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Cellular respiration, photosynthesis, cell communication, neurons synapses and signaling, endocrine system and hormones, immune system
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What are the products of linear electron transport and cyclic electron transport?
What is the role of cyclic electron transport?
Products:
Linear electron transport makes both NADPH and ATP
Cyclic electron transport produces only ATP
Role:
Cyclic electron transport: to increase the production of ATP to the ratio required by the Calvin cycle
These electrons are routed into an alternative pathway (the cyclic electron transport system), which creates ATP by contributing to the proton gradient that drives the conversion of ADP to ATP by ATP synthase
What are the major inputs and outputs of the Calvin cycle?
Inputs:
CO2 (from atmosphere)
ATP and NADPH (from the photosynthetic electron transport chain)
Outputs:
carbohydrates (triose phosphates)
ADP and NADP+ are also released
What are the three major phases in the Calvin cycle and the role of the enzyme rubisco?
Three major phases:
1) Carboxylation:
CO2 enters the Calvin cycle and is added to the 5-carbon compound RuBP in a reaction catalyzed by the enzyme rubisco
generating 3-phosphoglycerate (3-PGA)
2) Reduction
the 3-PGA is reduced through the conversion of ATP to ADP and NADPH to NADP+
producing triose phosphate
some of the triose phosphate molecules exit the cycle and are used by the cell to provide energy (by respiration) or to synthesize larger molecules
3) Regeneration
triose phosphate molecules are used to regenerate RuBP through reactions that require ATP
Then the cycle starts again with more CO2
The Calvin cycle requires both ATP and NADPH. Which of these molecules provides the major input of energy needed to synthesize carbohydrates?
NADPH supplies the major input of energy that is used to synthesize carbohydrates in the Calvin cycle
What are two strategies that plants use to limit the formation and effects of reactiev oxygen species?
Antioxidants:
neutralize reactive oxygen species
ex: ascorbate and beta-carotene
Xanthophylls:
slows the formation of reactive oxygen species by reducing excess light energy
they accept absorbed light energy directly from chlorophyll and convert this energy to heat
ex: yellow-orange pigments
How is photorespiration similar ot cellular respiration and how does it differ?
Like cellular respiration, photorespiration consumes O2 and releases CO2
Unlike cellular respiration, it consumes rather than produces ATP
Why does rubisco have such low catalytic rate (that is, why is it so slow)?
Rubisco faces a fundamental trade-off between selectivity and speed because it can use both CO2 and O2 substrates. High selectivity of CO2 over O2 requires that the reaction have a high energy barrier, leading to lower catalytic rate
What are the four major stages of cellular respiration? Briefly describe each one.
Cellular respiration is a series of chemical reactions that converts the energy stored in fuel molecules into a chemical form that can readily be used by cells
occurs in four stages
Glycolysis:
glucose is partiallybroken down, and a modest amount of energy (in the form of ATP andreduced electron carriers) is released
Pyruvate oxidation:
pyruvate (the breakdown product of glucose from stage 1) is converted to acetyl-coenzyme A, and carbon dioxide and electron carriers are produced
Citric acid cycle:
acetyl-CoA is broken down, and carbon dioxide, ATP, and reduced electron carriers are produced
Oxidative phosphorylation:
electron carriers generated in stages 1-3 donate their electron acceptor and, in the process, harness the energy of the electrons to produce a large amount of ATP
in aerobic respiration, oxygen is the final electron acceptor, so it is consumed, and water is produced
What is an oxidation-reduction reaction? Why is the breakdown of glucose in the presence of oxygen to produce carbon dioxide and water an example of an oxidation-reduction reaction?
