actively transported across a membrane, establishing a gradient. Protons diffuse
through ATP synthase, powering ATP synthesis
o (3) ATP, NADPH, and CO2 are used during the Calvin cycle to produce
carbohydrates through a series of reactions
Topic 3.6 – Cellular Respiration
 Fermentation and cellular respiration are processes that allow organisms to use energy
stored in biological macromolecules
o Cellular respiration and fermentation are characteristics of all forms of life
o Cellular respiration and fermentation release chemical energy from organic
molecules, like glucose
o Oxygen is not used during the process of fermentation but is used during the
process of cellular respiration
o Fermentation and anaerobic respiration are not the same processes
 Cellular respiration in eukaryotes involves a series of coordinated enzyme-catalyzed
reactions that capture energy from biological macromolecules
o Cellular respiration involves the release of chemical energy through the
breakdown of glucose and creates an energy-storing molecule called ATP
o ATP is used by all cells to do biological work
o Cellular respiration involves multiple metabolic pathways
 Glycolysis – occurs in the cytoplasm
 Pyruvate oxidation – occurs in mitochondria
 Krebs Cycle (The Citric Acid Cycle) – occurs in mitochondria
 Electron transport – occurs in mitochondria
 The electron transport chain transfers energy from electrons in a series of coupled
reactions
o Electron transport chain reactions occur in the membranes of chloroplasts and
mitochondria, and in the cell membranes of prokaryotes
o An electron transport chain (ETC) facilitates a series of coupled reactions used
during cellular respiration
o Electron transport chains allow for a more controlled and efficient transfer of
energy
o Electron transport chains use electron energy to establish
electrochemical/proton gradients across membranes
o Electrons are delivered by electron carriers, called NADH and FADH2, to the ETC
o ATP synthase uses the electrochemical/proton gradient to synthesize ATP
 Key Takeaways
o (1) All living things use fermentation and cellular respiration to produce ATP
o (2) Eukaryotes coordinate cellular respiration in three metabolic stages which
are glycolysis, pyruvate oxidation and Krebs cycle, and oxidative phosphorylation
o (3) NADH and FADH2 deliver electrons to the ETC which uses the electron energy
to create an electrochemical gradient of protons.
Topic 5.1 - Meiosis
 Key Terms
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Genome: Cell’s genetic informatic
Somatic: Cells of the body (not gametes)
Chromosomes: tightly packed DNA
Diploid (2n): 2 full sets of chromosomes
 Body cells are diploid (e.g., skin cells, leaf cells, hypha cell)
o Haploid (1n): 1 set of chromosomes
 Gametes, sex cells, are haploid
o Sister Chromatids: Replicated strands of DNA held together at the centromere
Meiosis ensures the formation of haploid gamete cells in sexually reproducing diploid
organism
Meiosis results in daughter cells with half the number of chromosomes as the parent
cells
o The diploid parent cell produces four haploid daughter, sex cells
Meiosis involves two rounds of a sequential series of steps (Meiosis 1 and Meiosis II)
Meiosis 1
o Prophase 1
 Nuclear Envelope begins to disappear
 Fibers begin to form
 DNA coils into visible duplicated (or double chromosomes made of sister
chromatids)
 Double chromosomes pair up based on size, shape, centromere location,
genetic information
 While paired, chromatids exchange genetic information with chromatids
from the other chromosome (nonsister chromatids exchange genetic
information)
o Metaphase 1
 Double chromosomes remain in pairs
 Fibers align pairs across the center of the cell
o Anaphase 1
 Fibers separate chromosome pairs
 Each double chromosome, from the pair, migrates to opposite sides of
the cell
o Telophase 1
 Nuclear envelope reappears and establishes two separate nuclei
 Each nucleus contains only one double chromosome from each pair
 Nucleus only contains half of the total information the parent
nucleus contained
o Cytokinesis will separate the cell into two daughter cells
o Daughter cells are haploid and genetically different from each other and the
parent cell
Meiosis II
o Prophase II
 Nuclear Envelope begins to disappear
AP Biology
 Fibers begin to form
o Metaphase II
 Fibers align double chromosomes across the center of the cell
o Anaphase II
 Fibers separate sister chromatids
 Chromatids (single chromosomes) migrate to opposite sides of the cell
o Telophase II
 Nuclear envelope reappears and establishes separate nuclei
 Each nucleus contains single chromosomes
 Chromosomes will begin to uncoil
o Cytokinesis will separate the two cells into four daughter cells
 Daughter cells are haploid and genetically different from each other and parent cell
 Mitosis and meiosis are similar in the way genetic information is passed to daughter
cells.
