Navneeth Nalajala
BIO 131
October / November 2025
BIO 131
Test 3 Study Guide
Navneeth Nalajala
Test Date: Wednesday, November 5, 2025
Chapters covered:
• Chapter 10: Photosynthesis
• Chapter 11: Cell-Cell Interactions
• Chapter 12: The Cell Cycle
Special Features in this edition:
• Glossary included for quick reference. I’m placing it at the beginning for ease of
access.
• The N2 review is back!
Reminder: Make sure to review Mastering Biology for practice questions!
Good luck for Test 3 -Nav
Bio 131 Chapter 10 Glossary
Photosynthesis
Photosynthesis Overview
Action Spectrum — Wavelengths that drive
light-capturing reactions; peaks show most effective wavelengths for photosynthesis
Fluorescence — Excited electrons return to
ground state, releasing energy as light or heat
Chromatography — Technique separating
pigments based on solubility and size
Photosynthesis — Process converting light
energy into chemical energy; CO2 + H2 O +
Light −−→ (CH2 O)n + O2
Light-Capturing Reactions — Require light;
oxidize water → release O2 ; produce ATP and
NADPH
Calvin Cycle — Uses CO2 , ATP, and NADPH
from light reactions; reduces CO2 → carbohydrates; doesn’t require light directly
Photosystems
Photosystem — Large protein complex of
chlorophyll and accessory pigments in thylakoid
membrane
Antenna Pigments — Pigments that collect
light energy and transfer it via resonance to reaction center
Resonance Energy Transfer — Energy (not
electron) transfer between pigments; moves
from higher to lower energy
Reaction Center — Central pair of special
chlorophyll molecules that transfer excited electron to electron acceptor
Special Pair — Pair of chlorophyll molecules
in reaction center; P680 in PSII, P700 in PSI
Chloroplast Structure
Thylakoids — Flattened membranous sacs inside chloroplasts where light reactions occur
Grana — Interconnected stacks of thylakoids
Lumen — Space inside a thylakoid; site of proton accumulation
Stroma — Fluid-filled space between thylakoids and inner membrane; site of Calvin cycle
Light & Pigments
Photons — Discrete packets of electromagnetic radiation (light)
Pigments — Molecules that absorb certain
wavelengths of light; only see non-absorbed
wavelengths
Chlorophyll and — Primary pigments; absorb blue and red light; appear green; have
ring head (with Mg) that absorbs light and isoprenoid tail
Carotenoids
—
Accessory
pigments
(carotenes, xanthophylls); absorb blue/green
light; appear yellow/orange/red; protect
against UV damage
Absorption Spectrum — Measures how
wavelength influences amount of light absorbed
by a pigment
Photosystem II
Light-Harvesting Complex — Mobile accessory structure that transmits resonance energy
to antenna pigments
Pheophytin — Chlorophyll-like molecule lacking Mg; accepts electrons from PSII reaction
center
PQ
(Plastoquinone) — Lipid-soluble
quinone; transports electrons in thylakoid membrane; picks up protons from stroma, releases
in lumen
Cytochrome Complex — Oxidizes PQ; releases protons into lumen for ATP synthesis
Photophosphorylation — ATP synthesis in
chloroplasts initiated by light
1
Water Splitting — Reaction where water is
oxidized: 2 H2 O −−→ 4 H+ + 4 e – + O2 ; replaces
electrons in PSII
Oxygenic Photosynthesis — Oxidizes water
to generate O2
Anoxygenic Photosynthesis — Uses different electron donors (like H2 S); no oxygen produced
reduced
Rubisco — Ribulose-1,5-bisphosphate carboxylase/oxygenase; enzyme fixing CO2 in
Calvin cycle; most abundant enzyme on Earth
Photorespiration — Wasteful process when
rubisco reacts with O2 instead of CO2 ; consumes energy, releases fixed CO2
C4 & CAM Pathways
Photosystem I
C3 Pathway — Standard Calvin cycle; first
stable product is 3-carbon 3PGA
C4 Pathway — Extra fixation step before
Calvin cycle; fixes CO2 into 4-carbon compound; concentrates CO2 near rubisco
PEP Carboxylase — Enzyme fixing CO2 to
PEP in mesophyll cells; high affinity for CO2 ;
used in C4 pathway
Mesophyll Cells — Cells near leaf surface
where PEP carboxylase fixes CO2 in C4 plants
Bundle-Sheath Cells — Cells surrounding
vascular tissue where rubisco operates in C4
plants
Plasmodesmata — Channels connecting mesophyll and bundle-sheath cells
CAM
Plants — Crassulacean acid
metabolism; temporal separation of CO2 fixation; open stomata at night, fix CO2 ; release
CO2 during day for Calvin cycle
Ferredoxin — Protein that receives excited
electrons from PSI reaction center
Ferredoxin–NADP+ Reductase — Enzyme
transferring electrons and protons to convert
NADP+ to NADPH
NADPH — Electron carrier storing highenergy electrons for Calvin cycle
Plastocyanin (PC) — Protein linking PSII
and PSI; shuttles electrons through lumen; can
transfer 1000+ e- /sec
Electron Flow
Z-Scheme — Model linking PSII and PSI; electrons flow from water through both photosystems to NADP+
Noncyclic Electron Flow — Linear electron
path from H2 O to NADP+ ; produces ATP and
NADPH
Cyclic Electron Flow — Electrons from
PSI return to ETC; generates ATP but not
NADPH; provides extra ATP
Enhancement Effect — Combined red + blue
light produces greater response than sum of individual wavelengths
Calvin Cycle
3-Phosphoglycerate (3PGA) — 3-carbon
organic acid; first stable product after carbon
fixation
RuBP — Ribulose-1,5-bisphosphate; 5-carbon
molecule that reacts with CO2 in fixation phase
Fixation Phase — Calvin cycle phase where
CO2 reacts with RuBP → 2 molecules of 3PGA
Reduction Phase — Calvin cycle phase where
3PGA is phosphorylated by ATP and reduced
by NADPH → G3P
Regeneration Phase — Calvin cycle phase
using ATP to regenerate RuBP from G3P
G3P (Glyceraldehyde-3-Phosphate) —
Phosphorylated 3-carbon sugar; product of re-
Carbon Fixation
Stoma (pl. Stomata) — Leaf opening bordered by guard cells; allows CO2 in and O2 out
Guard Cells — Paired cells bordering stomatal pore
Carbon Fixation — Addition of carbon from
inorganic CO2 to organic compound; carbon is
2
duction phase; used to make glucose or regenerate RuBP
Gluconeogenesis — Process using G3P to
make glucose
Sucrose — Glucose + fructose; transportable
sugar synthesized in cytosol
Starch — Polymerized glucose; stored in
chloroplasts and roots; broken down at night
3
Bio 131 Chapter 11 Glossary
Cell-Cell Interactions
Extracellular Structures
rounding ECM fibers
Elastin — ECM protein allowing tissue expansion and contraction (e.g., in lungs)
Integrins — Membrane proteins binding to
ECM; anchor cells to extracellular components
Laminins — Extracellular cross-linking proteins; bind integrins to other ECM components
S-Layer — Dense coat of proteins on archaeal
cell surface; replaces peptidoglycan
Ground Substance — Stiff surrounding material in fiber composites; resists compression
Fiber Composite — Structural organization
with cross-linked filaments (resist tension) embedded in ground substance
Cell-Cell Connections
Plant Cell Walls
Multicellularity — Cells forming direct physical connections; basis of tissue structure
Epithelia — Tissues forming external and internal surfaces; function as barriers
Tight Junction — Cell-cell attachment with
specialized proteins that ”stitch” adjacent
membranes together; forms watertight seal
Desmosome — Strong cell-cell attachment in
epithelial and muscle cells; linking proteins connect membranes; anchored by intermediate filaments
Selective Adhesion — Characteristic where
cells adhere specifically to cells of same tissue
type
Cadherins — Linking proteins in desmosomes;
bind to same-type cadherins on adjacent cells
Primary Cell Wall — Initial fiber layer secreted by young plant cells; contains cellulose
microfibrils
Microfibrils — Cellulose strands bound together with H-bonds; form crisscrossed network
Pectins — Hydrophilic polysaccharides filling
spaces in microfibrils; attract water; keep cells
moist; made in rough ER
Turgor Pressure — Pressure inside cell from
water influx; drives cell expansion
Expansins — Proteins secreted by young
plants; disrupt H-bonds in microfibrils to loosen
wall structure
Secondary Cell Wall — Additional layer secreted as plants mature; composition varies by
cell function (e.g., wax for waterproofing)
Middle Lamella — Gelatinous pectins filling
extracellular space between adjacent plant cell
walls; degradation causes cell separation
Cell Communication
Gap Junctions — Protein channels connecting adjacent animal cells; allow rapid passage of
ions and small molecules
Plasmodesmata — Membrane-lined channels
connecting adjacent plant cells through cell
walls; plasma membrane and cytoplasm continuous; smooth ER tubules pass through
Hormones — Information-carrying molecules
secreted into fluids; act on distant target cells;
include peptides, steroids, gases
Signal Receptor — Protein that changes
shape and activity after binding to signaling
Animal Extracellular Matrix
Extracellular Matrix (ECM) — Fiber composite secreted by animal cells; more proteinrich than plant cell walls
Collagen — Glycoprotein forming fibrous component of ECM; most abundant ECM protein
Proteoglycans — Highly glycosylated proteins forming gel-like ground substance sur4
molecule
