EVOLUTION, THE THEMES OF BIOLOGY, AND SCIENTIFIC INQUIRY

Biology ● The scientific study of life

● A subject of enormous scope, and exciting new biological discoveries are
being made every day

Unifying Themes ● Organization

● Information
● Energy and Matter
● Interactions
● Evolution

Properties of Life ● Order

● Evolutionary Adaptation
● Regulation
● Energy Processing
● Growth and Development
○ Inherited information carried by genes controls the pattern of
growth and development of organisms.
● Response to the Environment
● Reproduction
○ Organisms reproduce their own kind

Levels of Biological The Biosphere

Organization - Consists of all life on Earth and all the places where life exists
Ecosystems
- Consists of all the living things in a particular area, along with all the
nonliving components of the environment with which life interacts.
Communities
- The array of organisms inhabiting a particular ecosystem
- Species
- A group whose members can only reproduce with other members
of the group
- The set of populations that inhabit a particular area
Populations
- Consists of all the individuals of a species living within the bounds of a
specified area that interbreed with each other
Organisms
- Individual living things
Organs
- Body parrots that are made of multiple tissues and have specific functions in
the body
- Within an organ, each tissue has a distinct arrangement and contributes
particular properties to organ function
Tissues
- A group of cells that work together, performing a specialized function
Cells
- Life’s fundamental unit of structure and function
- Some organisms consist of a single cell, which performs all the functions of
life
- Other organisms are multicellular and feature a division of labor among
specialized cells
Organelles
- The various functional components present in the cells
 Molecules
- A chemical structure consisting of two or more units called atoms
- Chlorophyll
- The pigment that makes a leaf green
- Absorbs sunlight during photosynthesis
- Within each chloroplast, millions of chlorophyll molecules are
organized into systems that convert light energy to the chemical
energy of food

Emergent Properties - Are due to the arrangement and interactions of parts as complexity increases
- Systems Biology
- The exploration of a biological system by analyzing the
interactions among its parts

Structure and Function - At each level of the biological hierarchy, we find a correlation between
structure and function
- Because correlations of structure and function are common in all living
things, analyzing a biological structure gives us clues about what it does and
how it works

The Cell: An Cell

Organism’s Basic Unit -Smallest unit of organization that can perform all activities required for life
of Structure and -All cells share certain characteristics
Function - Every cell is enclosed by a membrane that regulates the passage of
materials between the cell and its surroundings
Cell Theory
- First developed in the 1800s, based on the observations of many scientists
- States that all living living organisms are made of cells, which are the basic
unit of life
- The action of organisms are all based on the activities of cells
Two Main Forms of Cells
● Prokaryotic Cells
○ Found in two groups of single-celled microorganisms
■ Bacteria
● Singular, bacterium
■ Archaea
● Singular, archaean
○ Lack a nucleus or other membrane-enclosed organelles
○ Generally smaller than eukaryotic cells
● Eukaryotic Cells
○ Contains membrane-enclosed organelles
○ Some organelles are found in the cells of all eukaryotes
■ Other organelles are specific to particular cell types
 DNA - Genetic material within chromosomes
(deoxyribonucleic acid) - Each chromosome contains one very long DNA molecule with hundreds or
thousands of genes, each a section of the DNA of the chromosome
- Transmitted from parents to offsprings, genes are the units of inheritance
- They encode the information necessary to build all of the molecules
synthesized within a cell, which in turn establish that cell’s identity
and function
-

CELL STRUCTURE AND FUNCTIONS, MEMBRANE, CELLULAR PROCESSES

Cell - An organism’s basic unit of structure and function

- Possesses a highly organized structure that enables it to carry out its vital
function

MODERN CELL - Cells are the smallest living unit in all organisms
THEORY - All cells come from other pre-existing cells
- All living things are made of cells (1 or more)

TWO TYPES OF Eukaryotic Cells

CELLS ● Complex, structurally organized cells
● DNA is in an organelle called the Nucleus, with a double membrane
● Possess a true nucleus enclosed in a nuclear envelope
● Have membrane-bound organelles
● Have extensive internal membranes that divide the cell into compartments
called Organelles
○ The plasma membrane and organelle membranes also participate
directly in the cell’s metabolism by containing enzymes that carry
out important chemical reactions
● Genetic material is organized into chromosomes
● Generally larger in size compared to prokaryotic
● Found in multicellular organisms
○ Plant
■ Cellulose cell wall
■ Chloroplasts and vacuoles
○ Animal
■ Rigid cell wall
■ May have flagella
○ Protist
■ They can have a cell wall, without differentiated tissues
○ Fungal
■ Chitin cell wall
■ They are heterotrophs

Prokaryotic Cells
● Simple, structurally uncomplicated cells
● The DNA is in a region that is not membrane-enclosed, called the Nucleoid
● Lack of a true nucleus
● Lack of membrane-bound organelles
● Genetic material is in the nucleoid
○ Typically a single, circular DNA molecule
○ Typically smaller in size
● Found in two groups of single-celled organisms
 ○ Bacteria
■ A diverse range of single-celled microorganisms found in
various environments
○ Archaea
■ Are a group of single-celled microorganisms that often
thrive in extreme environments

