metabolism - the sum of all chemical reactions occurring in a cell or organism

metabolic pathway - begins with a specific molecule and ends with a product

• each step is catalyzed by an enzyme

catabolic pathways release energy by breaking down complex molecules into similar compounds

• ex: cellular respiration, the breaking down of glucose in the presence of oxygen,

anabolic pathways consume energy to build complex molecules from simpler ones

• the synthesis of a protein from an amino acid is an example of anabolism

enzyme - a catalytic protein - biological catalysts that speed up biochemical reactions

• most are proteins

  • tertiary shape must be maintained for functionality

• enzyme names often indicate the substrate or chemical reaction involved

  • enzyme names often end in -ase

  • ex) sucrase is an enzymes that digests sucrose

• enzymes are reusable

  • not chemically changed by the reaction

  • cells typically maintain a specific enzyme concentration

• enzymes can facilitate synthesis or digestion reactions

  • structure is specific resulting in each enzyme only facilitating one type of reaction

• catalyst - a chemical agent that speeds up a reaction without being consumed by the reaction

• hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction

substrate - the reactant that an enzyme acts on (that enzyme’s substrate)

• The enzyme binds to its substrate, forming an enzyme-substrate complex

  • active site has a unique shape to fit its respective substrate

    • physical and chemical properties of the substrate must be compatible

    • small changes can occur to align with substrate

  • may or may not have chemical charges

• active site - the region on the enzyme where the substrate binds

Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction

*The substrate must have a complementary shape/conformation and charge to its respective enzyme for the reaction to be facilitated

substrate concentration:

• initial increases in substrate concentration increases reaction rate

  • more substrates mean more opportunity to collide with enzyme

• substrate saturation will eventually occur

  • results in no further increase in rate

  • reaction rate will remain constant if saturation levels are maintained

• increased concentration of products decrease opportunity for addition of substrate

  • matter takes up space

  • more product in an area means lower chance of enzyme-substrate collisions

  • slows reaction rate

enzyme concentration:

• changes in enzyme concentration can also impact reaction rate

• less enzyme = slower reaction rate

  • less opportunity for substrates to collide with active sites

• more enzyme = faster reaction rate

  • more opportunity for substrates to collide with active sites

activation energy (E_A) (free energy of activation) - the initial energy needed to start a chemical reaction

• often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings

  • typically reactions resulting in a net release of energy require less activation energy compared to reactions resulting in net absorption of energy

• endergonic - chemical reactions that require a net input of energy

  

• exergonic - chemical reactions that have a net loss of energy

  

Enzymes catalyze reactions by lowering the E_A barrier

• enzymes lower the activation energy requirement of all enzyme-mediated reactions, accelerating the rate of reactions

Enzymes are sensitive to local conditions, and under certain circumstances, can lose their shape (denaturation - changes in the conformational shape (of the enzyme))

• Denatured proteins are biologically inactive, and for enzymes this means they will not catalyze chemical reactions

• Occasionally, denaturation is reversible

Enzyme structure can be affected by general environmental factors, such as temperature and pH

• Each enzyme has an optimal temperature in which it can function

  • range in which enzyme-mediated reactions occur fastest

  • reaction rates change when optimum temps aren’t maintained

  • environmental increase in temp - initially increases reaction rate

    • increased speed of molecular movement

    • increased frequency of enzyme-substrate collisions

    • temp increases outside of optimum range result in enzyme denaturation

  • environmental decrease in temp - generally slows down reaction rate

    • decreased frequency of enzyme-substrate collisions

    • does not disrupt enzyme structure, no denaturation

• Each enzyme has an optimal pH in which it can function

  • pH measures the concentration of hydrogen ions in a solution

    • measured on a logarithmic scale

    • small changes in pH values equate to large shifts in hydrogen ion concentration

      • ex) pH 6 has 10x more hydrogen ions in solution compared to pH 7

  • range in which enzyme-mediated reactions occur the fastest

    • changing pH outside of this range will slow/stop enzyme activity

  • enzyme denaturation can occur as a result of increases and decreases outside of optimum

  • changes in hydrogen ion concentration can disrupt hydrogen bond interactions that help maintain enzyme structure

• Optimal conditions favor the most active shape for the enzyme molecule

pH affects enzyme structure due to the increased number of protons in solution

• This alters H-bonds in the protein’s structure, causing it to lose its secondary and tertiary structures

Temperature increases the kinetic energy of the enzymes and substrates, increasing collisions and reaction rate (up to a point)

• Once the optimum temperature is surpassed, the enzyme will begin denaturing and the reaction rate will decrease

Concentration of substrate and enzymes affect reaction rate as well

Cells produce molecules as needed, and cease producing them when demand is met and homeostasis is restored

• Negative feedback allows the cell to avoid wasting energy and resources

• Negative feedback is where the product of the pathway inhibits the process responsible for its production
  