Type of enzyme-linked receptor; dimerizes upon
hormone binding; autophosphorylates at tyrosine residues
Ras — Single-unit G protein; lipid-anchored
membrane protein; activated by RTK bridge
proteins; triggers phosphorylation cascade
Phosphorylation Cascade — Sequence of
protein modifications where kinases activate
other kinases; culminates in cell response
Signal Processing
Signal Transduction — Process triggered
when signaling molecule binds at cell surface;
converts extracellular signal to intracellular response
G Proteins — Signal receptors spanning
plasma membrane; regulated by GTP/GDP; activated by signal receptor
Second Messenger — Small, nonprotein
signaling molecule produced by activated Gproteins; diffuses rapidly through cell
Protein Kinases — Enzymes that activate
other proteins by adding phosphate groups; often activated by second messengers
Enzyme-Linked Receptors — Receptors
that transduce signals by directly catalyzing reactions
Receptor Tyrosine Kinases (RTKs) —
Signal Regulation
Signal Deactivation — Mechanisms shutting
down signaling pathways; includes GTP hydrolysis, phosphatases, enzyme degradation
Crosstalk — Interactions among different signaling pathways; allows integration of multiple
signals; modifies cell response
Quorum Sensing — Use of signaling pathways
to respond to population density in prokaryotic/eukaryotic microbes
5
Chapter 12 Glossary
The Cell Cycle
Cell Structure & Replication
Telophase — Nuclear envelope reforms; chromosomes de-condense
Cytokinesis — Division of cytoplasm to form
two daughter cells
Chromatid — Each double-stranded DNA
copy in a replicated chromosome
Sister Chromatids — Identical chromatid
copies attached at the centromere
Centromere — Attachment point where sister
chromatids join
Chromatin — Complex of DNA and histone
proteins forming chromosomes
Kinetochore — Protein complex that attaches
to the centromere and binds microtubules
Cellular Structures
Spindle Apparatus — Structure of microtubules that moves and separates chromosomes
Microtubules — Cytoskeletal fibers made of
and tubulin dimers; part of spindle
Centrosome — Microtubule organizing center
(MTOC) containing a pair of centrioles
Centrioles — Paired cylindrical structures
within the centrosome
Cleavage Furrow — Indentation in animal
cells during cytokinesis formed by actin filaments
Cell Plate — Structure in plant cells where
new cell wall forms during cytokinesis
Cell Cycle Phases
M Phase — Phase when cells separate chromosomes; includes mitosis and cytokinesis
Interphase — Period between M phases; chromosomes uncoil, cell prepares to divide
S Phase — Synthesis phase during interphase
when DNA is replicated
G1 Phase — Gap 1 phase; cell growth before
DNA synthesis
G2 Phase — Gap 2 phase; cell growth after
DNA synthesis, before mitosis
G0 — Non-dividing state where cells are permanently stuck in G1
Regulatory Molecules
MPF — M-phase-promoting factor; cyclin-Cdk
dimer that triggers M phase
Cyclin — Regulatory protein whose concentration fluctuates during cell cycle
CDK — Cyclin-dependent kinase; enzyme active only when bound to cyclin
p53 Protein — Tumor suppressor that stops
cell cycle or induces apoptosis if DNA is damaged
Rb Protein — Retinoblastoma protein; inhibits E2F transcription factor at G1 checkpoint
E2F — Transcription factor that activates
genes needed for S phase
Ubiquitin — Protein tag marking cyclins for
degradation by proteasome
Mitosis Stages
Prophase — Chromatin condenses; spindle apparatus forms from microtubules
Prometaphase — Nuclear envelope disintegrates; microtubules attach to kinetochores
Metaphase — Chromosomes align on the
metaphase plate; equal pulling forces
Metaphase Plate — Imaginary plane where
chromosomes line up during metaphase
Anaphase — Sister chromatids separate and
move to opposite poles as microtubules shrink
6
Cell Cycle Control
Cancer & Division
Cell-Cycle Checkpoint — Control point
where regulatory molecules decide if cell proceeds with division
G1 Checkpoint — Major checkpoint determining if cell divides or enters G0 ; checks size,
nutrients, DNA integrity
G2 Checkpoint — Checkpoint ensuring all
DNA is replicated and undamaged before mitosis
Growth Factors — Small proteins that stimulate cell division by promoting passage through
G1 checkpoint
Binary Fission — Bacterial cell division process; similar to mitosis but without it
Cancer — Disease caused by uncontrolled cell
division due to checkpoint failure
Tumor — Mass of cells formed by continuous,
uncontrolled division
Benign Tumor — Noninvasive tumor that remains localized
Malignant Tumor — Invasive, metastatic tumor that spreads to other tissues
Metastasis — Migration of cancer cells from
primary tumor to form secondary tumors in new
tissues
7
Navneeth Nalajala
Bio 131
October god knows when, 2025
Bio 131 Notes
Chapter 10: Cellular Respiration
1
Photosynthesis
1.1
Photosynthesis Uses Sunlight
In photosynthesis, energy in sunlight is tranformed into chemical energy: C – O bonds in
CO2 are turned into C – C and C – H bonds of carbohydrates.
The overall reaction is CO2 + H2 O + Light Energy →
(CH2 O)n + O2
Remember this contrasts heavily from cellular respiration, which uses redox reactions to
produce CO2 and water from glucose and O2 . Photosynthesis uses redox reactions to produce
sugar and O2 from CO2 and H2 O.
Figure 1: Electron tranfer reduces and oxidizes products in photosynthesis
1.2
Photosynthesis as a Linked Set of 2 Reactions
Light-Capturing Reactions
Calvin Cycle
Require Light
Uses CO2 , ATP, and NADPH
from light reactions
Water is oxidized
O released.
Reduces CO2
2
Electrons elevated to high energy and used to form: ATP and
NADPH
carbohydrates
Does not require light directly,
but depends on products of light
reactions
Both sets depend on each other. Light reactions produce ATP and NADPH required by
the Calvin cycle. The Calvin cycle regenerates ADP, Pi , and NADP+ required by the light
reactions.
10.1
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1.3
Bio 131
October god knows when, 2025
Photosynthesis in Chloroplasts
A chloroplast is enclosed by an outer and inner membrane. The interior is dominated by
flattened. membranous sacs called thylakoids.
Grana interconnected stacks of thylakoids
Lumen space inside a thylakoid
Stroma fluid-filled space between the thylakoids and the inner membrane
Pigments molecules that absorb certain wavelengths of light1
The Nav Review
⋄ Photosynthesis: Converts sunlight
energy into chemical energy in C – C
and C – H bonds of carbohydrates.
⋄ Overall reaction: CO2 + H2 O +
Light Energy −−→ (CH2 O)n + O2
⋄ Chloroplast structure:
⋄ Contrast with respiration: Photosynthesis makes sugar and O2 from
CO2 and H2 O; respiration breaks
down sugar to make CO2 and water.
⋄ Thylakoids: Flattened membranous sacs.
⋄ Two linked reactions:
⋄ Lumen: Inside thylakoids.
⋄ Light reactions:
Require
light, oxidize water
O2 , produce ATP and NADPH.
⋄ Calvin
1
ATP/NADPH from light reactions, reduces CO2
carbohydrates, regenerates ADP, Pi,
NADP+.
cycle:
Uses
we only see the wavelengths not absorbed
10.2
⋄ Grana: Stacked thylakoids.
⋄ Stroma: Fluid between thylakoids and inner membrane.
⋄ Pigments: Absorb specific
wavelengths of light.
Navneeth Nalajala
Bio 131
October god knows when, 2025
2
Pigments Capturing Light Energy
2.1
Electromagnetic Radiation
⋄ Light is a type of electromagnetic radiation
⋄ Can be wavelike and particle-like.
⋄ Light exists in discrete packets called photons
2.2
Pigments
Sunlight includes all wavelengths in the visible portion of the electromagnetic spectrum.
When a photon strikes an object, the photon can be absorbed, transmitted, or reflected.
2.2.1
Chromatography
Separates pigments in an extract.
Figure 2: Chromatography example
1. Spots of raw extact are placed on the bottom of support that is coated in a thin layer
of silica gel, cellulose, or similar porus material.
2. Coated support is placed in a covalent solution.
3. As the solvent moves upward, it carries the pigment molecules with it.
4. the variability in size and/or solubility of pigment molecules carries them at different
rates.
5. Researchers cut out a single region of the porous meterial, extract the pigment, and
then use a spectrophotometer to record the wavelengths absorbed.
10.3
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2.2.2
Bio 131
October god knows when, 2025
Absorbing Different Wavelengths
Chlorophylls
Carotenoids
Absorb blue and red regions of
the spectrum
Absorb wavelengths in the blue
and green parts of the spectrum
Makes plants look gree
Appear yellow, orange, or red
called chlorophyll α and β
Found in plants as carotenes and
xanthophylls
Action spectrum for photosynthesis are the wavelengths that drive the light-capturing
reactions. Engelmann2 found that violet-to-blue and red light are the most effective for
photosynthesis.
Absorption spectrum measures how the wavelength of photons influences the amount of
light aborbed by a pigment.On the graph below, peaks are wavelengths where absorbance/photosynthetic
activity is high, and vice versa for the troughs.