o Both processes involve:
 Nuclear envelope disappearing
 DNA coiling into chromosomes
 Aligning chromosomes in the center of the cell
 Using fibers to separate chromosomes
 Nuclear envelope reappearing
 Chromosomes uncoiling
 Followed by cytokinesis and production of daughter cells
 Mitosis and meiosis differ in the number of resulting cells and the genetic content of the
cells.
o Mitosis produces two daughter cells that are genetically identical to the parent
cell.
o Meiosis produces four haploid daughter cells that are genetically varied from
each other and the parent cell
 Key Takeaways
o (1) Diploid cells have pairs of chromosomes (a full set), one from each parent,
and are represented by 2n. Haploid cells have a single set of chromosomes,
represented by n.
o (2) The purpose of meiosis is to produce haploid gametes
o (3) Meiosis involves two rounds of cell division. In meiosis I, pairs of
chromosomes separate, resulting in two haploid cells containing only one of the
double chromosomes from each pair. In meiosis II, double chromosomes
separate, resulting in four haploid cells, each with single chromosomes.
o (4) Mitosis and meiosis are similar in the overall process (PMAT) of how genetic
information is passed on to daughter cells. However, mitosis produces two
genetically identical cells and meiosis produces four haploid genetically varied
cells.
Topic 5.2 – Meiosis and Genetic Diversity
 Meiosis generates genetic diversity
o Meiosis results in four haploid gametes (sex cells) that are genetically different
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o Certain processes take place during and after meiosis that generate genetic
diversity
 Crossing over increases genetic diversity among gametes
o Crossing over occurs in prophase I of meiosis 1
o Nonsister chromatids of double homologous chromosomes exchange segments
o Results in recombinant chromatids
o Formation of recombinant chromatids increases genetic diversity
 Random assortment of chromosomes serves to increase variation
o The order of the homologous pairs during metaphase 1 affects which
chromosomes end up in each gamete
o Crossing over continues during metaphase I
o Different combinations of chromosomes in each gamete increase genetic
variation
 Fertilization of gametes serves to increase variation
o When fertilization occurs, information from each parent is contributed to the
fertilized egg
o Typically one gamete from each parent fuse together to form a diploid offspring
o Fertilization is random in that any gamete can contribute to the diploid nature of
genomes in offspring; this increases the potential for genetic diversity
 Key Takeaways
o (1) Crossing over in prophase 1 occurs when nonsister chromatids exchange
segments. This results in recombinant chromosomes.
o (2) Random assortment of chromosomes in metaphase I can result in different
combinations of chromosomes in gametes.
o (3) During sexual reproduction, any gamete from one parent can combine with
any gamete from another parent, resulting in genetically different offspring. This
increases the genetic diversity within a population of organisms.
Topic 5.3 – Mendelian Genetics
 Heritable information provides for continuity of life
o Nucleic acids (DNA and RNA) are carriers of genetic information
o Genetic information is transferred to other cells during cell division
o Transmission of genetic information from one generation to the next provides
for continuity of life
 Shared, conserved, fundamental processes, and features support the concepts of
common ancestry for all organisms.
o Major features of the genetic code are shared by all modern living systems
 All organisms use nucleic acids to store and transmit genetic information
 All organisms have ribosomes and use ribosomes to synthesize proteins
based on nucleic acid sequences
o Core metabolic pathways are conserved across all currently recognized domains
 Glycolysis is a conserved pathway
 Mendel’s laws describe the inheritance of genes and traits on different chromosomes
o A gene is a unit of heredity coding for a trait
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 Can be transferred from one generation to the next
A trait is a genetically determined characteristic of an organism
 Genes determine traits
An allele is a specific variation of a gene
 Organisms inherit alleles from both parents
 Organisms can inherit different alleles for the same gene
 Often represented by using letters (ex. A, a)
 Dominant allele – always shows in the phenotype if inherited
(uppercase letter)
 Recessive allele – only shows in the phenotype when the
dominant allele has not been inherited (lowercase letter)
Genotype is the combination of inherited alleles
 Typically represented by two letters
 Homozygous – genotype containing two of the same alleles (ex.