Prokaryotic Cells Similarities Eukaryotic Cells

Have no nucleus Have DNA (Genetic Have well-defined

Material) nucleus

No membrane-bound Have cytoplasm Have membrane-bound

organelles - Gel-like organelles
substance that
fills the cell and
holds
organelles,
ribosomes, and
other cellular
structures

Generally smaller and Have ribosomes Bigger and more

less complex - Cellular complex
structures
responsible for
protein synthesis
(translation)

Genetic material (DNA) Have cell membrane Have multiple linear

is a single, circular - Essential for chromosomes enclosed
chromosome located in maintaining within the nucleus
the nucleoid region cellular
homeostasis

Have cell walls Undergo a more complex

process known as mitosis
(for somatic cells) or
meiosis (for reproductive
cells)

Undergo a simple form Reproduce both

of cell division called asexually and sexually
Binary Fission

Reproduce asexually Have a complex

cytoskeleton

Cellular Processes - Occur through stepwise chemical reactions

- Some chemical reactions are spontaneous and release energy while others
require energy
Metabolism
● An organism’s metabolism transforms matter and energy
○ 2 types of metabolism
■ Catabolic
● Uses energy to break down
■ Anabolic
● Requires energy to grow and build
● An organism’s metabolism transforms matter and energy
● The free-energy change of a reaction occurs spontaneously
○ Exergonic Chemical Reactions (-∆𝐺)
■ Spontaneous
■ Require no energy
○ Endergonic Chemical Reactions (+∆𝐺)
■ Non-spontaneous
■ Require energy
● ATP powers cellular work by coupling exergonic reactions to endergonic
reactions
● Enzymes speed up metabolic reactions by lowering energy barriers
● Regulation of enzyme activity helps control metabolism
○ Activators
■ Molecules that increase the activity of an enzyme
○ Inhibitors
■ Molecules that decrease the enzyme activity

Cellular Respiration
● The metabolic process that employs a catabolic pathway that uses oxygen to
drive the generation of Adenosine Triphosphate by extracting energy from
sugars or glucose, fats, and other fuels.
● The complete version of this is Aerobic Respiration, which requires
oxygen
● Glycolysis
○ Occurs in the cytoplasm
○ The breaking down of glucose to produce energy and pyruvate
○ Basically, it oxidizes glucose
■ Oxidation is when electrons are removed
○ The pyruvate then moves into the mitochondrial matrix to undergo
what is called Pyruvate Oxidation, where pyruvate turns into the
two-carbon acetyl-CoA
● The Krebs Cycle
○ Occurs in the mitochondrial matrix
○ acetyl-CoA combines with a four carbon oxaloacetate in order to
form the six carbon citrate
● The Electron Transport Chain
○ Occurs in the inner mitochondrial membrane
○ The electron transport chain is a series of redox reactions
○ Redox is a reduction of oxygen.
■ Transfers electrons. Electrons are usually passed first to
NAD+, reducing it to NADH
○ At the end of the electron transport chain, the final electron
acceptor (accepts electrons transferred to it from another
compound) O2 or oxygen, combines with protons to produce water
(H2O). Meanwhile, protons move back into the mitochondrial
matrix and ATP Synthase utilizes that for ATP synthesis
● Fermentation
○ The pathway for when there are no suitable electron acceptors and
 is not dependent on oxygen. It occurs in both prokaryotic and
eukaryotic cells
○ Glycolysis
■ During glycolysis, two NAD+ electron carriers are
reduced to two NADH molecules and 2 net ATPs are
produced
○ NADH+ must be oxidized back so that glycolysis can continue and
cells can continue making 2 ATPs
● Photosynthesis
○ Process of converting the energy of sunlight into chemical energy
stored in sugars.
○ Takes place in specialized cellular structures called chloroplasts,
which contain the pigment chlorophyll
○ Autotrophs - The Producers
■ They produce their own organic molecules from CO2 and
other inorganic raw materials
○ Heterotrophs - The Consumers
■ They are unable to make their own food and live on
compounds produced by others

○ Light Reaction
■ Light is captured
■ Water is split (based on chemical equation)
■ Products of this reaction
● Oxygen
● ATP
● NADPH
○ Calvin Cycle/Dark Reaction
■ Needs ATP and NADPH (products of light-dependent
reactions)
■ Does not directly capture light
■ Happens in the stroma
○ Organic compounds produced by photosynthesis provide the
energy and building material for Earth’s ecosystems
● Cell Communication
○ The process of information exchange through chemical signals
○ Three Stages of Cell-Signaling
■ Signal Reception
● Ligands secretion and signal reception of pair
receptor
■ Signal Transduction
● Alteration in receptor’s activity and shape
■ Cellular Response
● Change within the target cell
 ○ Cell-Signaling Pathways
■ Local Signaling
● Direct Contact
○ Cell junction and cell-surface molecules
● Paracrine Signaling
○ ligand=growth factors
● Synaptic Signaling
○ Nervous system
○ Ligand = neurotransmitters
■ Long-distance Signaling
● Endocrine Signaling
○ Circulatory system
○ Ligand = hormones
○ Integration of Multiple Cell-Signaling Pathways
■ Apoptosis
● “Programmed cell death”
● Outside (signal from nearby cell), inside
(protein-protein interactions)

BASIC FEATURES OF ● CELL MEMBRANE (Plasma Membrane)