Figure 3: Strong correlation between abosrption spectra and action spectrum
2.2.3
Parts of the Pigment
⋄ Chlorophyll α and β are similar and structure
⋄ Both have 2 parts: a long isoprenoid ”tail” and a ”head” which is a large ring structure
with a magnesium atom in the middle.
⋄ The trail interacts with proteins embedded in the thylakoid membrane; the head is
where the light is absorbed.
2
scientist that ran experiments on photosynthesis in algae
10.4
Navneeth Nalajala
Bio 131
October god knows when, 2025
Figure 4: Structure of pigments
2.3
Carotenoids
Carotenoids are called accessory pigments because they absorb light and pass the energy on
to chlorophyll. Both xanthophylls and carotenes3 are found in chloroplasts.
⋄ In fall, where the leaves of deciduous trees die, their chlorophyll degrades first, leaving
carotenoids show in the color of leaves.
⋄ The variation in color shows how these accessory pigments can extend the range of
wavelengths to drive photosynthesis (aside from wavelengths absorbed by chlorophyll)
⋄ Many herbicides work by inhibiting enzymes that are involved with carotenoid synthesis.
⋄ Plants without carotenoids rapidly lose their chlorophyll, turn white, and die.
⋄ The primary function of carotenoids is to protect the plant.
High-energy ultraviolet photons can knock electrons from
atoms, forming free radicals that damage molecules.
Carotenoids protect plants by stabilizing these radicals;
without them, chlorophyll would be destroyed.
2.4
Electrons During Light Absorption
⋄ When a chlorophyll molecule absorbs a photon, the photon’s energy is transferred to
the bonds in the chlorophyll molecule’s head region.
⋄ In response an electron bumps up to a higher energy state.
3
Both of these are types of carotenoids
10.5
Navneeth Nalajala
Bio 131
October god knows when, 2025
⋄ the states are incremental rather than continuous. The levels are a property of electron
configuration in a particular pigment.
Figure 5: Possible energy states of electrons in chlorophyll
The image shows how chlorophyll can absorb red/blue photons. All the energy from the
photon is directly turned into the energy state. There is not a state of energy that
directly corresponds to the energy from a green photon. Thus, it is not absorbed.
A quick note about fluorescence: Ultraviolet light can eject electrons and form free radicals,
while infrared light mainly produces heat. When pigments absorb photons with the right
energy, electrons become excited but quickly return to the ground state, releasing energy as
heat or light (fluorescence). In chloroplasts, most excited electrons drive photosynthesis;
only a few cause fluorescence.
2.5
Photosystems
Chlorophyll molecules in the thylakoid membrane function as groups, not individually.
They, along with accessory pigments, form large protein complexes called photosystems.
Most pigments act as antenna pigments that collect light and direct energy toward a
central reaction center.
2.5.1
Antenna Pigments and Resonance Energy Transfer
⋄ When an antenna pigment absorbs a photon, the energy-not the electron-is transferred to a nearby pigment.
⋄ This is called resonance energy transfer.
⋄ Energy moves only between pigments that absorb different wavelengths, always
from higher to lower energy photons.
10.6
Navneeth Nalajala
Bio 131
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⋄ Proteins organize pigments to tune their absorption range and ensure energy moves
efficiently.
⋄ As energy transfers, potential energy decreases, and the original excited electron
returns to the ground state.
⋄ This energy transfer is like a wave of excitement that moves through pigments toward
the reaction center.
2.5.2
The Reaction Center
⋄ When energy reaches the reaction center, it is absorbed by a pair of special chlorophyll
molecules(called the special pair).
⋄ These molecules transfer an excited electron to an electron acceptor.
⋄ The acceptor becomes reduced (gains energy), marking the conversion of light energy to chemical energy.
⋄ In darkness, this redox step cannot occur—it is endergonic.
⋄ When light excites the electron, the reaction becomes exergonic, making the electron
transfer spontaneous.
2.5.3
Four Possible Fates of Excited Electrons
⋄ Fluorescence: Electron falls back to ground state, releasing light and/or heat.
⋄ Heat: Energy is lost purely as thermal motion.
⋄ Resonance: Energy excites a nearby pigment (common in antenna pigments).
⋄ Redox: Electron is transferred to an electron acceptor (in reaction centers).
Figure 6: Four fates for excited electrons in photosynthetic pigments
10.7
Navneeth Nalajala
Bio 131
October god knows when, 2025
The Nav Review
⋄ Electromagnetic
radiation:
Light behaves as waves and particles; exists as photons.
⋄ Green photons not absorbed;
UV can cause radicals; infrared
mainly produces heat.
⋄ Pigments: Molecules that absorb
certain wavelengths; sunlight can be
absorbed, transmitted, or reflected.
⋄ Fluorescence occurs when energy is released as light/heat.
⋄ Chromatography: Separates pigments based on solubility and size;
absorbance measured with spectrophotometer.
⋄ Photosystems: Groups of chlorophyll + accessory pigments forming
protein complexes in thylakoid membrane.
⋄ Chlorophylls:
⋄ α and β absorb blue and red
light; appear green.
⋄ Structure: head (ring + Mg,
absorbs light) + tail (interacts
with thylakoid proteins).
⋄ Carotenoids:
⋄ Accessory pigments (xanthophylls, carotenes);
absorb
blue/green light.
⋄ Extend usable light range, protect against UV-induced free
radicals.
⋄ Responsible for fall leaf colors
when chlorophyll degrades.
⋄ Electron excitation: Photon absorption raises electron to higher energy state; states are discrete.
10.8
⋄ Antenna pigments: Collect
light; energy transferred via
resonance energy transfer.
⋄ Reaction center:
Special
pair chlorophylls transfer excited electron to acceptor, converting light
chemical energy.
⋄ Fates of excited electrons:
⋄ Fluorescence: electron returns,
releasing light/heat.
⋄ Heat: lost as thermal energy.
⋄ Resonance: excites nearby pigment.
⋄ Redox: transferred to electron
acceptor (reaction center).
Navneeth Nalajala
3
Bio 131
October god knows when, 2025
Discovery of Photosystems I and II
I want to preface with a quick note about the enhancement effect. Robert Emerson found
that the combined response to both blue and red light is greater than the individual sums.
After some time it was discovered that there are two types of reaction centers, each absorbing
different wavelengths of light. This is the case for cyanobacteria and the chloroplasts of
eukaryotes.
3.1
How Does Photosystem II Work?
⋄ Begins with a mobile accessory structure called the light-harvesting complex which
transmits resonance energy to an antenna pigment inside the photosystem.
⋄ The antenna pigments transfer energy to the pair of pigments in the reaction center4 .
⋄ Pheophytin comes into play at this point5 . Unlike other pigments, does not get
excited by photons.
⋄ It procedes to accept excited electrons by taking from the reaction center special pair.
The redox reaction between pheophytin and the special pair is a key step.
⋄ After the transfer, the oxidized6 special pair becomes a strong electron acceptor.
⋄ The electron is not pulled back by the special pair because it is quickly shuttled away
by a quinone molecule to an ETC. Thylakoid ETC is similar to mitochondrial ETC.
Figure 7: Photosystem II. Quinone molecule is identified as PQ in this case.
4
If you are confused, refer back to section 2.5
Structurally identical to chlorophyll except for that it lacks a magnesium atom in the head
6
oxidized because it donates the electron to pheophytin
5
10.9
Navneeth Nalajala
3.1.1
Bio 131
October god knows when, 2025
More on Photosystem II
Figure 8: Photosystem II. Quinone molecule is identified as PQ in this case.
⋄ PQ is a quinone that is lipid soluble (can freely move in the thylakoid membrane) to
transport electrons.
⋄ The cytochrome complex oxidizes the PQ to release protons into the thylakoid lumen
for ATP synthesis.
⋄ PQ also picks up protons when reduced. These protons are pulled from the chloroplast
stroma. After being oxidized by the cytochrome complex, PQ drops off the protons in
the thylakoid lumen.
⋄ pH in the thylakoid is less compared to the stroma.
The rest of the photosystem II follows the ETC and ATP synthase of mitochondria. Since the
synthesis of ATP in chloroplasts is initiated by light, it is called photophosphorylation.
Similar to oxidative phosphorylation in plant and animal mitochondria, but here the ATP
will remain within the organelle and is used to produce carbohydrate.
3.2
The Replacement of Electrons in the ETC
Photosystem II obtains electrons by oxidizing water.
From the simplified overall reaction:
CO2 + H2 O + Light Energy −−→ (CH2 O)n + O2
We know that the atoms of O2 come from H2 O. This reaction7 can be written as:
2 H2 O −−→ 4 H+ + 4 e – + O2
7
Also called the ”splitting of water”
10.10
Navneeth Nalajala
Bio 131
October god knows when, 2025
Since oxygen is very electronegative, the reaction is highly endergonic.
The energy to oxidize water comes from photosystem II. When excited electrons are removed
from the special pair, the redox potential of the oxidized pigments is so strong that it can
pull electrons from water.
3.3
Oxygenic Photosynthesis
Anoxygenic Photosynthesis
Oxidize water to generate O2
Use different electron donors
(H2 S)
Produce oxygen
No oxygen produced
How Photosystem I Works
⋄ Heliobacteria, like purple bacteria,8 have a single photosystem that uses sunlight to
excite electrons to high energy levels.
⋄ Instead of sending these electrons through an electron transport chain to pump protons,
heliobacteria use them directly to reduce NAD+ to NADH:
NAD+ + 2 e− + H+ −−→ NADH
⋄ In cyanobacteria and chloroplasts, a similar process occurs—but instead of NAD+ ,
the molecule NADP+ is reduced to form NADPH.