AA, aa)
 Heterozygous – genotype containing two different alleles (ex. Aa)
Phenotype is the physical result or expression of the genotype
Law of Segregation
 Chromosomes carry alleles
 Homologous chromosomes carry alleles for the same trait
 When chromosomes are separated into daughter cells during meiosis,
the alleles for each trait are also separated
 Separation of alleles allows for genetic variation among gametes
 Mendel’s experimental design involved specific crosses (P, F1, and F2)
 Reappearance of the recessive phenotype in the F2 generation is
evidence of segregation of alleles
Law of Independent Assortment
 Two or more genes assort independently of each other
 One trait is not automatically inherited with another trait
 Alleles for separate traits can be packaged in every possible combination
into gametes
Rules of probability can be applied to analyze passage of single-gene traits from
parent to offspring
 Understanding Mendel’s law of segregation allows for the use of
mathematical calculations to determine the probable inheritance of an
allele
 To determine the probability of A or B happening, add the probability of
A to the probability of B
 To determine the probability of A and B happening, multiply the
probability of A and the probability of B.
 A monohybrid cross is an examination of how one trait is inherited
 A dihybrid cross is an examination how two traits are inherited
 Punnett squares are typically used to illustrate the probable outcomes of
a cross
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o A pedigree is a visual representation tracing the history of a trait through familial
generations.
 Helps to identify types of inheritance
 Circles represent biological females, squares represent biological males
 Shaded shapes are affected individuals, unshaded shapes are unaffected
individuals
 Perpendicular lines branching off horizontal lines represent offspring
 Generations indicated with Roman numerals
o Patterns of inheritance can often be predicted from data, including pedigrees
 Autosomal dominant traits
 Show a pattern of affected offspring with affected parents
 Autosomal recessive traits
 Show a pattern of affected offspring with unaffected parents
o Key Takeaways
 (1) Mendel’s law of segregation states that alleles are segregated into
separate gametes during meiosis
 (2) Mendel’s law of independent assortment states that genes are not
linked
 (3) A monohybrid cross examines the inheritance of one trait and a
dihybrid cross examines the inheritance of two traits
 (4) Understanding Mendel’s laws allows for the application of
mathematical calculations and laws of probability to predict genetic
events
 (5) Pedigrees show inheritance patterns within families and can be used
to predict inheritance of traits in subsequent generations
o Chi-Square Test
 Scientists use hypothesis testing to determine of investigative results are
due to the independent variable or due to chance
 A chi-square goodness-of-fit test evaluates numerical data from two
groups to determine if the observed results are significantly varied from
the expected results
 The steps required of a chi-square goodness-of-fit test include
establishing a question and hypotheses, determining the observed and
expected values, calculating the chi-square value, identifying the critical
value, and drawing a conclusion determining whether the null hypothesis
should be rejected or if the data fail to reject the null.
Topic 5.4 – Non-Mendelian Genetics
 Patterns of inheritance of many traits do not follow the ratios predicted by Mendel’s
laws.
o Genes that are adjacent and close to one another on the same chromosome and
that are inherited together are known as linked genes.
o Traits that are determined by genes located on sex chromosomes are known as
sex-linked traits.