ALL CELLS ○ Selective barrier
● CYTOSOL
○ Semifluid, jellylike substance in which subcellular components are
suspended
● CHROMOSOMES
○ Carry genes in the form of DNA
● RIBOSOMES
○ Complexes that make proteins according to instructions from the
genes

PARTS OF A FIMBRIAE
PROKARYOTIC - Attachment structures on the surface of some prokaryotes (not visible on
CELL TEM)
NUCLEOID
- Region where the cell’s DNA is located (not enclosed by a membrane)
RIBOSOMES
- Complexes that synthesize proteins
PLASMA MEMBRANE
- Membrane enclosing the cytoplasm
CELL WALL
- Rigid structure outside the plasma membrane
GLYCOCALYX
- Outer coating of many prokaryotes, consisting of a capsule or a slime layer
CILIA AND FLAGELLA
- Both cellular extensions containing microtubules
 - Cilia are shorter and more numerous than flagella
- Cilia have alternating power and recovery strokes. Flagella have an
undulating motion
- Can be used to propel cells through water
- Cilia can be used to move fluid over the surface of a tissue layer
- Some cilia are nonmotile and act as signal-receiving antennas for the cell
- Bending of cilia and flagella is produced by motor proteins called Dyneins
that walk along microtubules using ATP for energy

PARTS OF AN ENDOPLASMIC RETICULUM

ANIMAL CELL - Network of membranous sacs and tubes
- Active in membrane synthesis and other synthetic and metabolic processes
- Has rough (ribosome-studded) and smooth regions
- ROUGH ER
- Many cells secrete proteins that are produced by ribosomes
attached to rough ER
- Most secretory proteins are glycoproteins
- Proteins with carbohydrates covalently bonded to them
- The carbohydrates are attached to the proteins in the ER lumen by
enzymes built into the ER membrane
- After secretory proteins are formed, the ER membrane keeps them
separate from proteins in the cytosol, which are produced by free
ribosomes
- Secretory proteins depart from the ER wrapped in the membranes
of vesicles that bud like bubbles from a specialized region called
transitional ER
- Vesicles in transit from one part of the cell to another are called
Transport Vesicles
- SMOOTH ER
- Synthesis of lipid
- Detoxification of drugs and poisons
- Storage of calcium ions
NUCLEUS
● Houses most of the genes in the eukaryotic cell, which contain the
instructions for building and maintaining the cell
● Directs protein synthesis by synthesizing messenger RNA (mRNA) that
carries information from the DNA
● Nuclear Envelope
○ Double membrane enclosing the nucleus
○ Allow proteins and RNAs to enter and exit the nucleus
○ Perforated by pores
○ Continuous with ER
● Nuclear Lamina
○ A netlike array of protein filaments that maintains the shape of the
nucleus
● Nuclear Matrix
○ A framework of protein filaments extending throughout the nuclear
interior that may help organize the genetic material
● Nucleolus
○ Nonmembranous structure involved in production of ribosomes
○ A nucleus has one or more nucleoli
○ Where the ribosomal RNA (rRNA) is synthesized
● Chromatin
○ Material consisting of DNA and proteins
○ Visible in a dividing cell as individual condensed chromosomes
PLASMA MEMBRANE
- Membrane enclosing the cell
RIBOSOMES
- Complexes that make proteins
- Free in cytosol or bound to rough ER or nuclear envelope
- Cellular components that carry out protein synthesis
- Can be found either free in the cytoplasm or bound to the endoplasmic
reticulum
- Bound ribosomes make proteins that are destined for insertion into
membranes, for packaging within certain organelles such as
lysosomes, or for export from the cell (secretion)
GOLGI APPARATUS
- Organelle active in synthesis, modification, sorting, and secretion of cell
products
- Products of the ER are modified and stored and then sent to other
destinations
- Consists of a group of associated, flattened membranous
sacs—cisternae—looking like a stack of pita bread
1. Vesicles move ER to Golgi
2. Vesicles coalesce to form new cis Golgi cisternae
3. Cisternal maturation: Golgi cisternae move in a cis-to-trans direction
4. Vesicles form and leave Golgi, carrying specific products to other locations
or to the plasma membrane for secretion
5. Vesicles transport some proteins backward to less mature Golgi cisternae,
where they function
6. Vesicles also transport certain proteins back to ER, their site to function
LYSOSOME
- Digestive organelle where macromolecules are hydrolyzed
- Lysosomal enzymes work best in the acidic environment found in lysosomes
● Phagocytosis
a. Lysosome contains active hydrolytic enzymes
b. Lysosome fuses with food vacuole
c. Hydrolytic enzymes digest food particles
● Autophagy
a. Lysosome fuses with vesicle containing damaged organelles
b. Hydrolytic enzymes digest organelle components
MITOCHONDRION
- Organelle where cellular respiration occurs and most ATP is generated
- Dynamic organelles that move around, change their shapes, and fuse or
divide
- Have two membranes
- Outer Membrane
- Inner Membrane
- Folded into cristae, which increases its surface area and
enhances the productivity of cellular respiration
- The cristae contain the electron transport chain and ATP synthase, two
protein complexes that are essential for cellular respiration
- Mitochondria contain enzymes and other other proteins that are involved in
cellular respiration
PEROXISOME
- Organelle with various specialized metabolic function
- Produces hydrogen peroxide as a by-product and then converts it to water
MICROVILLI
- Membrane projections that increase the cell’s surface area
CYTOSKELETON
 -Reinforces cell’s shape
-Involved in cell motility, location and movements of cell parts
-Interacts with motor proteins for organelle movement
-Dynamic can be quickly dismantled and reassembled made up o f three
main types of fibers:
- Microtubules
- Thickest, tubulin proteins growth by addition and
shrinkage of dimers
- Microfilaments
- Made up of actin proteins
- Can form linear filaments or structural networks
- Structural role is to bear tension (pulling forces)
- Involved in cell motility
- Essential for muscle contraction
- Intermediate filaments
- Made up of a variety of proteins, including keratins
- More permanent fixtures of cells than microfilaments and
microtubules
- Reinforcing the shape of the cell and fixing the position of
certain organelles, such as the nucleus
- Functions in cell movement
- Components are made of protein
CENTROSOME
- Region where the cell’s microtubules are initiated
- Contains a pair of centrioles
FLAGELLUM
- Motility structure present in some animal cells
- Composed of a cluster of microtubules within an extension of the plasma
membrane