⋄ Both NADH and NADPH are electron carriers: they store energy by holding
high-energy electrons that can later power other reactions.
Figure 9: Photosystem I produces NADPH
8
These bacteria have only one photosystem.
10.11
Navneeth Nalajala
3.3.1
Bio 131
October god knows when, 2025
Steps of Photosystem I in Chloroplasts
1. Antenna pigments absorb photons (light energy) and transfer that energy to the
reaction center in Photosystem I.
2. The reaction center chlorophylls use this energy to excite two electrons—one for each
absorbed photon.
3. The excited electrons leave the reaction center and move through a series of carriers,
eventually reaching a protein called ferredoxin.
4. The enzyme ferredoxin–NADP+ reductase then transfers the two electrons and
one proton to convert NADP+ into NADPH:
NADP+ + 2 e− + H+ −−→ NADPH
In summary: Photosystem I uses light energy to produce NADPH, a molecule that carries
the electrons needed to build sugars in later stages of photosynthesis.
3.4
The Z Scheme: Photosystem II and I working together
Figure 10: The Z scheme model links photosystems I and II.
1. Process starts with photons exciting electrons in photosystem II’s antenna pigments.
2. The special pair, each molecule called P6809 , passes excited electrons to pheophytin.
3. Note the equation at the bottom of photosystem II that shows how electrons are
replaced. The H+ ions contribute to the electrochemical gradient.
4. The 4 electrons are transferred down the ETC (first diagonal line). Electrons are
stepped down in potential energy through redox reactions.
9
the name P680 represents the optimal wavelength absorbed-680 nm
10.12
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Bio 131
October god knows when, 2025
5. Each reduced ”PQ” picks up protons from the stroma and transfes them to teh lumen
after being oxidized by the cytochrome-complex.
6. ATP synthase uses the proton force to make ATP.
7. When electrons reach the end of the cytochrome complex, they are passed to the
protein plastocyanin ”PC”.
8. Each reduced PC diffuses through the lumen of the thylakoid and donates one electron
to an oxidized reaction center pigment in photosystem I.
⋄ Plastocyanin forms a link between each system.
⋄ A single PC can shuttle over 1000 electrons/sec
⋄ It replaces electrons that are carried away from the special pair of pigments in
the photosystem I reaction center.
⋄ The special pair here is called P700.
9. Electrons that flow into P700 are excited and transferred to the protein ferredoxin,
which passes electrons to catalyze reduction of NADP+ to NADPH.
10. Note: for each O2 molecule produced by photosystem II, 4 electrons have been tranferred along the Z scheme to make 2 NADPH.
3.5
The Enhancement Effect
When chloroplasts are only illuminated with the red portion of the spectrum, only photosystem II can run at a maximum rate.
Photosystem I’s efficiency is reduced and this leads to a lower rate of electron flow. The
same is true for wavelengths in the far-red portion with the efficiencies flipped.
But when both wavelengths are available at the same time, both photosystems work at a
maximum rate.
3.6
Noncyclic Electron Flow between Water and NADP+
Figure 11: Complete path of electrons from photosystem II to photosystem I
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Electrons that pass from water to NADP+ move through a chain of redox reactions in a
linear fashion, referred to as noncyclic electron flow.
⋄ In both mitochondria and chloroplasts, redox reactiosn are used to build a proton
gradient for ATP production.
⋄ In mitochondrial ETC, electron potential energy starts high and then steadily drops
as electrons are transfered to the terminal electron acceptor, which has the lowest
potential energy.
⋄ In chloroplasts, the electron donor (H2 O) has much lower potential energy than the
reduced terminal electron acceptor(NADPH).
3.7
Cyclic Electron Flow
Recent evidence indicates and alternative path called cyclic electron flow (occurs in green
algae and land plants). ATP is produced in both cyclic and non-cyclic photophosphorylation.
Figure 12: Alternative to the Z scheme.
In cyclic electron flow:
⋄ Electrons excited in photosystem I are transferred back to the ETC, generating ATP
through photophosphorylation instead of reducing NADP+ .
⋄ Cyclic electron flow coexists with noncyclic electron flow and produces additional ATP.
10.14
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A Quick Note On Oxygen
The importance of O2 cannot be overstated. In cells, O2 is so electronegative that it creates
a huge potential energy drop for the ETCs involved in cellular respiration.
So, organisms that use O2 as an electron acceptor can produce ATP more efficiently.
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⋄ Enhancement effect: Combined
blue + red light excites both photosystems, giving higher electron flow
than individual wavelengths.
⋄ Photosystem II (PSII):
⋄ Light-harvesting complex
antenna pigments
reaction
center (special pair).
⋄ Pheophytin accepts electrons
from special pair.
⋄ Electrons shuttled to PQ
cytochrome complex
thylakoid lumen (protons pumped
for ATP).
⋄ Water is oxidized
electrons
replace those in PSII, releasing
O2 .
⋄ Photophosphorylation
produces ATP.
⋄ Photosystem I (PSI):
⋄ Antenna pigments absorb light
reaction center P700.
⋄ Electrons excited
ferre+
doxin
NADP reduced to
NADPH.
⋄ NADPH stores high-energy
electrons for sugar synthesis.
⋄ 4 electrons from 2 water
molecules
2 NADPH, 1 O2 .
⋄ Oxygenic vs. anoxygenic photosynthesis:
⋄ Oxygenic: water oxidized
produced.
O
2
⋄ Anoxygenic:
other electron
donors (H2 S), no O2 produced.
⋄ Noncyclic electron flow:
⋄ Electrons flow linearly from
H2 O
NADP+ .
⋄ Produces ATP + NADPH.
⋄ Redox reactions establish proton gradient for ATP synthase.
⋄ Cyclic electron flow:
⋄ Electrons from PSI
ATP, not NADPH.
ETC ⋄ Coexists with noncyclic flow;
produces extra ATP.
⋄ Oxygen in bioenergetics:
⋄ Z-scheme:
⋄ PSII electrons
PC
PSI
+
NADP .
⋄ Plastocyanin links PSII and
PSI; each PC can shuttle 1000
e− /sec.
ETC ATP
ferredoxin 10.15
⋄ Highly electronegative; allows
efficient ATP production in respiration.
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How do Cells Capture CO2?
CO2 cannot diffuse directly into plants because of a waxy coating called a cuticle. This layer
prevents water from evaporating out of tissues but also prevents gases from leaving.
⋄ The surface of a lead is dotted with openings bordered by two distinctively shaped
cells called guard cells.
⋄ The opening between these paired cells is called a pore.
⋄ The entire structure is called a stoma (plural: stomata)
⋄ An open stoma allows CO2 to diffuse into air-filled spaces and excess O2 to diffuse out.
4.1
The Calvin Cycle Fixes Carbon
Carbon fixation is the addition of carbon atoms from inorganic carbon dioxide to an
organic compound.
⋄ Carbon fixation is a redox reaction. The carbon atom in CO2 is reduced.
4.2
Rubisco
All photosynthetic organisms that use the Calvin cyle to fix carbon require the CO2 -fixing
enzyme ribulose-1,5 biphosphate carboxylase/oxygenase (commonly called rubisco).
⋄ The rubsico enzyme is roughly cube-shaped and has 16 polypeptides that form 8 active
sites to fix CO2 .
⋄ Fun fact: Thought to be the most abundant enzyme on earth.
⋄ Oxygen and CO2 compete at the enzyme’s active sites, which slows the rate of CO2
reduction.
Figure 13: Rubisco can react with CO2 or O2 .
Photorespiration is the reaction sequence that resembles respiration, because it consumes
oxygen and produces carbon dioxide.
Because photorespiration requires energy and releases fixed CO2 , it undoes photosynthesis.
Some of products from photorespiration are involved in plant signaling and development.
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The C4 Pathway
Researchers found a 4-carbon compound rather than a 3-carbon one. This new set of reactions is called the C4 pathway, different from Calvin’s C3 pathway.
Figure 14: C4 plants fix carbon twice: first into a four-carbon compound, then into a
three-carbon compound via the Calvin cycle.
4.4
Two Pathways in Two Cell Types
The C4 pathway does not replace the Calvin cycle; it adds an extra fixation step. C4 plants
fix CO2 in two ways:
⋄ By PEP carboxylase in mesophyll cells near the surface of leaves.
⋄ By rubisco in bundle-sheath cells surrounding the vascular tissue.
Vascular tissue transports water and nutrients, while the two cell types10 coordinate to make
photosynthesis more efficient.
4.4.1
Steps of the C4 Pathway (Hatch–Slack Model)
Hal Hatch and Roger Slack proposed a four-step model explaining how CO2 fixed into a
four-carbon compound is later released to feed the Calvin cycle:
1. Carbon Fixation in Mesophyll Cells: PEP carboxylase fixes CO2 to phosphoenolpyruvate (PEP), a three-carbon molecule:
PEP carboxylase
PEP + CO2 −−−−−−−−−→ Oxaloacetate (4 C)
2. Transport: The resulting four-carbon molecules are transported to bundle-sheath
cells through channels called plasmodesmata.
3. CO2 Release: The four-carbon molecules are oxidized to release CO2 . Because
bundle-sheath cells are less permeable to gases, CO2 concentrations increase, promoting
carbon fixation by rubisco to form 3PGA and start the Calvin cycle.