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o Linked genes and sex-linked traits do not follow predicted ratios associated with
Mendel’s laws and can be identified by quantitative analysis
Genes that are adjacent and close to one another on the same chromosomes may
appear to be genetically linked.
o Linked genes
 Typically inherited together
 Less likely to be separated during crossing over in meiosis
The probability that genetically linked genes will segregate as a unit can be used to
calculate the map distance between them
o Map distance
 Tells you how close together a pair of linked genes is
 Determined by how frequently a pair of genes participates in a single
crossover event
o Linked genes have a recombination frequency of less than 50%
o Ex. If a pair of linked genes has a recombination frequency of 5%, they are close
together on the chromosome. These linked genes are considered 5 map units
apart.
o Map units can be used to determine the distance between genes on a
chromosome
Some traits are determined by genes on sex chromosomes and known as sex-linked
traits
o Sex-linked traits are located on sex chromosomes
 Sex chromosomes determine biological sex in animals
 Sex chromosomes are nonhomologous
 Sex chromosomes can have different letter designations (X/Y, Z/W)
o Sex-linked traits deviate from Mendel’s model of inheritance
o In humans
 Biological females contain two X chromosomes (XX)
 Biological males contain an X and a Y chromosome (XY)
 The Y chromosomes carries very little genetic information; therefore,
most sex-linked alleles are only carried on the X chromosome
 Alleles are shown as a superscript on the X chromosome (e.g., X^A
or X^A)
 Biological females can be considered carriers (heterozygous) of a
recessive sex-linked allele.
 Biological males are more likely to have phenotypes associated with
recessive sex-linked alleles
Key Takeaways
o (1) Linked genes are genes located on the same chromosome that are typically
inherited together
o (2) Map distance tells you how close together a pair of linked genes is. The
smaller the map distance, the closer together the genes are on the chromosome
and the more likely those genes will be inherited together
o (3) Sex-linked traits are traits determined by genes located on sex chromosomes.
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o (4) Sex-linked traits differ from Mendelian traits because each parent does not
contribute sex-linked alleles to every biological offspring, like with Mendelian
inheritance; biological sex will determine which sex-linked alleles are inherited.
 Many traits are the product of multiple genes and/or physiological processes happening
in combination
o Many traits are the product of multiple genes acting in varying combinations
 These traits do not segregate in Mendelian patterns
o Human hair color is an example of a trait determined by multiple genes
 Alleles inherited from each parent for each gene have an additive effect
in determining the phenotype
 A dominant allele codes for dark pigment, a recessive allele does not
 The figure below shows possible genotypes and phenotypes if hair color
was coded for by genes A, B, and C
 Some traits result from non-nuclear inheritance
o Chloroplast and mitochondria contain their own non-nuclear genome
o Chloroplast and mitochondria are randomly assorted to gametes and daughter
cells during cell division
o Mitochondria are transmitted to the egg and not sperm in animals
 Such traits are maternally inherited
o Mitochondria and chloroplast are transmitted in the ovule and not in the pollen
in plants
 Such traits are maternally inherited
o Traits determined by chloroplast and mitochondrial DNA do not follow simple
Mendelian rules
o Non-nuclear inheritance patterns can be determined through pedigree analysis
 Key Takeaways
o (1) Inheritance determined by multiple genes has a larger number of possible
genotypes and a larger range of phenotypes possible compared to inheritance
determined by a single gene. These traits do not segregate in Mendelian
patterns.
o (2) Non-nuclear inheritance seen in chloroplasts and mitochondria is maternally
inherited. These traits do not segregate in Mendelian patterns.
Topic 5.5 – Environmental Effects on Phenotype
 The same genotype can result in multiple phenotypes
o Environmental factors can influence gene expression
 If the environmental conditions change, the expression of the gene can
change
o Phenotypic plasticity is the ability of one genotype to produce more than one
phenotype.
o Phenotypic diversity can be due to environmental factors and not necessarily
due to genetic diversity.
 Organisms can have the same genes but show different forms based on
external factors.
o Ex. Flower color based on soil pH
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In hydrangea plants, the color of the flower is determined by the pH of
the soil.
 The same genes can yield different color flowers depending on the
environmental conditions (pH of the soil) during flower development.