PARTS OF A PLANT NUCLEUS

CELL - Nuclear Envelope
- Nucleolus
- Chromatin
CELL WALLS
- Extracellular structures that protect the plant cell, maintain its shape, and
prevent excessive uptake of water.
- Made up of microfibrils of cellulose embedded in a matrix of other
polysaccharides and proteins and synthesized by an enzyme called cellulose
synthase
- Young plant cells secrete a thin and flexible primary cell wall
- Middle Lamella
- A thin layer rich in sticky polysaccharides that glues adjacent plant
cells together (pectin)
- Some mature cells also add a secondary cell wall between the plasma
membrane and the primary wall
- The secondary wall, often deposited in several laminated layers,
has a strong and durable matrix that affords the cell protection an
support
ROUGH ENDOPLASMIC RETICULUM
SMOOTH ENDOPLASMIC RETICULUM
RIBOSOMES
GOLGI APPARATUS
MITOCHONDRION
PEROXISOME
 - Play a role in a variety of metabolic reactions, including fatty acid oxidation,
detoxification, and sugar production
- Essential for protecting the cell from the toxic effects of hydrogen peroxide
- Contains enzymes that remove hydrogen atoms from various substrates and
transfer them to oxygen, producing hydrogen peroxide as a by-product
- Breaking down fatty acids into smaller molecules that can be used as fuel
for cellular respiration
- Detoxifying alcohol and other harmful compounds
- Converting fatty acids to sugar in plant seeds
- Peroxisomes also contain an enzyme that converts H2o2 to water, which is
necessary because H2O2 is itself toxic
PLASMA MEMBRANE
CELL WALL
- Outer layer that maintains cell’s shape and protects cell from mechanical
damage
- Made of cellulose, other polysaccharides, and protein
PLASMODESMATA
- Cytoplasmic channels through cell walls that connect the cytoplasms of
adjacent cells
CHLOROPLAST
- Photosynthetic organelle
- Converts energy of sunlight to chemical energy stored in sugar molecules
- Contain the green pigment chlorophyll, along with enzymes and other
molecules that function in the photosynthetic production of sugar
- Member of a family of plastids
- Contents are partitioned from the cytosol by an envelope consisting of two
membranes
CYTOSKELETON
- Microfilaments
- Microtubules
CENTRAL VACUOLE
- Prominent organelle in older plant cells
- Functions include storage, breakdown of waste products, and hydrolysis of
macromolecules
- Enlargement of the vacuole is a major mechanism of plant growth

THE NUCLEUS NUCLEUS

- Contains most of the genes in the eukaryotic cell
- Usually the most conspicuous organelle, averaging 5µ𝑚 in diameter
- Within the nucleus, the DNA is organized into discrete units called
Chromosomes
- Structures that carry the genetic information
NUCLEAR ENVELOPE
- Encloses the nucleus, separating its contents from the cytoplasm
- A double membrane
- Each a lipid bilayer with associated proteins, are separated by a
space of 20-40 nm
- Perforated by pore structure that are about 100 nm in diameter
- Pore Complex
- Regulates the entry and exit of proteins and RNAs, as well as large
complexes of macromolecules
- Nuclear side is lined by the Nuclear Lamina
- A netlike array of protein filaments that maintains the shape of the
nucleus by mechanically supporting the nuclear envelope
 VACUOLES ● Vacuoles
○ Large vesicles derived from the endoplasmic reticulum and Golgi
apparatus
○ Selective in transporting solutes
○ The solution inside a vacuole differ in composition from the
cytosol
○ Vacuoles that contain pigments the red and blue pigments of petals
help attract pollinating insects to flowers
● Food Vacuoles
○ Formed by phagocytosis
● Hydrolytic Vacuoles
○ Carry out enzymatic hydrolysis
● Storage Vacuoles
○ Hold reserves of important organic compounds
● Contractile Vacuoles
○ Pump excess water out of the cell, thereby maintaining a suitable
concentration of ions and molecules inside the cells
● Central Vacuole
○ Develops by the coalescence of smaller vacuoles
○ Solution inside the central vacuole, called cell sap, is the plant
cell’s main repository of inorganic ions, including potassium and
chloride
○ Plays a major role in the growth of plant cells, which enlarge as the
vacuole absorbs water, enabling the cell to become larger with a
minimal investment in the new cytoplasm