4. Regeneration: The remaining three-carbon compound returns to the mesophyll cell,
where it is used to regenerate PEP, completing the cycle.
10
mesophyll and bundle-sheath
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Figure 15: Rubisco can react with CO2 or O2 .
4.4.2
Purpose and Efficiency
⋄ The C4 pathway acts as a CO2 concentrator. It increases the ratio of CO2 to O2
near rubisco, reducing photorespiration and improving Calvin cycle efficiency.
⋄ PEP carboxylase has a much higher affinity for CO2 than rubisco, allowing C4 plants
to fix carbon efficiently even with limited gas exchange.
C4 photosynthesis is an evolutionary adaptation that helps plants like maize and sugarcane
thrive in hot, dry climates.
4.5
CAM Plants
CAM stands for crassulacean acid metabolism and resembles the C4 pathway in some ways.
It’s goal is to limit the effects of dehydration.
⋄ Similar in most aspects, but occurs at a different time.
⋄ CAM occurs in cacti and other species that keep their stomata closed during the day.
⋄ At night, when it is cooler and more humid, CAM plants open their stomata and take
in large quantities of CO2 .
⋄ The CO2 is temporarily fixed into organic acids and stored in central vacuoles of the
cells.
⋄ During the day the acids are processed in reactions that release the CO2 and feed the
calvin cycle.
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Figure 16: CAM plants
C4 plants stockpile CO2 by fixing and storing organic acids where rubisco is not active, CAM
plants store CO2 when rubisco is inactive. This is a separation of space vs. time.
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⋄ Stomata:
⋄ Leaf openings bordered by
guard cells.
⋄ Opening = pore; whole structure = stoma (pl. stomata).
⋄ C4 Pathway Steps (Hatch–Slack
Model):
1. PEP carboxylase fixes CO2
oxaloacetate (4C).
⋄ CO2 diffuses in; O2 diffuses out.
2. 4C compounds transported to
bundle-sheath cells via plasmodesmata.
⋄ Carbon Fixation / Calvin Cycle:
3. CO2 released
rubisco fixes
carbon (3PGA).
⋄ CO2 added to organic compounds; carbon is reduced.
4. Remaining 3C returns to mesophyll
regenerate PEP.
⋄ Requires rubisco (16 polypeptides, 8 active sites).
⋄ Rubisco reacts with O2
photorespiration, which wastes
energy and CO2 .
⋄ C3 vs. C4 Pathway:
⋄ PEP carboxylase:
⋄ High affinity for CO2 , efficient
even with low gas exchange.
⋄ CAM Plants:
⋄ Temporal separation of CO2
fixation.
⋄ C3 = Calvin cycle.
⋄ C4 = extra step fixes CO2 into
4C compound in mesophyll
cells via PEP carboxylase,
transported to bundle-sheath
cells
rubisco uses CO2 for
Calvin cycle.
⋄ Reduces photorespiration; acts
as CO2 concentrator.
10.19
⋄ Open stomata at night
fix
CO2 into organic acids stored in
vacuoles.
⋄ During day release CO2 from
acids
feed Calvin cycle.
⋄ Space vs. time strategy: C4
separates where, CAM separates when rubisco is active.
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5
Captured CO2 is Reduced to Make Sugar
5.1
3-Step Process of the Calvin Cycle
3-phosphoglycerate(3-Carbon oganic acid) is the first stable product formed after carbon
fixation. It is also one of the 10 intermediates in glycolysis.
Figure 17: Number of reactants and products resulting from three turns.
Of the 6 G3Ps made in the reduction phase, 1 is used to make other molecules while the
other 5 are used to regenerate 3x RuBP.
The complete Calvin Cycle has 3 phases:
1. Fixation phase The Calvin cycle begins when CO2 reacts with RuBP. It fixes carbon
and makes 2x of 3PGA11 .
2. Reduction phase The 3PGA is phosphorylated by ATP and then reduced by accepting electrons from the NADPH as the phosphate is removed. Results in a phosphorylated 3-carbon sugar glyceraldehyde-3-phosphate (G3P). Some of the G3P that is
synthesized is drawn off to make other molecules like glucose.
3. Regeneration phase The rest of the G3P keeps the cycle going by being a substrate
for the third phase in the cycle: reactions that use ATP to make more RuBP.
⋄ All three phases take place in the stroma of chloroplasts.
⋄ 3 turns fix 3x of CO2 .
⋄ Each mole of CO2 requires energy from 3 moles of ATP and 2 moles fo NADPH to fix
and reduce to sugar.
11
3-phosphoglycerate (a 3 carbon organic acid)
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Regulation of Photosynthesis
⋄ The presence of light triggers proteins for photosynthesis.
⋄ When sugar levels are high, the production of proteins needed for photosynthesis is
inhibited, but the production of proteins to process/store sugar is stimulated.
⋄ Rubsico is activated by regulatory molecules that are produced when light is available,
but limited in conditions of low CO2 availability-photorespiration is favored.
5.3
The Sugars of Photosynthesis
The products of the Calvin cycle go through several reaction pathways to produce every
molecule needed. One of these sequences uses G3P to make a monosaccharide glucose. This
process is called gluconeogenesis. Often combined with fructose(also made from G3P) to
make sucrose.
If photosynthesis is rapid and sucrose is abundant, glucose is polymerized to make starch,
which is stored in the cells of leaves and roots. Starch production takes place inside chloroplasts; sucrose synthesis takes place in the cytosol. At night, the starch is broken down into
glucose to sustain the plant.
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The Nav Review
⋄ Calvin Cycle Overview:
⋄ Fixes CO2
produces sugar in
chloroplast stroma.
⋄ 3 phases: Fixation, Reduction, Regeneration.
⋄ 3 turns of the cycle fix 3 CO2 ;
each CO2 uses 3 ATP + 2
NADPH.
⋄ Fixation Phase:
⋄ CO2
reacts with RuBP
2
molecules
of
3phosphoglycerate (3PGA).
⋄ ATP used to regenerate RuBP
from remaining G3P
cycle
continues.
⋄ Sugar Products:
⋄ G3P
glucose (via gluconeogenesis).
⋄ Glucose + fructose
sucrose
(transportable sugar).
⋄ Excess glucose starch (stored
in chloroplasts; broken down at
night).
⋄ Regulation:
⋄ Reduction Phase:
⋄ 3PGA
phosphorylated
by
ATP, reduced by NADPH
glyceraldehyde-3-phosphate
(G3P).
⋄ 1 G3P used for biosynthesis
(glucose, sucrose), 5 G3P used
to regenerate RuBP.
⋄ Regeneration Phase:
⋄ Light triggers production of
photosynthesis proteins.
⋄ High sugar
inhibits photosynthesis protein production, stimulates sugar processing/storage proteins.
⋄ Rubisco activated in light; limited CO2 favors photorespiration.
Last updated: 2025/11/01 13:35:59 -04’00’
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Bio 131 Notes
Chapter 11: Cell-Cell Interactions
1
The Cell Surface
1.1
The Structure and Function of the Extracellular Layer
Rarely are cells bounded by just the plasma membrane. Most cells secrete products that are
assembled beyond the membrane.
⋄ The structure of the cell walls around prokaryotic cells is very different compared to
bacteria and archaea.
⋄ In bacteria, cell walls are made of peptidoglycan1 .
⋄ Archaea cell walls are not unified but they all lack peptidoglycan.
⋄ Often, archaea cell walls are made as a dense coat of proteins on the surface of the cell,
called an S-layer.
⋄ In contrast, all types of extracellular layers in eukaryotes have the same level of organization.
⋄ These are fiber composites: have a cross-linked network of long filaments embedded in
a stuff surrounding material called a ground substance.
⋄ The rods/filaments are effective at withstanding tension. Functionally similar ot
steel rods in reinforced concrete.
⋄ The stiff ground substance is effective at withstanding compression.
1.2
The Cell Wall in Plants
1.2.1
Primary Cell Walls
When plants first form, they secrete an initial fiber called a primary cell wall.
⋄ The fibrous component of the cell wall consists of long strands of cellulose.
⋄ These strands are bound into microfibrils, which are cross-linked with H-bonds to
other filaments.
⋄ Microfibrils are synthesized directly into the extracellular space by a complex of enzymes, where they form a crisscrossed network.
⋄ The spaces in microfibrils are filled with polysaccharides such as pectins2 . Because
these are hydrophillic, they attract and hold water to keep cells moist.
1
2
We talked about this for Test 1
used to thicken jams actually
11.1
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⋄ Pectins are made in the rough ER and are secreted into the extracellular space.
Figure 1: Cell walls in plants are fiber composites
⋄ Normally, the concentration of the solute is higher inside the cell than outside, so water
increases the volume.
⋄ This turgor pressure pressurizes the inside of the cell.
⋄ Young plants excrete expansins into their cell wall.
⋄ These disrupt the H-bond in the cross link of microfibrils to loosen the structure.
⋄ Turgor pressure forces the wall to grow longer and basically allow for cell growth.
1.2.2
Secondary Cell Walls
⋄ As plants mature, they secrete an additional layer of material, called a secondary cell
wall.
⋄ Makeup varies between cells and correlates with function.
⋄ For example, cells on the surface of the lead have a secondary cell wall of waxes to be
waterproof.
Figure 2: The two cell wall layers
11.2
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1.3
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Extracellular Matrix in Animals
Most animal cells secrete a fiber composite called a extracellular matrix (ECM).