Oxidation-reduction reactions are used to store or release chemical energy
oxidation → the loss of electrons
reduction → the gain of electrons
this gain and loss always happen in a single reaction in which electrons are transferred from one molecule to another
in many reactions, electrons are not completely transferred between molecules
instead → there is a change in electron density around an atom
occurs when glucose is broken down in the presence of oxygen
produces carbon dioxide and water
the carbon atoms in glucose are oxidized
they go from sharing electrons equally in the carbon-carbon bonds to partially losing electrons in the carbon-oxygen bonds of the carbon dioxide molecule
the opposite is true of oxygen, which is reduced in the same reaction
the oxygen atoms go from sharing electrons equally to partially gaining electrons when water is formed
For each of the following pairs of molecules, indicate which member of the pair is reduced and which is oxidized, and which has more chemical energy and which has less chemical energy: NAD+/NADH: FAD/FADH2; CO2/C6H12O6.
The reduced forms have more chemical energy than their corresponding oxidized forms
Reduced molecules:
NADH
FADH2
C6H12O6
Oxidized molecules:
NAD+
FAD
CO2
What are two different ways in which ATP is generated in cellular respiration?
Substrate-level phosphorylation:
a phosphorylated organic molecule directly transfers a phosphate group to ADP
this pathway produces only a small amount of the total ATP generated in the process of cellular respiration
Oxidative phosphorylation:
produces most of the ATP generated in cellular respiration (stage 4 of cellular respiration)
ATP is generated indirectly through:
the reduction of electron carriers
the transfer of electrons from electron carriers to the electron transport chain
the subsequent synthesis of ATP from ADP and inorganic phosphate
What is the overall chemical equation for glycolysis?
Glucose + 2NAD+ + 2ADP + 2Pi → 2 pyruvate + 2ATP + 2NADH + 2H+ + 2H2O
At the end of glycolysis, but before the subsequent stages of cellular respiration, which molecules contain someof the chemical energy held in the original glucose molecule?
Contained in pyruvate, ATP, and NADH
Where does pyruvate oxidation take place?
Inside the mitochondrial matrix
At the end of pyruvate oxidation, but before the subsequent stages of cellular respiration, which molecules contain someof the chemical energy held in the original glucose molecule?
acetyl-CoA and NADH
At the end of the citric acid cycle, but before the subsequent stages of cellular respiration, which molecules contain someof the chemical energy held in the original glucose molecule?
ATP, NADH, and FADH2
What is the function of running the citric acid cycle in reverse?
Used to generate intermediates in the synthesis of other molecules and to incorporate carbon into organic molecules
Animals breathe in air that contains more oxygen than the air they breathe out. Where is oxygen consumed?
Oxygen is consumed in cellular respiration
oxygen is the final electronacceptor in the electron transport chain and is converted to water
How does the movement of electrons along the electron transport chain lead to the generation of a proton gradient?
The movement of electrons along the electron transport chain in the inner mitochondrial membrane is coupled to the transfer of protons through several enzyme complexes and electron carriers
Electrons donated by NADH enter through complex I, and electrons donated by FADH2 enter through complex II
From complexes I and II, coenzyme Q (CoQ) picks up electrons and transfers them to complex III
Complex III donates electrons to cytochrome c, which in turn transfers them to complex IV, which then donates them to the final electron acceptor, oxygen
As the electrons pass through the complexes, protons are pumped into the intermembrane space
This creates a concentration and charge gradient, providing a source of potential energy that is then used to drive the synthesis of ATP