 Acidic soil (low pH) yields blue or lavender flowers
 Basic soil (higher pH) yields pink or red flowers
o Ex. Phenotypic plasticity in stomate density
 In many plant species, the number of stomates can be determined by the
amount of CO2 in the atmosphere
 The same genes can yield different numbers of stomates depending on
the atmospheric conditions
 Low amounts of CO2 lead to more stomates
 High amounts of CO2 lead to fewer stomates
 Key Takeaways
o (1) Phenotypic plasticity is the ability of one genotype to produce more than one
phenotype
o (2) The same genotype can result in multiple phenotypes due to changes in
environmental conditions.
o (3) Environmental factors can influence how genes are expressed. This leads to
phenotypic plasticity.
Topic 5.6 – Chromosomal Inheritance
 Segregations, independent assortment, and random fertilization result in genetic
variation.
o The law of segregation explains the separation of alleles during gamete
formation.
 Each gamete carries only one allele for each gene therefore each gamete
receives only one parental allele.
 Segregation of parental alleles into gametes provides opportunity for
more varied combinations of alleles when fertilization occurs.
o Independent assortment suggests that genes for two or more traits will be
sorted into gametes independently; genes are not linked.
 Inheritance of each gene is random and not connected to inheritance of
any other gene.
 Assortment of genes independently into gametes provides more possible
gene combinations when fertilization occurs.
 Ex. Pea color and pea shape
o Random fertilization refers to the concept that any of the genetically unique
sperm created by a male can join with any of the genetically unique eggs created
by a female.
 This will produce offspring with a genetically unique combination of
chromosomes.
 Mutated alleles can be inherited.
o Chromosomes can carry mutated alleles.
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o The law of segregation and independent assortment explain how mutated alleles
can be randomly distributed into gametes.
o Mutations contribute to genetic diversity in offspring.
o Mutations can manifest as genetic disorders when the variations negatively
affect the functioning of the offspring.
Human genetic disorders can be attributed to specific chromosomal changes
o Nondisjunction is the failure of chromosomes to fully separate during the
formation of gametes.
 This results in too many or too few chromosomes in the sex cells.
o Ex. – Triple X Syndrome
 Usually caused by a malformation of egg or sperm cells
 Nondisjunction resulting in reproductive cells with more than 1
chromosomes
 Resulting in offspring with more than 2 sex chromosomes
Key Takeaways
o (1) The segregation of parental alleles into gametes provides opportunity for
more varied combinations of alleles when fertilization occurs.
o (2) The assortment of genes independently into gametes provides more possible
gene combinations when fertilization occurs.
o (3) Nondisjunction is the failure of chromosomes to fully separate during the
formation of gametes. This results in too many or too few chromosomes in the
sex cells.
o (4) Random fertilization leads to genetic variation in offspring of sexually
reproducing organisms.
o (5) Certain human genetic disorders can be attributed to chromosomal
inheritance and can result in genetically varied offspring.
The chromosomal basis of inheritance provides an understanding of gene transmission.
o Certain genetic disorders can be caused by a single mutated allele or a specific
chromosomal change that is passed from parents to offspring.
o Parents to offspring inheritance can be analyzed to determine patterns of gene
transmission
o Mutations or mis-formations in gametes can result in disorders being present in
offspring that were not present in parents.
o Example – Huntington’s disease
 Huntington’s disease is a progressive and eventually fatal neurological
disorder.
 Caused by a single defective gene on Chromosome 4
 Inheritance is autosomal dominant
 This means that if you inherit the affected chromosome from a
parent, you will get the disease.
Key Takeaways
o (1) Chromosomes are inherited as full units and passed from parents to offspring
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o (2) Patterns of inheritance of traits, diseases, or disorders can be analyzed to
determine how chromosomes were inherited
o (3) Visual representations such as pedigrees can be used to help us predict the
causes or effects of changes in chromosomal inheritance from parents to
offspring.