EXTRACELLULAR ● Proteoglycan Molecules

MATRIX ○ Has a small core protein with many carbohydrate chains covalently
attached
○ The ECM interacts with cells through integrins, cell-surface
receptor proteins that are built into the plasma membrane
○ Can regulate a cell’s behavior by communicating with it through
integrins
○ Can influence the activity of genes in the nucleus

CELL JUNCTIONS ● Sites of direct physical contact between adjacent cells

● Plasmodesmata are channels that connect the cytoplasm of adjacent plant
cells
● Light junctions, desmosomes, and gap junctions are three main types of cell
junction in animal cells
● Tight junctions seal the space between adjacent cells, preventing leakage of
materials across the tissue
● Desmosomes anchor adjacent cells together, providing strength and support
to tissues
● Gap junctions allow small molecules, ions, and electrical signals to pass
directly between adjacent cells

Relationships among 1. The nuclear envelope is connected to the rough ER, which is also
organelles of the continuous with the smooth ER
endomembrane system 2. Membranes and proteins produced by the ER move via transport vesicles to
the Golgi
3. The Golgi pinches off transport vesicles and other vesicles that give rise to
lysosomes, other types of specialized vesicles, and vacuoles
4. The lysosome is available for fusion with another vesicle for digestion
5. A transport vesicle carries proteins to the plasma membrane for secretion
 6. The plasma membrane expands by fusion of vesicles; proteins are secreted
from the cell by exocytosis

MEMBRANE STRUCTURE AND FUNCTION

FLUID MOSAIC ● The membrane is a mosaic of protein molecules embedded in the

MODEL phospholipid bilayer
● The phospholipid is an amphipathic molecule
● Serves as a stable boundary between aqueous compartment sheltering
hydrophobic tails from water and exposing hydrophilic tails
● Membrane proteins are also amphipathic
● Membranes are not static sheets of molecules, but are fluid

MEMBRANE ● Decreases as temperature decreases as phospholipids in the membrane

FLUIDITY become more closely packed at a lower temperatures
● Membranes with unsaturated fatty acids are more fluid than the saturated
fatty acids since the kinks in the unsaturated fatty acid tails prevent them
from packing together as closely as the saturated fatty acid tails
● Cholesterol makes membranes less fluid at high temperatures, but it also
lowers the temperature at which the membrane solidifies since cholesterol
hinders the close packing of phospholipids

EVOLUTION OF ● The composition of cell membrane lipids varies between species which
DIFFERENCE IN could be evolutionary adaptations
MEMBRANE LIPID
COMPOSITION

MEMBRANE ● Two major populations of membrane proteins

PROTEINS ○ Integral Proteins
■ Penetrate the hydrophobic interior of the lipid bilayer
■ Transport substances across the membrane, passively or
actively
■ Enzymatic activity or catalyzing reactions that take place
at or within the membrane
■ Cell signaling by transmitting signals from the outside of
the cell to the inside, or vice versa
■ Cell adhesion by helping cells adhere to each other or to
the extracellular matrix
○ Peripheral Proteins
■ Structural support
● Stabilizes the membrane and provide structural
support for the cell
■ Cell signaling
● By transmitting signals from the inside of the cell
to the outside, or vice versa

\
GLUCOSE TRANSPORTER (GLUT) PROTEIN
- Transports glucose across the plasma membrane of cells
SODIUM-POTASSIUM PUMP
- Transports sodium ions out of the cell and potassium ions into the cell
- Helps to maintain the cell’s membrane potential and to regulate cell volume
RHODOPSIN PROTEIN
- A light-sensitive protein in the retina of the eye
- When it absorbs light, it triggers a signal transduction cascade that leads to
 vision
THE T-CELL RECEPTOR (TCR) PROTEIN
- On the surface of T cells
- Responsible for recognizing antigens
CCR5 PROTEIN IN HIV INFECTION
- A co-receptor that HIV needs to bind to in order to infect cells
- People with a mutation in the CCR5 gene are resistant to HIV infection
because their cells do not express CCR5

MEMBRANE ● Molecules that contain carbohydrates and are attached to the cell membrane
CARBOHYDRATES ● Important for cell-cell recognition
IN CELL-CELL ○ The ability of cells to distinguish one type of neighboring cell from
RECOGNITION another
● Vary from species to species, among individuals of the same species, and
even from one cell type to another in a single individual

MEMBRANE ● The biological membrane has emergent properties, including selective

STRUCTURE permeability
RESULTS IN ● Selective Permeability
SELECTIVE ○ The ability of the membrane to allow some substances to cross
PERMEABILITY more easily than others
○ Controls the exchange of molecules and ions with its surroundings
● Hydrophobic Substances
○ Soluble in lipids and pass through membranes rapidly, but polar
molecules and ions need specific transport proteins
● Nonpolar Molecules
○ Can dissolve in the lipid bilayer of the membrane and cross it easily
● Polar Molecules
○ Cannot cross the lipid bilayer easily
● Transport Proteins
○ Allow specific ions and polar molecules to cross the cell membrane
by providing a hydrophilic channel or by shuttling them across the
membrane
○ 2 Types of Transport Proteins
■ Channel Proteins
● Provide a hydrophilic channel that certain
molecules or ions use as a tunnel
■ Carrier Proteins
● Bind to their passengers and change shape to
shuttle them across the membrane