How is a proton gradient used to generate ATP?
The protons accumulated in the innermembranespace cannot passively diffuse across the membrane, so they diffuse through a transport channel called ATP synthase
This enzyme is composed of two subunits:
F0 - the channel through which protons flow
F1 - the catalytic unit that synthesizes ATP
Proton flow through the channel causes it to rotate
which converts the energy of the proton gradient into mechanical rotational energy (kinetic energy)
The rotation of the F0 subunit leads to the rotation of the F1 subunit
Rotation causes conformational changes in the F1 subunit that allow it to catalyze the synthesis of ATP from ADP and Pi
Uncoupling agents are proteins spanning the inner mitochondrial membrane that allow protons to pass through the membrane and bypass the channel of ATP synthase. Describe the consequences of uncoupling agents for the proton gradient and ATP production.
Uncoupling agents decrease the proton gradient and, therefore, decrease levels of ATP
The energy of the proton gradient is not used for oxidative phosphorylation, but instead is dissipated as heat
Uncoupling agents are found naturally in certain tissues, such as fat, for heat generation
They can also act as poisons
Bread making involves ethanol fermentation and typically uses yeast, sugar, flour, and water. Why are yest and sugar used?
Yeast cells are eukaryotes
In bread making, yeast can use sugar as a food source for ethanol fermentation.
The carbon dioxide produced in the process causes the bread to rise
The ethanol is removed in the baking process
What are two different metabolic pathways that pyruvate can enter?
Pyruvate Oxidation (aerobic):
needs oxygen
Pyruvate is converted to acetyl-CoA
Is the starting substrate for the citric acid cycle
During the citric acid cycle, the chemical energy in the bonds of acetyl-CoA is transferred to ATP by substrate-level phorphorylation and to the electron carriers NADH and FADH2
Fermentation (anaerobic):
occurs without oxygen
all ermentation pathways rely on the oxidation of NADH to NAD+
Lactic acid fermentation:
electrons from NADH are transferred to pyruvate to produce lactic acid and NAD+
Ethanol fermentation:
pyruvate releases carbon dioxide to form acetaldehyde
electrons from NADH are transferred to the molecule to produce ethanol and NAD+
What are three types of organic molecules tha tcontain high potential energy in their bonds and therefore can act as “fuel” molecules?
Carbohydrates, lipids, and proteins
they have high potential energy in their chemical bonds
What happens to chemical reactions that generate ATP when level of ATP are high in a cell?
When ATP levels are high, the cell has a high amount of free energy. In this case, pathways that generate ATP re slowed, or down-regulated
How does muscle tissue generate ATP during short-term and long-term exercise?
Short-term exercise:
converts storedglycogen to glucose
glucose is rapidly broken down anaerobically to pyruvate
which then feeds into the lactic acid fermentation pathway
Long-term exercise:
the liver releases glucose into the blood
which is taken up by muscle cells and oxidized to produce ATP
adipose tissue releases fatty acids that are also taken up by muscle cells and broken down by β-oxidtaion
these proceses are slower than anaerobic pathways
however, the end result is the production of more ATP than the fermentation pathway can produce
What is the overall goal of cellular respiration?
To harvest chemical energy from organic fuel molecules (like glucose) to produce ATP, which powers cellular work
What does the mnemonic OIL RIG stand for in the context of redox reactions?
OIL - oxidation is loss of electrons
RIG - reduction is gain of electrons
What is the summary chemical equation for aerobic cellular respiration?
C6H12O6 (glucose) + 6 O2 → 6 CO2 + 6 H2O + Energy (ATP + heat)
What are the three main stages of cellular respiration?
Glycolysis
The Citric Acid Cycle (Krebs’ Cycle)
Oxidative Phosphorylation (Electron Transport Chain)
Where does each stage of cellular respiration occur in a eukaryotic cell?
Glycolysis - cytoplasm
Pyruvate Oxidation & Citric Acid Cycle - mitochondrial matrix
Oxidative Phosphorylation - inner mitochondrial membrane
What is the net energy yield of Glycolysis per glucose molecule?
2 ATP (net gain; 4 produced, 2 consumed)
2 NADH (high-energy electron carriers)
What happens during the Transition Step (Pyruvate Oxidation)?
Two molecules of pyruvate (from glycolysis) are turned into two molecules of acetyl-CoA
this process also releases 2 CO2 and produces 2 NADH
What are the main products of the Citric Acid Cycle (Krebs Cycle) per glucose molecule?
2 ATP
6 NADH and 2 FADH2 (which carry energy to the ETC)
4 CO2 (released as waste)
What is the role of NAD+ in cellular respiration?
It acts as an electron carrier. It picks up electrons and hydrogen ions (protons) from food to become NADH (NAD+ is reduced), carrying them to the ETC
What is the final electron acceptor in the aerobic electron transport chain?
Oxygen (O2), which combines with H+ ions to form water (H2O)
How does ATP Synthase produce ATP?
It uses the exergonic flow of H+ ions (protons) moving down their concentration gradient to power the phosphorylation of ADP into ATP
What is the total net ATP yield of aerobic respiration per glucose molecule?
Approx. 36-38 ATP
2 from Glycolysis
2 from Citric Acid Cycle
32-34 from the ETC
What is the primary purpose of Fermentation if it does not produce additional ATP?
To regenerate NAD+ from NADH, allowing glycolysis to continue producing a small amount of ATP in the absence of oxygen
What are the end products of Lactic Acid Fermentation in human muscle cells?