Topic 6.1 – DNA and RNA Structure
 DNA, and in some cases RNA, is the primary source of hereditary material
o Genetic information is stored as the sequence of bases in DNA and RNA
o Genetic information is transmitted from one generation to toe next through
DNA, or in some cases RNA
o DNA is packaged into chromosomes before genetic information is passed from
parent to daughter cells
o Many viruses use RNA molecules to encode genetic information
 DNA, and sometimes RNA, exhibits specific nucleotide base pairing.
o DNA and RNA are structurally similar in the following ways:
 Both are polymers containing nucleotides
 Both are chain-like molecules
 Both follow base pairing rules
 When DNA nucleotides pair with each other, adenine pairs with
thymine and guanine pairs with cytosine
 When RNA nucleotides pair with DNA nucleotides, there is one
base pair change in which RNA’s uracil nucleotides pair with
DNA’s adenine nucleotides
 Specific nucleotide base pairing is conserved through evolution
o DNA and RNA both follow conserved base pairing rules in which pyrimidines pair
only with specific purines
o Pyrimidines have a single ring structure. Examples are uracil, cytosine, and
thymine.
o Purines have a double ring structure. Examples are adenine and guanine.
 Prokaryote and eukaryote genomes differ in certain aspects.
o Prokaryotic organisms typically have circular chromosomes while eukaryotic
organisms have multiple, linear chromosomes
o Prokaryotic genomes are typically smaller than eukaryotic genomes
o Prokaryotes and eukaryotes can contain plasmids, which are small extrachromosomal, double-stranded, circular DNA molecules
 Prokaryotic plasmids are found in the cytosol while eukaryotic plasmids
are found in the nucleus
 Key Takeaways
o (1) DNA, and in some cases RNA, is the primary source of heritable information.
o (2) DNA and RNA store information as nitrogen base sequences. Base pairing
occurs with specific pyrimidines always pairing with specific purines. This base
pairing is conserved through evolution.
AP Biology
o (3) Prokaryotes typically have circular chromosomes while eukaryotes have
linear chromosomes. Prokaryotic genomes are typically smaller than eukaryotic
genomes. Prokaryotic plasmids are found in the cytosol while eukaryotic
plasmids are found in the nucleus.
Topic 6.2 – Replication
 DNA replication ensures continuity of hereditary information
o Genetic information is copied during DNA replication
 Occurs before cell division
 Allows transmission of a complete genome from one generation to the
next
o Specific replication mechanisms ensure the continuity of hereditary information
 DNA replication is semiconservative
o Semiconservative replication results in a DNA molecule containing one original
strand and a newly synthesized compliment
 Each original strand serves as a template for the synthesis of a new
complementary strand
 Directionality in a DNA molecule influences the replication process
o Each DNA strand has a terminal phosphate group on one end and a terminal
hydroxyl group (-OH) on the other end.
 Phosphate terminus is referred to as the 5-prime end (5’)
 Hydroxyl terminus is referred to as the 3-prime end (3’)
o The two strands of a DNA molecule run antiparallel to each other where the 5’
end of one strand is opposite the 3’ end of the complimentary strand
o Nucleotides can only be added to a growing strand in a 5’-3’ direction
 One strand will always be synthesized continuously = leading strand
 One strand will always be synthesized discontinuously, in fragments =
lagging strand
 Enzymes are involved in DNA replication
o Helicase unwinds the DNA strands
o Topoisomerase relaxes the supercoil at the replication fork
 Replication fork – the location where the two strands are separated
o DNA polymerase synthesizes new strands
 Requires RNA primers to initiate synthesis
 Attaches the 3’ end of the template strand
 Builds strands in a 5’-3’ direction
o Ligase joins DNA fragments on the lagging strand
 Key Takeaways
o (1) DNA replication ensures the continuity of hereditary information, allowing
transmission of genetic information between generations
o (2) DNA replication is semiconservative. One strand acts as a template for a new,
complimentary strand of DNA
o (3) DNA is synthesized in the 5’ to 3’ direction. DNA is synthesized continuously
on the leading strands and discontinuously on the lagging strand.
o (4) Enzymes are involved in DNA replication
AP Biology
 Helicase – unwinds DNA strands
 Topoisomerase – relaxes the supercoil ahead of the replication fork
 DNA polymerase – synthesizes new DNA strands
 Ligase – joins DNA fragments of the lagging strand
Topic 6.3 - Transcription and RNA Processing
 Genetic information flows from DNA to RNA to protein
o Genetic information is typically stored in DNA molecules
o RNA molecules are used to facilitate protein synthesis using DNA information
o Ribosomes contain RNA and assemble proteins
 Transcription is the process in which an enzyme directs the formation of an mRNA
molecule
o DNA strands are separated during transcription.