⋄ ECM organization follows the same principles as the cell walls. However, animal ECM
is more protein relative to carbohydrate than a cell wall.
⋄ The fibrous component is mostly made of glycoproteins called collagen.
⋄ Most ECM proteins go outside the cell through exocytosis.
⋄ The ground substance that surrounds collagen and other fibrous components of the
ECM is called proteoglycans.
⋄ These are highly glycosylated and form gel.
⋄ For example, the ECM around cells in our lungs has large amounts of elastin to allow
the ECM to expand and contract3
⋄ Collagen and other ECM proteins support cell structure through their attachments.
⋄ Membrane proteins called integrins bind to extracellular cross linking proteins called
laminins 4 which bind other components of the ECM.
⋄ Anchorage to the ECM makes sure cells are in the right place and is extremely important.
The Nav Review
⋄ Extracellular layers: Most cells
are surrounded by secreted layers beyond the plasma membrane.
⋄ Prokaryotic cell walls:
⋄ Bacteria: made of peptidoglycan.
⋄ Archaea: lack peptidoglycan;
often have an S-layer protein
coat.
⋄ Eukaryotic extracellular layers:
Fiber composites = filaments (resist
tension) + ground substance (resist
compression).
⋄ Plant cell walls:
⋄ Primary: cellulose microfibrils
3
4
remember structure=function!
Don’t mix laminins with lamins from the nucleus
11.3
crosslinked with H-bonds; filled
with pectins for hydration.
⋄ Secondary: added later; composition varies by cell function
(e.g., wax for waterproofing).
⋄ Turgor pressure + expansins
enable wall stretching and
growth.
⋄ Animal ECM:
⋄ Fibrous proteins (mainly collagen) + proteoglycan gel.
⋄ Supports cell structure and location through integrins and
laminins.
⋄ Elastic ECM (e.g., lungs) allows expansion/contraction.
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How do Adjacent Cells Connect and Communicate?
Direct physical connections between cells are the basis of multicelluarity. These connections, along with the ECM, maintain the structure and function of tissues.
2.1
Cell-Cell Attachments in Multicellular Organisms
Materials that bind cells together are important in epithelia, which are tissues that form
external and internal surfaces. Epithelia function as barriers between internal and external
environments.
2.1.1
Indirect Cell-Cell Attachments
The extracellular space in the walls of adjacent plant cells is full of gelatinous pectins called
the middle lamella. If enzymes degrade the middle lamella, it can cause cells to separate,
just like when leaves detach and fall.
In contrast to indirect intercellular connections through integrins and the ECM, several
membrane proteins allow for direct cell-cell attachments in epithelia
Figure 3: The structures in cell-cell adhesion
2.2
Tight Junctions Make Waterproof Seals
A tight juntion is a cell-cell attachment composed of specialized proteins in the plasma
membranes of animal cells.
⋄ Long chains of this protein form on the surface of the cell and attach to the same
protein on adjacent cell.
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⋄ The right interactions will pull the membranes close together5
⋄ This forms a watertight seal.
⋄ Commonly found in cells that form a barrier. Ex: the epithelial cells that line the
stomach.
⋄ Can be dynamic and used for different purposes.
2.3
Desmosomes Make Secure Adhesions
A desmosome is a strong cell-cell attachment that is common in animal epithelial and
muscle cells. Could be likened to the rivets that hold sheet metal together.
Figure 4: Linking components of desmosomes
⋄ Comprise of linking proteins and cytosilic anchoring proteins.
⋄ The proteins span the membrane and connect adjacent cells and their anchoring proteins.
⋄ Cytoskeletal intermediate filaments help reinforce desmosomes by attaching to the
intracellular anchoring proteins.
2.4
Cell-Cell Adhesions Are Selective
Selective adhesion is the characteristic of a cell to adhere to cells of the same tissue type.
The concept of cell-cell adhesion proteins was discovered through experiments on antibodies.
Cadherins are the linking proteins in desmosomes. Each cadherin can bind to cadherins
of the same type- this ensures that cells of the same tissue type attach specifically to one
another.
2.5
Cells Communicate via Cell-Cell Gaps
There are two general mechanisms as to how cells respond to information:
1. Signals can regulate gene expression.
2. Signals can activate/inactive certain proteins in the cell.
5
could think of it as the proteins ”stiching” the membranes together.
11.5
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2.5.1
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Gap Junctions Conenct Animal Cells via Protein Channels
⋄ In many animal tissue, structures called gap junctions connect adjacent cells.
⋄ In a gap junction, specialized proteins assemble in the membranes of adjacent cells,
creating interconnected channels that allow substances to move between cells.
⋄ Gap junctions are communication portals by allowing the rapid passage of ions/molecules.
Example: For the muscle cells in our heart, the flow of ions through gap junctions
acts as a signal to coordinate contractions.
Figure 5: Linking components of desmosomes
2.5.2
Plasmodesmata Connect Plant Cells via Membrane-Lined Channels
⋄ In plants, gaps through cell walls allow direct connections between the cytoplasm of
adjacent cells.
⋄ These connections are called plasmodesmata.
⋄ In these connections, the plasma membrane and cytoplasm of the two cells are continuous.
⋄ Tubular extensions from the smooth ER run through these membrane-lined channels.
⋄
Gap junctions and plasmodesmata allow adjacent cells to transmit information.
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The Nav Review
⋄ Cell connections: Direct physical contacts + ECM maintain tissue
structure and function.
⋄ Proteins span membranes, link
to anchoring proteins + intermediate filaments.
⋄ Indirect cell-cell attachments:
⋄ Function like rivets, giving mechanical stability.
⋄ Plants:
middle lamella =
gelatinous pectins; degradation
cell separation.
⋄ Animals: integrins + ECM mediate indirect connections.
⋄ Tight junctions:
⋄ Selective adhesion:
⋄ Cells adhere specifically to others of same tissue type.
⋄ Cadherins = linking proteins;
bind same-type cadherins.
⋄ Cell communication:
⋄ Chains of proteins in adjacent
membranes “stitch” cells together.
⋄ Form watertight seals; common in epithelial barriers (e.g.,
stomach lining).
⋄ Can be dynamic for different
cellular needs.
⋄ Desmosomes:
⋄ Strong adhesion in epithelial
and muscle cells.
11.7
⋄ Signals regulate gene expression or protein activity.
⋄ Gap junctions: protein channels connect animal cells
rapid ion/molecule passage; coordinate heart muscle contractions.
⋄ Plasmodesmata: membranelined channels connect plant
cells; plasma membrane + cytoplasm continuous; smooth ER
tubules pass through.
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3
How Do Distant Cells Communicate?
3.1
Cell-Cell Signaling in Multicellular Organisms
October 28, 2025
One method of distant signaling is via hormones - information carrying molecules are
secreted into fluids and act on distant target cells. Usually small and include peptides,
steroids, and even gases.
3.2
Signal Reception
⋄ Hormones and other types of molecules deliver their message by binding to receptor
molecules.
⋄ A signal receptor is a protein that changes its shape and activity after binding to a
signaling molecule.
⋄ Identical receptors in diverse cells and tissues allows long-distance signals to coordinate
activities.
Example: When startled, adrenal glands relesase epinephrine, increasing heart
rate, releasing glucode, and inreasing breathing rate.
⋄ Most lipid-soluble signaling molecules can diffuse across the hydrophobic region of the
membrane and enter the cytosol of their target cells. The receptors are inside the cell.
⋄ Large/hydrophillic signaling molecules are lipid-insoluble and cannot cross the membrane. The receptors are usually in the plasma membrane.
There are also two more important points to note about receptors regardless of where they
are located:
1. Receptors are dynamic The number of receptors/ability of a receptor to bind tightly
to a signaling molecule can decline due to intensive/frequent stimulation. So the sensitivity of a cell to a particular hormone can change over time.
2. Receptors can be blocked Many drugs can block the interaction between hormones
and their receptors.
3.3
Signal Processing
The way the cell responds depends on where the receptors are located (cytosol or membrane
surface).
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Processing Lipid-Soluble Signaling Molecules
Example: Example steroid hormones that are lipid-soluble signaling molcules
are estrogens and cortisol.
Figure 6: Lipid-Soluble Molecules
The molecules have to be carried through the bloodstream with hydrophilic proteins. After
reaching their target cells, these molecules are released from the carrier proteins, diffuse
through the membrane, and enter the cytosol.
Often, a hormone-receptor complex is formed in the cytosol and then transported to the
nucleus to change gene expression. See the image for more information.
3.3.2
Processing Lipid-Insoluble Signaling Molecules
Hormones in this group do not directly participate in intracellular activities. When a signaling molecule binds at the cell surface, it triggers a signal transduction. The long and
complex series after is called a signal transduction pathway.
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Figure 7: Signal transduction converts an extracellular signal to an intracellular signal
There are 2 major types of signal transduction systems distinguished based on how they are
initiated:
G-Protein Coupled Receptors
⋄ G proteins are signal receptors that span the plasma membrane.
⋄ When G-proteins are activated by a signal receptor, they produce a second messenger. It is a small, nonprotein signaling molecule.
⋄ G proteins are regulated by GTP/GDP. When GTP binds, it changes the protein’s
shape.
⋄ G-proteins are inactivated when GTP loses its phosphate group.
⋄ Here are the steps of the pathway:
1. Signaling molecule arrives and binds to the receptor in the plasma membrane,
which is in turn attached to the G-protein.