Lactic acid (lactase)
ATP (produced via glycolysis)
What are the end products of Alcohol Fermentation in yeast?
Ethanol
CO2
ATP
What is beta-oxidation?
The process by which fatty acids are broken down into Acetyl-CoA, producing NADH and FADH2 for the ETC
How is cellular respiration regulated?
Through feedback mechanisms;
Concentrations of ATP, NAD+, and NADH serve as indicators of available energy and can slow or speed up the pathways.
One key regulatory enzyme mentioned is phosphofructokinase (PFK)
How is the efficiency of cellular respiration described in terms of energy loss?
Approx. 40% of the energy from glucose is captured as ATP, which 60% is lost as heat
Describe the relationship between photosynthesis and cellular respiration.
They are reciprocal processes: photosynthesis uses CO2, H2O, and sunlight to produce O2 and organic molecules, which are then used as inputs for cellular respiration
What are the two distinct phases of Glycolysis?
Energy Investment Phase:
Consumes 2 ATP to split glucose
Energy Harvest Phase:
produces 4 ATP and 2 NADH
What is substrate-level phosphorylation?
The direct transfer of a phosphate group from a fuel molecule (substrate) to ADP by an enzyme to form ATP, occurring in glycolysis and the Citric Acid Cycle
What is the role of NAD+ and NADH in cellular respiration?
They act as electron carriers.
NAD+ is the oxidized ("empty") state that picks up electrons and a proton to become NADH (reduced state), which then carries them to the Electron Transport Chain (ETC).
What are the specific outputs of the Transition Step (Pyruvate Oxidation) per glucose molecule?
2 Acetyl-CoA, 2 Co2, and 2 NADH
Define Chemiosmosis.
The use of energy stored in a hydrogen ion (H+) gradient across a membrane to drive cellular work, specifically ATP synthase
How does ATP Synthase convert energy forms?
It converts the potential energy of the proton gradient into mechanical (kinetic) energy as the rotor spins, which then catalyzes the formation of chemical energy in ATP
What is the difference between Fermentation and Anaerobic Respiration?
Anaerobic respiration uses an ETC with a final electron acceptor other than oxygen (like sulfate or nitrate)
Fermentation does not use an ETC at all
What is a key chemical difference between Lactic Acid and Alcohol Fermentation?
Alcohol fermentation releases CO2 as a byproduct (in addition to ethanol)
Lactic acid fermentation does not release CO2
Why is fermentation considered an evolutionarily ancient pathway?
It occurs in the cytoplasm and doesn't require membrane-bound organelles or oxygen, which was absent in Earth's early atmosphere.
What is the difference between Liver and Muscle glycogen storage?
Muscle cells store glycogen for their own contraction; the liver stores glycogen to be released as glucose for the rest of the body.
What are the products of beta-oxidation?
It breaks lipids into glycerol and acetyl-CoA, producing NADH and FADH2. It does not produce ATP directly.
Which enzyme is specifically mentioned as a key regulator of respiration?
Phosphofructokinase (PFK)
If you want to produce carbohydrates that contain the heavy oxygen (18O) isotope, should you water your plants with H218O or inject C18O2 into the air?
You should label the oxygen in CO2 (that is, inject C18O2) because the entire CO2 molecule is used in synthesizing carbohydrates, whereas H2O donates only the electrons needed for the reduction phase of the Calvin cycle. The extraction of electrons from water releases O2 as a by-product.
In what ways are photosynthesis and cellular respiration similar and in what ways are they different?
Photosynthesis:
energy from sunlight is captured in chemical forms (NADPH and ATP) that are used to synthesize carbohydrates from CO2
H2O is the ultimate electron donor and O2 is produced as a by-product
Cellular Respiration:
carbohydrates are oxidized to CO2, releasing energy that is ultimately used to synthesize ATP
O2 is the ultimate electron acceptor and H2O is produced as a by-product
How do antena chlorophylls differ from reaction center chlorophylls?
Antenna chlorophylls:
transfer absorbed energy from one antenna chlorophyll molecule to another, and ultimately the reaction center
Reaction center chlorophylls:
transfer electrons to an electron acceptor, resulting in the oxidation of reaction center chlorophyll molecules
Why are two photosystems needed when H2O is used as an electron donor?
Photosystem II is needed to pull electrons from water
Photosystem I is needed to raise the energy of these electrons enough that they can reduce NADP+ to NADPH
How is energy from sunlight used to produce ATP?
ATP is produced by ATP synthase when there is a high enough concentration of protons in the lumen compared to that in the stroma.
Photosynthetic electron transport results in a high concentration of protons in the lumen in two ways:
(1) as a result of splitting water
(2) from the coupled movement of electrons and protons that involves both plastoquinone and the cytochrome-b6f complex
Because sunlight powers the movement of electrons through the photosynthetic electron transport chain, it is the energy source for producing ATP in photosynthesis
What is the general definition of photosynthesis?
The process of converting light (kinetic) energy into chemical (stored) energy. It captures sunlight and converts it into solar energy, initially stored in a carbohydrate.
Is photosynthesis an endergonic or exergonic process?
It is an endergonic process.
The energy boost required to drive the reaction is provided by light.
State the overall redox equation for photosynthesis.
6 CO2 + 6 H2O + light energy → C6H12O6 + 6 O2