 One strand serves as the template strand, also known as the noncoding
strand, minus strand, or antisense strand.
 The other strand is the non-template strand, also known as the coding
strand.
 The strand serving as the template strand depends on the gene being
transcribed.
 The gene targeted for transcription is located on the coding
strand
o The enzyme RNA polymerase synthesizes messenger RNA (mRNA) in the 5’ to 3’
direction by reading the template in the 3’ to 5’ direction
 mRNA molecule is the transcribed copy of a particular gene
 There are 3 types of RNA molecules
o Messenger RNA (mRNA) carries genetic information from DNA to the ribosomes.
 Information is used to direct protein synthesis at the ribosomal site
 A codon is a three-base sequence found on mRNA
o Transfer RNA (tRNA) is recruited to the ribosomes to help create a specific
polypeptide sequence as directed by mRNA.
 There are various tRNA molecules, each carrying a specific amino acid
 An anti-codon is a three-base sequence on tRNA
 Correct base pairing of tRNA anti-codons with mRNA codons will result in
the release and addition of an amino acid to a growing polypeptide
o Ribosomal RNA (rRNA) molecules are functional units of ribosomes responsible
for protein assembly
 Base-pairing of anti-codons and codons occurs in the ribosomes
 Creates primary polypeptides as tRNA releases amino acids
 Key Takeaways
o (1) Genetic information flows from DNA to RNA to protein.
o (2) Transcription is the process by which RNA polymerase uses the noncoding
strand of DNA as a template to produce an mRNA molecule
o (3) RNA polymerase synthesizes mRNA in the 5’ to 3’ direction while reading
DNA in the 3’ to 5’ direction
AP Biology
o (4) There are three types of RNA molecules, each with their own structure
accounting for difference in function
 mRNA – carries copy of gene to ribosomes
 tRNA – recruited to the ribosomes in order to build the primary amino
acid sequence (polypeptide) dictated by the mRNA sequence
 rRNA – the functional building block of ribosomes responsible for protein
assembly
 A series of enzyme-regulated modifications occur to the mRNA transcript in eukaryotic
cells.
o Addition of a poly-A tail
 100-200 adenine nucleotides
 Increases stability
 Helps with exporting from nucleus
o Addition of GTP cap
 Modified guanine nucleotide
 Protects the transcript
 Helps ribosomes attach to mRNA
 A series of enzyme-regulated modifications occur to the mRNA transcript in eukaryotic
cells
o Introns are sequences of an mRNA transcript that do not code for amino acids
 Are excised during RNA processing
 Not included in the mature mRNA transcript
o Exons are sequences of an mRNA transcript that code for amino acids
 Sequences are retained during RNA processing
 Different exons are connected in the mature mRNA transcript
o The process of splicing introns and connecting retained exons in the mature
mRNA transcript is called alternative splicing
o There are many different exons on a primary transcript
 Different mRNA transcripts can be produced from one primary transcript.
 Exons can be retained in different variations
 Different mRNA transcripts lead to different proteins
 Key Takeaways
o (1) Addition of a poly-A tail, addition of a GTP cap, excision of introns, splicing,
and retention of exons are examples of enzyme-regulated modifications to
mRNA.
o (2) Alternative splicing is when introns are excised from a primary mRNA
transcript and exons are retained and joined together.
o (3) Different combinations of exons can be retained in a mature mRNA
transcript. Different exon combinations encode for different proteins.
Topic 6.4 – Translation
 Translation of mRNA generates polypeptides
o Translation is the process by which an mRNA sequence is used to generate a
polypeptide
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o Translation occurs on ribosomes
 Prokaryotes only have cytosolic ribosomes
 Eukaryotes have cytosolic ribosomes and ribosomes bound to the rough
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Translation involves energy and many sequential steps
o Translation involves three main steps
 In prokaryotic organisms, translation occurs while the mRNA is being
transcribed
Retrovirus translation is a special case because of an alternate flow of information
o Retroviruses introduce viral RNA, not DNA, into host cells.