PASSIVE ● Diffusion of a substance across a membrane with no energy investment

TRANSPORT ● Rules of diffusion
○ In the absence of any other forces, a substance will diffuse from
where it is more concentrated to where it is less concentrated
● A substance diffuse down its concentration gradient
● Diffusion of a substance across a biological membrane
○ It requires no energy
● Concentration gradient itself represents potential energy

WATER DIFFUSION ● Water diffusion across cell membranes is called OSMOSIS

○ Movement of water across a selectively permeable membrane from
an area of high water concentration (low solute concentration) to an
area of low water concentration (high solute concentration)
 TONICITY ● Ability of a surrounding solution to cause a cell to gain or lose water
● Depends on the concentration of nonpenetrating solutes in the solution
relative to the concentration of nonpenetrating solutes inside the cell
○ If the solution is isotonic to the cell, there will be no net movement
of water across the plasma membrane
○ If the solution is hypertonic to the cell, the cell will lose water and
shrivel
○ If the solution is hypotonic to the cell, the cell will gain water and
swell

FACILITATED ● Passive transport of molecules across a membrane with the help of

DIFFUSION transport proteins
○ Specific for molecules they transport and provide channels or
corridors that allow the molecules to cross the membrane more
easily
■ Channel Proteins
● Simply provide corridors that allow specific
molecules or ions to cross the membrane
■ Carrier Proteins
● Bind to their passengers and change shape in a
way that shuttles them across the membrane

ACTIVE TRANSPORT ● Used energy to move solutes against their concentration gradients
● Powered by ATP hydrolysis
● Carried out by carrier proteins, not channel proteins
● Important for maintain ion concentrations inside cells and for transporting
nutrient intro cells
● Electrogenic Pumps
○ Generate voltage across membranes by pumping ions against their
concentration gradients
● Cotransport
○ A type of active transport that couples the downhill diffusion of
one solute to the uphill transport of another solute

BULK TRANSPORT BULK TRANSPORT

ACROSS THE - Movement of large molecules and particles into and out of the cell vesicles
PLASMA - Important for variety of cellular processes, including secretion, signaling,
MEMBRANE nutrient uptake, and membrane remodeling
OCCURS BY EXOCYTOSIS
EXOCYTOSIS AND - Process of releasing vesicles from the cell into extracellular fluid
ENDOCYTOSIS ENDOCYTOSIS
- Process of engulfing material from the extracellular fluid and forming
vesicles inside the cell
THREE TYPES OF ENDOCYTOSIS
● Phagocytosis
○ Engulf large particles
● Pinocytosis
○ Small particles and fluids
● Receptor-Mediated Endocytosis
○ Take in specific molecules that bind to receptors on the cell surface

GENETICS

MEIOSIS ● Sexual Reproduction

○ Two organisms are needed to produce an offspring
 ○ Usually, sexually producing organisms have diploid cells, meaning
two sets of chromosome in each cell
○

CELL SIGNALING

Cell Signaling ● Signal Reception

○ A signaling molecule binds to a receptor, causing it to change
shape
○ Reception occurs when a signaling molecule binds to a receptor
protein on a target cell’s surface to initiate a chemical signal
detection
■ G protein-coupled receptors (GPCRs)
■ Receptor tyrosine kinesis (RTKs)
■ Ligand-gated ion channels
● Signal Transduction
○ Cascades of molecular interactions transmit signals from receptors
to relay molecules in the cell
○ Begins when signaling molecule binds to a receptor protein
○ Transduction converts the signal to a form that can bring about a
specific cellular response
■ Phosphorylation Cascades
■ Second Messengers
● Cellular Response
○ Cell signaling leads to regulation of transcription or cytoplasmic
activities
○ Cell-signaling processes ensure that cellular activities occur in the
right cells, at the right time, and in proper coordination with other
cells of the organism
■ Nuclear Response
■ Apoptosis

Signal Reception Cell-Surface Transmembrane Receptors

Feature GPCR Tyrosine Kinase Ion Channel

Location Cell surface Cell surface Cell surface or

 internal membranes

Activation Binding to a Binding to a ligand Binding to a ligand,

signaling voltage change, or
molecule mechanical stimuli

Effect Activation of a G Activation of a Opening or closing of

protein, which tyrosine kinase an ion channel, which
leads to a change cascade, which leads leads to a change in
in cellular to a change in cellular ion flow across the
behavior behavior membrane

Examples Yeast mating Epidermal growth Nicotinic

factors, factor receptor acetylcholine
neurotransmitters, (EFGR), insulin receptor,
and epinephrine receptor, voltage-gated sodium
(adrenaline) and platelet-derived channel, TRP
many other growth factor channels
hormone receptor (PDGFR)

G-Protein Coupled Receptor (GPCR)

● Protein receptors on cell surface that work with G protein to transmit signals
from outside the cell to the inside
● Involved in many important body functions, including vision, smell, and
taste
● Bind to signaling molecules, such as hormones and neurotransmitters,
changes shape and activates a G protein. The G protein activates other
proteins in the cell, leading to a change in cellular behavior. GPCRs are also
important drug targets because they are involved in so many important body
functions