In the redox process of photosynthesis, which molecule is oxidized and which is reduced?
Water (H2O) is oxidized (loses electrons), and Carbon Dioxide (CO2) is reduced (gains electrons) to form sugar.


Define Autotrophs vs. Heterotrophs.
Autotrophs: "Self-feeders" that use photosynthesis to capture energy from the sun (photoautotrophs) or energy from sulfur/ammonia (chemoautotrophs).
Heterotrophs: "Other feeders" that depend on organic compounds produced by others for energy.
Where specifically does photosynthesis occur in a plant?
In the chloroplasts, which are primarily located in the mesophyll cells of leaves

How does CO2 enter and O2 exit the leaf?
Through microscopic pores called stomata on the underside of the leaf.

Define the Stroma and Thylakoids.
Stroma: The dense fluid within the chloroplast where the Calvin cycle occurs (the "sugar factory").
Thylakoids: An elaborate system of interconnected membranous sacs where the light reactions take place

What are Grana?
Stacks of thylakoids

What is the primary purpose of the light reactions?
To convert solar energy into the chemical energy of ATP and NADPH.
What are the three main types of pigments in chloroplasts?
Chlorophyll a: Directly participates in light reactions; absorbs blue-violet and red light.
Chlorophyll b: Accessory pigment; absorbs blue and orange light.
Carotenoids: Accessory pigments that absorb blue-green light and provide photoprotection.

What happens during "Photolysis"?
Enzymes split H2O into hydrogen ions (protons), electrons, and oxygen (O2). The electrons replace those lost by chlorophyll, and O2 is released as a byproduct.
Distinguish between Photosystem II (PS II) and Photosystem I (PS I).
PS II: Functions first; reaction center P680; best at absorbing 680 nm wavelength.
PS I: Functions second; reaction center P700; best at absorbing 700 nm wavelength.

What is the role of NADPH in the light reactions?
It acts as an "electron taxi," carrying high-energy electrons from the light reactions to the Calvin cycle.

What is the primary product of the Calvin cycle?
G3P (Glyceraldehyde 3-phosphate), a three-carbon sugar.

Name the three phases of the Calvin cycle
Carbon Fixation: CO2 is attached to RuBP by the enzyme Rubisco.
Reduction: ATP and NADPH are used to convert the 3-carbon compounds into G3P.
Regeneration: The remaining G3P molecules are used to regenerate the CO2 acceptor, RuBP
How many times must the Calvin cycle turn to produce one net molecule of G3P?
Three times, fixing three molecules of CO2
Why is Rubisco considered a critical enzyme?
It is the enzyme that catalyzes the first step of the Calvin cycle (carbon fixation)
What is Photorespiration?
A wasteful process where Rubisco adds O2 instead of CO2 to the Calvin cycle, consuming energy without producing sugar. It often occurs in C3 plants on hot, dry days when stomata are closed.

How do C4 plants minimize photorespiration?
Through spatial separation. They fix CO2 into 4-carbon compounds in mesophyll cells using PEP carboxylase, then move them to bundle-sheath cells to release CO2 for the Calvin cycle.
How do CAM plants adapt to arid conditions?
Through temporal separation. They open stomata at night to fix CO2 into organic acids and close them during the day to use that stored CO2 for the Calvin cycle.