2. The receptor changes shape, kicks out GDP and allowed GTP to bind to the
G-protein.
3. The active binding will then split off. It can now go on to interact with nearby
enzymes(which can produce secondary receptors)
4. Secondary receptors are effective because they are small and can diffuse rapidly.
5. Some second messengers activate protein kinases, which are enzymes that activate other proteins by adding a phosphate group.
11.10
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Figure 8: G-protein receptors trigger the production of a second messenger
Some things to note: Second messengers are not restricted to a single role. Also, more than
one type of second messenger may be involved with a cell’s response.
Enzyme Linked Receptors
Enzyme-linked receptors transduce hormonal signals by directly catalyzing a reaction.
Receptor tyrosine kinases (RTKs) are the best example (see next page). The sequence
of protein modifications that culminate in a cell response is called a phosphorylation
cascade. The cascade flows ”downstream”.
11.11
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1. A hormone binds to 2 subunits of a RTK
and makes them form a dimer.
2. The change turns on catalytic activity,
allowing it to phosphorylate itself at tyrosine residues.
3. Proteins inside the cell bind to the RTK,
forming a bridge between the receptor
and a lipid-anchored membrane protein
called Ras, which is a single unit g protein.
4. When Ras is activated, it triggers phosphorylation and the activation of a protein kinase.
5. Each kinase goes on to phosphorylate
another kinase. See the figure to the left:
Figure 9
3.4
Signal Deactivation
Cells regulate their signaling pathways heavily. For example, once activated, G proteins
hydrolyze GTP to GDP, shutting off downstream enzymes. Phosphates and other enzymes
also deactivate signaling components. When these shutdown mechanisms fail, it can lead to
cancer.
Crosstalk
A quick note about crosstalk: interactions among different pathways that modify the cell
response. It is a network of signal transduction pathways to allow cells to respond to many
different cells. It allows for cells to respond to many signals at the same time.
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The Nav Review
⋄ Distant cell communication:
Hormones = signaling molecules secreted into fluids, act on distant target cells (peptides, steroids, gases).
⋄ Signal reception:
⋄ Molecules bind to receptors, proteins that change
shape/activity.
⋄ Lipid-soluble: diffuse through
membrane
cytosol/nucleus
receptors.
⋄ Lipid-insoluble:
brane receptors
duction.
bind mem-
signal trans-
intracellular response.
⋄ G-protein
(GPCRs):
coupled
receptors
⋄ G-protein spans membrane; activated by receptor
produces
second messenger.
⋄ Steps: Signal binds receptor
shape change GDPGTP
G-protein active enzyme
second messenger kinase
activation cellular response.
⋄ Enzyme-linked receptors:
⋄ Example: Receptor tyrosine kinases (RTKs).
⋄ Receptor dynamics:
⋄ Receptors can downregulate
with frequent stimulation.
⋄ Drugs can block receptors
hibit signaling.
signal
in-
⋄ Lipid-soluble signaling: Hormonereceptor complex often goes to nucleus
changes gene expression
(e.g., estrogens, cortisol).
⋄ Lipid-insoluble signaling: Signal
transduction converts extracellular
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⋄ Hormone binds
dimerization
autophosphorylation
bridge proteins
activate Ras
phosphorylation cascade
cellular response.
⋄ Signal deactivation: GTP hydrolysis, phosphatases, other enzymes
shut off pathway.
⋄ Crosstalk: Pathways interact integrate multiple signals
modify
cellular responses.
Navneeth Nalajala
4
Bio 131
October 28, 2025
Signaling Between Unicellular Organisms
Most unicellular organisms communicate about environmental changes. They closely monitor
population density. The use of signaling pathways to respond to population density in
prokaryotic/eukaryotic microbes is called quorum sensing.
It is based on signaling molecules that are secreted by cells and diffuse through the environment.
Last updated: 2025/11/01 13:30:27 -04’00’
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Navneeth Nalajala
Bio 131
October 30, 2025
Bio 131 Notes
Chapter 12: The Cell Cycle
1
How do Cells Replicate?
Figure 1: Chromosome morphology
⋄ Each of the double-stranded DNA copies in a replicated chromosome is called a chromatid.
⋄ Once mitosis begins, chromatids remain attached at their centromere.
⋄ Chromatid copies that remain attached at their centromere are called sister chromatids.
⋄ Even though a replicated chromosome has 2 chromatids, it is considered a single chromosome.
1.1
Cells Alternate Between M Phase and Interphase
M phase is when cells are in the process of separating their chromosomes. However, cells
spend majority of their time in interphase.
⋄ There are no dramatic changes in the nucleus.
⋄ Chromosomes uncoil into long, thin structures.
⋄ The cell prepares to divide/spends time growing.
The S Phase (synthesis phase) is a part of interphase. This is the period where genetic
material is copied.
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Figure 2: The 4 cycles in the cell cycle
The N2 Review
⋄ A chromatid is one of the two identical DNA copies in a replicated chromosome.
⋄ Sister chromatids remain attached at the centromere until separated during
mitosis.
⋄ A replicated chromosome with two chromatids is still considered a single chromosome.
⋄ M phase is when chromosomes are actively separated.
⋄ Interphase is the majority of the cell cycle; chromosomes are uncoiled and the
cell grows.
⋄ S phase is part of interphase, where DNA is synthesized.
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2
Bio 131
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The M Phase
The M phase has two distinct events: the division of the nucleus and the division of the
cytoplasm.
Remember that mitosis divides the replicated chromosomes to form two daughter nuclei. Cytokinesis follows mitosis and divides the cytoplasm of the parent
cell to form 2 daughter cells.
Figure 3: An overview of the cell cycle
Just a quick review: DNA is the genetic material in chromosomes; chromosomes
are made up of chromatin(which is a complex of DNA and histone proteins); Sister
chromatids are identical copies of the same chromosome that are joined together.
2.1
The Events of Mitosis
2.1.1
Prophase
Mitosis begins with prophase, where chromatin condenses to form a more compact structure.
⋄ Prophase is also marked by the formation of the spindle apparatus.
⋄ It is a structure that produces mechanical forces that move replicated chromosomes
initially and pull chromatids apart at the end of mitosis.
⋄ The spindle apparatus is made of microtubules(part of the cytoskeleton).
⋄ Microtubules are made up of α and β tubulin dimers.
⋄ They have a plus and minus end, and originate from microtubule organizing centers
(MTOCs).
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⋄ In some cells, the MTOC is a centrosome, which is a structure that has a pair of
centrioles. 1
2.1.2
Prometaphase
Once chromosomes have condensed, the nuclear envelope disintegrates.
⋄ This allows microtubules to attach to chromosomes at structures called kinetochores.
⋄ Kinesin and dynein motors attached to kinetochores walk the chromosomes to the
middle.
2.1.3
Metaphase
At this point the chromosomes are lined up on the imaginary plane called the metaphase
plate.
⋄ Each chromosome is held by kinetochore microtubules from each side, each exerting
the same amount of pull.
⋄ The sister chromatids are connected to opposite poles, so it is a ”tug of war”.
2.1.4
Anaphase
The cohesins that hold sister chromatids together are cleaved by an enzyme. The chromosomes are then split apart.
⋄ The daughter chromosomes move to opposite poles as the microtubules shrink.
⋄ The two poles of the spindle are pushed/pulled farther apart.
⋄ Each side receives the same amount of chromosomes.
During anaphase, two types of movement work together to separate daughter chromosomes.
First, kinetochore microtubules shorten, pulling sister chromatids toward opposite poles.
At the same time, overlapping polar microtubules lengthen and motor proteins push the
spindle poles farther apart, fully separating the two sets of chromosomes.
2.1.5
Telophase
The nuclear envelope reforms and chromosomes begin to de-condense.
Below is a table of all the structures involved in mitosis.
1
Might want to read up on this a tad. The textbook has extensive information that is most likely not on
the exam
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Navneeth Nalajala
Bio 131
October 30, 2025
Figure 4
2.2
How Do Chromosomes Move During Anaphase?
2.2.1
Mitotic Spindle Forces
⋄ The microtubules are attached to the kinetochores of the chromosomes.
⋄ During anaphase, the plus ends of the microtubules switch from adding tubulin dimers
to removing them. As the plus ends shrink, the chromosomes are pulled along.
2.2.2
Kinetochores are Linked to Retreating Microtubule Ends
⋄ The kinetochore is a complex of many proteins that attaches to the centromere of the
chromosome.
⋄ The fibers from the kinetochore are tethered to a ring that is forced towards the minus
end of the microtubule. This is best seen in the image below.
Figure 5
2.3
Cytokinesis Results in 2 Daughter Cells
During cytokinesis, the cytoplasm divides to form 2 daughter cells.
In plant cells, polar microtubules left over organize the cell. Vesicles from the golgi carry
components for a new cell wall. The vesicles are moved with motor proteins. The cell plate
occurs in plants/animal cells have a cleavage furrow.
The cleavage furrow is formed through the contraction of actin filaments in the plasma
membrane.
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Navneeth Nalajala
2.4
Bio 131
October 30, 2025
Bacterial Cell Replication
Bacteria divide through a process called binary fission. It does not involve mitosis, but it
similar in a lot of ways.
Figure 6: Binary fission
Protein filaments attach to the replicating bacterial chromosomes, then filaments pull the
chromosomes apart.