Receptor Tyrosine Kinases (RTK)

● Surface proteins that help communicate with other cells
● Bind to signaling molecules, such as growth factors
● When an RTK binds to a signaling molecule, it attaches a phosphate group
to another protein

PHOTOSYNTHESIS

FUNCTION AND ● Photosynthesis feeds the biosphere as it converts light energy to the
STRUCTURE chemical energy of food
● Autotrophs or “producers”
○ Synthesize organic molecules from carbon dioxide
● Pants are photoautotrophs that use light energy
● Heterotrophs
○ Unable to make their own food
○ Live on compounds composed by others
● Chloroplasts
○ Sites of photosynthesis located within the mesophyll cells, the
tissue in the interior of the lead
● CO2 enters the leaf, and O2 exits, by way of the stomata

CHLOROPLAST ● The chloroplast has two membranes enclosing the stroma

● The stroma contains a third membrane system consisting of sacs called
 thylakoid that separate the stroma from the thylakoid space
● The sacs are sometimes arranged in columns called grana
● Chlorophyll
○ Responsible for the green color of leaves, is in the thylakoid
membranes
○ The absorption of light energy by chlorophyll drive s the synthesis
of organic molecules in the chloroplast

PROPERTIES OF ● Light
LIGHT ○ A form of electromagnetic energy
● The distance between the crests of the waves is called the wavelength
○ The shorter the wavelength, the greater the energy of the light
○ The wavelengths drive photosynthesis
● Photosynthetic Pigments
○ The molecules that absorb light energy
●

PHOTOSYSTEMS ● The photosystem in the thylakoid membrane is a protein and pigment

complex
● Captures light energy in the light harvesting complex and transfers it to a
reaction-center complex
● Two Types of Photosystems
○ PS I
■ Generates ATP
■ Reaction-center chlorophyll is P700
○ PS II
■ Splits water molecules and releases oxygen
■ Reaction-center chlorophyll is P680

PHOTOSYNTHESIS: ● Thylakoid Membranes

AN OVERVIEW ○ Sites of the light reactions, whereas the Calvin cycle occurs in the
stroma
● Light Reactions
○ Use solar energy to make ATP and NADPH for the Calvin Cycle
● Calvin Cycle
○ Incorporates CO2 into organic molecules for sugar conversion
● Photosynthesis
○ Redox process
○ Water is split, and electrons are transferred along with hydrogen
ions from the water to carbon dioxide, reducing it to sugar.
LINEAR ELECTRON ● The process by which light energy is converted into chemical energy in the
FLOW form of ATP and NADPH

The steps of linear electron flow are as follows:

● A photon of light strikes one of the pigment molecules in a light-harvesting
complex of PS 2
● The electron in the pigment molecules is excited and is transferred to the
primary electron acceptor of PS 2
● A water molecule is split into two electrons, two hydrogen ions, and an
oxygen atom
● The electrons from the split water molecule are transferred to the P680 pair
of chlorophyll A molecules in the PS 2 reaction-center complex
● The excited electrons from the P680 pair are transferred to PS 1 via an
electron transport chain
● The electron transport chain pumps protons into the thylakoid space,
creating a proton gradient
● The proton gradient is used to make ATP in a process called Chemiosmosis
● The electrons from PS 1 are transferred to NADP via ferredoxin
● The reduction of NADP and NADPH removes an Hydrogen ion from the
stroma

Cyclic Electron Flow

● Uses photosystem 1 but not photosystem
● There is no production of NADPH and no release of oxygen that results
from this process.
● Does generate ATP

PHOSPHORYLATION Chloroplasts vs Mitochondria

Feature Chloroplasts Mitochondria

 Energy source Light energy Chemical energy from
food molecules

Electron donor Water NADH and FADH2

Electron acceptor NADP+ Oxygen

Proton gradient direction Stroma to thylakoid Mitochondrial matrix to

space intermembrane space

ATP synthesis location Stroma-facing side of the Matrix-facing side of the

thylakoid inner mitochondrial
membrane

Process Photophosphorylation Oxidative

phosphorylation

End product ATP and NADPH ATP

CALVIN CYCLE The Calvin Cycle consists of three phases:

Phase 1: Carbon fixation of CO2 into organic molecules
● The product of the reaction is a six-carbon intermediate that is short-lived
because it is so energetically unstable that it immediately splits in half,
forming two molecules of 3-phosphoglycerate
Phase 2: Reduction
● Involves the reduction of 3-PGA to glyceraldehyde 3-phosphate (G3P)
● For every three molecules of CO2 that enter the cycle, there are six
molecules of G3P formed
Phase 3: Regeneration of the CO2 acceptor ribulose biphosphate or RuBP
● One molecule exits the cycle to be used by the plant cell, but the other five
molecules must be recycled to regenerate the three molecules of RuBP
● To accomplish this, the cycle spends three more molecules of ATP

PHOTOSYNTHESIS ● On hot, dry days, C3 plants close their stomata to conserve water, leading to
ALTERNATIVE photorespiration, which consumes ATP and releases CO2
MECHANISMS ● The C4 and CAM pathways are evolutionary solutions to this proble,
characterized by preliminary Co2 incorporation into organic acids before
transfer to the Calvin cycle
● C4 plants minimize the cost of photorespiration by incorporating CO2 into
four-carbon compounds in mesophyll cells. These compounds are exported
to bundle-sheath cells, where they releases carbon dioxide for use in the
Calvin cycle
● On the other hand, CAM or Crassulacean Acid Metabolism, open their
stomata at night. This incorporates CO2 into organic acids, which are stored
in mesophyll cells. During the day, the stomata close, and the CO2 is
released from the organic acids for use in the Calvin cycle