Give examples of C4 and CAM plants.
C4: Sugarcane
CAM: Pineapple and succulents

What are the four essential elements of cell signaling?
What are the four essential elements of cell signaling?
What are the four essential elements of cell signaling?
Signaling cell, a signaling molecule, a receptor protein, and a responding cell
What are the steps that occur when a signaling molecule binds to a receptor on a responding cell?
Receptor activation, signal transduction, response, and termination
If a hormone is released into the bloodstream so that it comes into contact with many cells, what determinds which cells in the body respond to the hormone?
Only cells that have receptors for the hormone respond to the signal, so signaling can be specific for particular cells.
These receptors are not present in every cell; different cell types express a different assortment of receptor types on their surface.
Thus, only a subset of cells responds to a given signaling molecule, even if that signaling molecule comes into contact with many cell.
What is one way in which endocrine, paracrine, autocrine, and contact-dependent signaling are similar to one another?
The steps involved are all the same: receptor activation, signal transduction, response, and termination
What is one way in which endocrine, paracrine, autocrine, and contact-dependent signaling are different from one another?
The distance between the signaling and responding cell.
Whether the signaling molecule is released by the signaling cell (endocrine, paracrine, autocrine signaling) or is a transmembrane protein (contact-dependent signaling)
How are receptors that bind polar and nonpolar signaling molecules similar, and how are they different?
Polar signaling molecules:
Cannot diffuse across the membrane and therefore bind to receptors on the cell surface
These receptors are usually transmembrane proteins with an extracellular domain, a transmembrane domain, and a cytoplasmic domain
The polar ligands bind with the receptor outside the cell, leading to a cellular response
Non-polar signaling molecules:
Can easily diffuse through the cell membrane
Once inside the cell, they bind to receptors in the cytoplasm or nucleus
In the case of steroid hormones, the ligand-receptor complex moves into the nucleus (if it is not there already) and leads to changes in gene expression
How can cells respond to external signaling molecules, even when those signaling molecules cannot enter the cell?
Cells respond to signals by means of specific transmembrane proteins called receptors that bind to the signal (ligand) at the receptor’s specific ligand-binding site
The binding of the ligand to its receptor causes a conformational change in the receptor, activating it
The activated receptor transmits the signal inside the cell, generating a response
The type of ligand and receptor determines how the cell responds to the signal
What are the three possible initial steps following the binding of a signaling molecule to a receptor?
G protein-coupled receptors bind and activate G proteins
Receptor kinases are activated and phosphorylate other proteins
Ion channels open or close
Is the term “G protein” just a shorter name for a g protein-coupled receptor? Explain your answer.
No. A G protein-coupled receptor is a transmembrane receptor that interacts with a G protein located inside the cell on the cytoplasmic side of the cell membrane
What are three ways in which a signal is amplified in a G protein-coupled receptor signaling pathway?
A single activated G protein-coupled receptor can activate multiple G proteins. Each active G protein activates an adenylyl cyclase molecule, each of which then generates a large amount of cAMP. Each cAMP molecule activates a molecule of protein kinase A (PKA). Once activated, each PKA enzyme phosphorylates and activates multiple protein targets.
What are three ways in which the response of a cell to a signal can be terminated?
The receptor itself could change its conformation to the inactive form
The protein interacting with the intracellular portion of the receptor could become inactivated (perhaps due to dephosphorylation)
Any of the downstream proteins (such as cAMP or protein kinase A) could become inactivated
What are the four essential elements required for any cellular communication?
Signaling cell: The cell that releases the signaling molecule.
Signaling molecule (Ligand): The molecule that carries the message.
Receptor protein: The protein on or in the responding cell that binds the signaling molecule.
Responding cell: The cell that changes its behavior in response to the signal.
List the four sequential steps of cell signaling in order.
Receptor activation: The signal binds to and activates a receptor.
Signal transduction: The signal is transmitted into the cell interior through a pathway.
Response: The cell performs a specific action (e.g., activating an enzyme or gene transcription).
Termination: The response is stopped so new signals can be received.
Define Endocrine signaling and provide examples.
Signaling where molecules travel great distances through the circulatory system (bloodstream) to reach target cells.
Ex: Adrenaline (from adrenal glands to heart/lungs), Insulin, Estrogen, and Testosterone.
Define Paracrine signaling and its typical molecules.
Signaling between cells that are close together; the signal moves via diffusion.
Molecules: Typically small, water-soluble molecules like growth factors.