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Bio 131
October 30, 2025
The N2 Review
⋄ M phase: Division of nucleus (mitosis) and cytoplasm (cytokinesis).
⋄ Mitosis steps:
⋄ Prophase: Chromatin condenses, spindle apparatus forms from microtubules, MTOCs/centrosomes organize microtubules.
⋄ Prometaphase: Nuclear envelope breaks down; microtubules attach to
kinetochores.
⋄ Metaphase: Chromosomes align at metaphase plate; sister chromatids attached to opposite poles.
⋄ Anaphase: Cohesins cleaved; kinetochore microtubules shorten, polar microtubules push spindle poles apart; daughter chromosomes move to opposite poles.
⋄ Telophase: Nuclear envelope reforms, chromosomes de-condense.
⋄ Chromosome movement: Kinetochore microtubules shrink at plus ends; kinetochores tethered to microtubule ends; polar microtubules push poles apart.
⋄ Cytokinesis: Cytoplasm divides; cleavage furrow in animals (actin filaments),
cell plate in plants (vesicles form new cell wall).
⋄ Bacterial replication: Binary fission; protein filaments attach to chromosomes
and pull them apart; no mitosis.
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3
Bio 131
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Control of the Cell Cycle
The variation in division of cells is due to the length of the G1 phase. In rapidly dividing
cells, G1 is basically eliminated. In non-diving cells, they are permanently stuck in G1 ,
although it is often referred to as G0 2 .
3.1
Cell-Cycle Regulatory Molecules
M-phase-promoting factor (MPF) is a signal that induces the M phase in cells.
Figure 7: The 4 cycles in the cell cycle
⋄ MPF is a dimer made of 2 subunits.
⋄ Cyclin is a regulatory proteins whose concentration fluctuates during the cell cycle.
⋄ CDK(Cyclin Dependent Kinase) - enzyme that is always present but only active
when bound to cyclin.
⋄ Cyclin levels increase during Interphase and peak at M phase. After M phase begins,
cyclin is quickly degraded, inactivating MPF.
⋄ If cyclin didn’t degrade, MPF would stay active and the cell would get stuck in M
phase.
3.1.1
How MPF Is Turned On
During interphase, cyclin concentration increases steadily. However, MPF does not trigger
M phase immediately because its Cdk subunit has two regulatory phosphorylation sites:
⋄ One site activates Cdk when phosphorylated.
2
nerve cells and muscle cells fall into this category
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⋄ The other site inhibits Cdk when phosphorylated.
After cyclin binds to Cdk, both sites become phosphorylated, keeping MPF inactive despite
rising levels. Late in G2 , a phosphatase removes the inhibitory phosphate, activating
the kinase. Active MPF then phosphorylates target proteins, leading to chromosome
condensation and spindle formation, initiating M phase.
3.1.2
How MPF Is Turned Off
During anaphase, an enzyme complex degrades MPF’s cyclin subunit, deactivating MPF.
This process demonstrates:
⋄ Negative feedback: MPF activation leads to its own deactivation.
⋄ Protein degradation control: The enzyme complex tags cyclin with ubiquitin,
marking it for destruction by the proteasome.
As a result, cyclin concentration drops rapidly after M phase and then gradually builds
again during interphase.
This can be quite complicated to understand but it a key part of the cell cycle regulation. I
recommend reading more about this/watching videos.
3.2
Cell-Cell Checkpoints Can Arrest the Cell Cycle
Figure 8: The 4 cell-cycle checkpoints
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Bio 131
October 30, 2025
A cell-cycle checkpoint is a critical control point where regulatory molecules determine if
a cell proceeds with division. Defects in these checkpoints can lead to uncontrolled division,
cell death, or tumor formation.
⋄ G1 Checkpoint (most important): Determines whether a cell will divide or enter
G0 .
⋄ Cell size: Must be large enough for viable daughter cells.
⋄ Nutrient availability: Cells halt if nutrients are scarce.
⋄ Social signals: External signals from other cells promote or inhibit division.
⋄ DNA integrity: The p53 protein stops the cycle or induces apoptosis if DNA
is damaged.
⋄ Defective p53
DNA damage persists potential for tumor formation.
⋄ G2 Checkpoint: Occurs after S phase, before mitosis.
⋄ Ensures all DNA is replicated and undamaged.
⋄ If issues exist, the phosphatase that activates MPF’s Cdk remains inactive, preventing entry into M phase.
⋄ M-Phase Checkpoints (2 total):
2. Anaphase Telophase: Cell exits M phase only after all chromosomes are
1. Metaphase
Anaphase: Sister chromatids separate only when all kinetochores are attached to the spindle. Prevents unequal chromosome distribution.
separated. Cyclins must be degraded to turn off MPF and allow cytokinesis.
Failure
cell remains in M phase.
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Navneeth Nalajala
Bio 131
October 30, 2025
The N2 Review
⋄ G1 variation: Rapidly dividing cells have short G1 , non-dividing cells stay in
G0 (e.g., nerve/muscle cells).
⋄ MPF: Dimer of cyclin (regulatory protein) + CDK (always present, active
when bound to cyclin).
⋄ Cyclin rises during interphase, peaks in M phase, then degraded.
⋄ Activation: Cdk has activating and inhibitory phosphorylation; phosphatase removes inhibitory phosphate in G2 .
⋄ Deactivation: Cyclin ubiquitinated and degraded by proteasome during
anaphase; negative feedback ensures MPF turns off.
⋄ Checkpoints: Regulate cell cycle and prevent errors.
⋄ G1 : Cell size, nutrients, social signals, DNA integrity (p53). Defective p53
tumors.
⋄ G2 : DNA fully replicated and undamaged; MPF not activated if problems
exist.
⋄ M-phase:
1. Metaphase
Anaphase: Chromatids separate only when all kinetochores attached.
2. Anaphase
Telophase: Cyclins degraded; cell exits M phase.
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4
Bio 131
October 30, 2025
Cancer: Out-of-Control Cell Division
Cancer is a general term fo disease caused by cells that divide uncontrollably.
There are at least 200 types of cancer.
4.0.1
Cancer and Loss of Cell-Cycle Control
Overview: There are two main categories of defects:
1. Overactive growth signals: Proteins that promote cell division are abnormally
active (e.g., Ras mutations keep signaling for mitosis).
2. Loss of tumor suppression: Genes that normally halt the cell cycle are inactivated
(e.g., defective p53 allows damaged DNA to divide).
4.0.2
Properties of Cancer Cells
⋄ Uncontrolled division: Cells divide continuously, forming a mass of cells called a
tumor.
⋄ Benign tumors: Noninvasive, remain localized.
⋄ Malignant tumors: Invasive and metastatic—spread through the bloodstream or
lymphatic system to form secondary tumors.
⋄ Metastasis: Migration of cancer cells from the primary tumor to new tissues; makes
surgical removal less effective.
4.0.3
Loss of Cell-Cycle Control
Most cancer cells fail at the G1 checkpoint, which normally prevents damaged or unneeded
cells from dividing.
4.0.4
Social Control and Growth Factors
⋄ In multicellular organisms, cells divide only when they receive social signals from
other cells—often in the form of growth factors.
⋄ Growth factors are small proteins that stimulate division by promoting passage through
the G1 checkpoint.
⋄ In culture, normal cells stop dividing without serum (which contains growth factors),
while cancer cells divide without it, showing loss of social control.
4.0.5
How the G1 Checkpoint Works
1. Growth factors stimulate the production of E2F (a transcription factor) and a specific
cyclin.
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Navneeth Nalajala
Bio 131
October 30, 2025
2. E2F activates genes for S phase but is initially inhibited by the Rb (retinoblastoma)
protein.
3. Cyclin binds to Cdk, forming an active cyclin–Cdk complex.
4. The complex phosphorylates Rb, causing it to release E2F.
5. Free E2F activates genes for DNA synthesis, allowing the cell to enter S phase.
Figure 9: Growth factors in cells
4.0.6
How Checkpoints Fail in Cancer
Cells become cancerous when G1 control fails, typically due to:
⋄ Overproduced G1 cyclins: Lead to constant Cdk activation, continuous Rb phosphorylation, and persistent E2F activity.
⋄ Defective Rb protein: Cannot bind E2F, leaving it permanently active, pushing the
cell into S phase uncontrollably.
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Bio 131
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The N2 Review
⋄ Cancer: Disease caused by uncontrolled cell division; over 200 types exist.
⋄ Defects causing cancer:
1. Overactive growth signals: e.g., Ras mutations constantly promote mitosis.
2. Loss of tumor suppression: e.g., defective p53 allows damaged DNA to
divide.
⋄ Tumor types:
⋄ Benign: noninvasive, localized.
⋄ Malignant: invasive, metastatic, spreads via blood/lymph.
⋄ G1 checkpoint failure: Main cause of uncontrolled division in cancer.
⋄ Social control / growth factors: Normal cells need growth factors to pass G1 ;
cancer cells divide without them.
⋄ G1 checkpoint mechanism:
1. Growth factors
E2F + cyclin production.
2. E2F inhibited by Rb.
releases E2F.
4. Free E2F activates S-phase genes DNA replication.
3. Cyclin–Cdk phosphorylates Rb
⋄ Checkpoint failures in cancer:
constant Cdk activation, persistent E2F.
⋄ Defective Rb cannot inhibit E2F uncontrolled S-phase entry.
⋄ Overproduced G1 cyclins
Last updated: 2025/11/01 13:21:55 -04’00’
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