CELLULAR PROCESSES

CELLULAR Metabolism
PROCESSES ● Matter and energy transformation
● Free Energy change in spontaneous reaction
● ATP powers from exergonic and endergonic reactions
 ● Enzyme functions and regulations
Respiration
● Catabolic pathways
● Glycolysis
● Citric acid cycle
● Oxidative phosphorylation
● Fermentation and anaerobic respiration
● Other metabolic pathways
Photosynthesis
● Photosynthesis function and process
● Light reactions
● Calvin cycle
● Carbon fixation
Communication
● Signal conversion
● Signal reception
● Signal transduction
● Cellular response
● Apoptosis
Cell Cycle
● Cell division
● Mitotic phase
● Eukaryotic cell cycle regulation

METABOLISM ● The collection of chemical reactions that occur in an organism

● It is an emergent property of life that arises from orderly interactions
between molecules
● An organism’s metabolism transforms matter and energy

Metabolic Pathways
● Catabolic (breaking down molecules, releasing energy)
○ Cellular Respiration - breaking down glucose & organic fuels in the
presence of oxygen to carbon dioxide and water
● Anabolic (building molecules, consuming energy)
○ Amino acid synthesis
● Energy Forms
○ Kinetic - energy from moving objects
○ Thermal - energy from random molecular motion
○ Potential - energy from stored and can be released
○ Chemical - potential energy stored in the bonds between atoms
Laws of Thermodynamics
● 1st Law of Thermodynamics
○ Conservation of energy
○ Energy cannot be created nor destroyed, only transferred or
transformed
● 2nd Law of Thermodynamics
○ Spontaneous processes requiring no outside input of energy,
increase the entropy (molecular disorder) of the universe

Free-Energy
● Energy that can do work under cellular conditions
● Tells us whether r not the reaction occurs spontaneously
● The change in free energy (DG) is related directly to enthalpy change
(DH) and to the change in entropy (DS): ∆𝐺 = ∆𝐻 − 𝑇∆𝑆
● Spontaneous (exergonic) reactions release free energy (∆𝐺 < 0), while
 non-spontaneous (endergonic) reactions require energy input (∆𝐺 > 0)
● ∆𝐺 = 𝐺 𝑓𝑖𝑛𝑎𝑙 𝑠𝑡𝑎𝑡𝑒 − 𝐺 𝑖𝑛𝑖𝑡𝑖𝑎𝑙 𝑠𝑡𝑎𝑡𝑒
ATP
● The cell’s energy shuttle
● Powers cellular work by coupling exergonic reactions to endergonic
reactions
● ATP hydrolysis releases free energy when it is converted to ADP and
Phosphate ion
● This free energy drives endergonic reactions by transferring the phosphate
group to specific reactants, forming a phosphorylated intermediate that is
more reactive

Activation Energy (EA)

● The initial energy input required to initiate a chemical reaction
● At the peak of the barrier is the transition state of bond breakage
● The reaction releases more energy than it consumes, making it a favorable
or spontaneous process
Enzymes
● Speed up metabolic reactions by lowering energy barriers
● Act as catalysts, an agent that speeds up a reaction without being consumed
by the reaction
● Form an enzyme substrate complex with a specific reactant
● Binds to the substrate on a region called the active site
● Undergoes a slight confrontational change, an induced fit to enhance their
ability to catalyze the chemical reaction
● Mechanisms to lower activation energy
○ Bringing substrates together, can stretch or distort substrates,
provide a favorable environment
● Enzyme activity is affected by
○ Temperature and pH - reaction increases with increasing
temperature and at optimal pH
○ Cofactors - non protein helpers used for electron transfer
● Enzyme Inhibitors
○ Competitive Inhibitors - resemble the substrate molecule and
compete for binding to the enzyme’s active site
○ Noncompetitive Inhibitors - bind to another part of the enzyme
causing a conformational change and disrupting the active site
○ Toxins and Poisons - sarin, a nerve gas that binds covalently to an
enzyme in the nervous system
○ Antibiotics - penicillin blocks an enzyme for bacterial cell wall
synthesis
○ Allosteric Regulation - protein’s function at one site is affected by
the binding of a regulatory molecule to a separate site
○ Conformational Change - with two distinct conformations: active
and inactive. The binding of regulatory molecules induces a
conformational change between these sites
○ Activator and Inhibitor Effects - activators stabilize the active
conformation, increasing enzyme activity; inhibitors stabilize the
inactive conformation, reducing enzyme activity
○ Signal Amplification - the binding of a single regulatory molecule
can affect the activity of all subunits due to subunit interactions,
providing an amplification mechanism

Cooperativity
● The binding of a substrate molecules to one subunit can increase the
 affinity for substrates at other subunits, amplifying the enzyme’s response to
substrate concentration
Feedback Inhibition
● The end product of a metabolic pathway can act as an allosteric inhibitor of
an early enzyme in the pathway, preventing overproduction of the end
product