 Reverse transcriptase is an enzyme that copies the viral RNA into viral
DNA
 This is a viral enzyme
 This enzyme is introduced into the host cell
 Once the enzyme converts the viral RNA into viral DNA, the DNA is
integrated into the host genome
o Once integrated, the viral DNA will be transcribed and
translated
o Transcription and translation of the viral DNA results in
assembly of new viral progeny
Nearly all organisms use the same genetic code
o Translation mechanisms are similar in nearly all organisms
 Nucleotides used to construct DNA and RNA molecules are common
among organisms
 This conservation is evidence of common ancestry
o Viral DNA and RNA molecules are chemically compatible with host-cell genomes
 This allows host-cell translation mechanisms to work with viral genomes
Key Takeaways
o (1) Translation is the process of generating polypeptides using the information
carried on an mRNA molecule
o (2) Translation occurs in three main steps: initiation, elongation, and termination
o (3) In prokaryotes, translation occurs while the mRNA is being transcribed
o (4) For a retrovirus genome to be translated, viral RNA must be converted into
viral DNA and then the viral DNA is integrated into the host genome. Reverse
transcriptase is the viral enzyme that converts viral RNA into viral DNA
o (5) The fact that nearly all organisms use the same genetic code is evidence of
common ancestry of all living organisms.
Translation involves many sequential steps
o Translation is the final process in the flow of information from DNA  RNA 
protein
 Involves converting RNA information into a protein
o The first step of translation is initiation
 rRNA in the ribosome interacts with the mRNA at the first start codon
AP Biology
o mRNA nucleotides are grouped together and read in triplets called codons
 Each codon encodes a specific amino acid
 Can be deduced by using a codon chart
 Many amino acids are encoded for by more than one codon
o tRNA molecules bring the correct amino acid to the correct place, specified by
the codon on the mRNA
 tRNA anti-codons must complement mRNA codons to help ensure the
correct amino acid is brought to the ribosome
o The second step of translation is elongation
 Each newly arrived tRNA brings another amino acid to be added to a
growing polypeptide chain.
 The rRNA adds the amino acids as tRNA brings them
o The last step of translation is termination
 Amino acids continue to be added to the growing polypeptide chain until
a STOP codon is reached
 Translation ends
 No more amino acids are added
 Newly synthesized polypeptide is released
 Key Takeaways
o (1) The salient features of translation include:
 rRNA in the ribosome interacts with a start codon of mRNA
 tRNA brings the correct amino acid to the correct place, as specified by
the mRNA sequence
 Each subsequent amino acid is added to the growing polypeptide chain
until a stop codon is reached on the mRNA
 The polypeptide is released
o (2) The primary molecules involved in translation are:
 mRNA
 tRNA
 rRNA
 Amino acids
Topic 6.5 – Regulation and Gene Expression
 Differences in the expression of genes account for phenotypic differences between
organisms
 Gene expression is the process by which instructions in the DNA are transcribed and
translated into a functional protein
o The flow of information is from DNA to RNA to protein
o Different types of chemical reactions regulate gene expression
 Regulatory sequences are stretches of DNA that interact with proteins
o Regulatory sequences are stretches of DNA that can be used to promote or
inhibit protein synthesis
o Regulatory proteins are used to assist with the promotion or inhibition of protein
synthesis
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o The interaction of regulatory sequences with regulatory proteins controls
transcription
Epigenetic changes can affect gene expression
o Epigenetic changes involve reversible modification of DNA or histones
 Histones are proteins used to wrap DNA around
 Slight chemical modifications of DNA and histones cause tight
packing or loose packing of DNA
o Packing and unpacking regulates gene expression
Observable cell differentiation results from the expression of genes for tissue-specific
proteins
o The cells within a multicellular organism have the same DNA sequences
o Tissues are groups of cells that have the same function
 The presence of specific proteins within the cells of tissues give the tissue
its function
o The phenotype of a cell or organism is determined by the combination of genes
that are expressed
 Cell differentiation refers to cells within the same organism having
different phenotypes
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