• Competitive inhibitors bind to the active site of an enzyme, competing with the substrate

  • molecules can bind reversibly or irreversibly to the active site of the enzyme

  • competes with the normal substrate for the enzyme’s active site

  • if inhibitor concentrations exceed substrate concentrations, reactions are slowed

  • if inhibitor concentrations are considerably lower than substrate concentrations, reactions can proceed normally

  • if inhibitor binding is irreversible, enzyme function will be prevented

  • if an inhibitor binds reversibly, enzyme can regain function once inhibitor detaches

• Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective

  • do not bind to the active site

  • bind to the allosteric site

  • binding causes conformational shape change to the active site

  • binding prevents enzyme function because the active site is no longer available

  • reaction rate decreases

  • increasing substrate cannot prevent effects of noncompetitive inhibitor binding

Allosteric regulation may either inhibit or stimulate an enzyme’s activity

• Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site

• This includes allosteric inhibition or regulation

• allosteric site - enzymes can have regions other than the active site to which molecules can bind

According to the first law of thermodynamics, the energy of the universe is constant

• Energy can be transferred and transformed, but it cannot be created or destroyed

• The first law is also called the principle of conservation of energy

According to the second law of thermodynamics

• During every energy transfer or transformation, some energy is unusable, and is often lost as heat

  • Every energy transfer or transformation increases the entropy (disorder) of the universe

Cells are not in equilibrium; they are open systems experiencing a constant flow of materials

• A catabolic pathway in a cell releases free energy in a series of reactions

  • within a chemical pathway, the product of one reaction can serve as a reactant in a subsequent reaction

  • the sequential reactions allow for a more controlled and efficient transfer of energy

• Metabolic pathways are how cells perform work

Cellular work can be

1. Transport work

2. Mechanical work

3. Chemical work

To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one

Most energy coupling in cells is mediated by ATP

• ATP (adenosine triphosphate) is the cell’s energy currency

ATP is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups

• The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis

• Energy is released from ATP when the terminal phosphate bond is broken

The three types of cellular work are powered by the hydrolysis of ATP

• In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction

ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP)

The energy to phosphorylate ADP comes from catabolic reactions in the cell

The ATP cycle is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways

All forms of life must be able to transfer energy from biological macromolecules into usable forms

• Organisms transfer the energy of organic compounds to ATP through fermentation or cellular respiration

  • cellular respiration and fermentation are characteristics of all forms of life

Organisms acquire organic compounds for energy in different ways; plants produce their own food while consumers obtain energy by ingesting food

Cells use chemical energy stored in organic molecules to regenerate ATP, which powers cellular work

Catabolic pathways yield energy by oxidizing organic fuels and the breakdown of organic fuels is exergonic

• Fermentation is a partial oxidation of sugars that occurs without O₂

  • products are lactic acid or ethanol

• Aerobic respiration consumes organic molecules and O₂ and yields ATP

• Anaerobic respiration is similar to aerobic respiration but consumes compounds other than O₂

  • still have pyruvate (diff from fermentation)

Cellular respiration includes anaerobic and aerobic processes, but is often used to refer to aerobic respiration

• Although carbohydrates, fats, and proteins are all oxidized as fuel, it is helpful to trace cellular respiration with the sugar glucose

stages of cell respiration:

1. Glycolysis (occurs in the cytoplasm)

   1. Pyruvate Oxidation (occurs in mitochondria)

2. The Citric Acid Cycle (Krebs Cycle) (occurs in mitochondria)

3. Oxidative Phosphorylation - electron transport chain (occurs in mitochondria)

Oxidative phosphorylation includes an ETC and chemiosmosis

• ETC reactions occur in membranes of chloroplasts and mitochondria, and in the cell membranes of prokaryotes

• ETC facilitates a series of coupled reactions used during cellular reparation

• ETC allow for a more controlled and efficient transfer of energy

• ETC use electron energy to establish electrochemical/proton gradient across membranes

• Electrons are delivered by electron carriers, aka NADH and FADH2, to the ETC

• ATP synthase uses the electrochemical/proton gradient to synthesize ATP

• electrochemical gradients are maintained as a result of biological membrane impermeability to charged molecules/ions

• oxidative phosphorylation - the process of making ATP using the stored energy of a proton gradient

  • NADH and FADH2 lose high energy electrons to the ETC = oxidation

  • ATP synthase adds an inorganic phosphate to ADP resulting in an ATP molecule = phosphorylation

• protons moving along the gradient (diffusion), through ATP synthase, powers ATP synthase

• energy is stored in proton gradients

• decoupling oxidative phosphorylation from electron transport refers to the proton gradient NOT being used by ATP synthase to produce ATP

  • when decoupling occurs, the energy stored in the gradient is released as heat

  • the heat from decoupling can be used by endothermic organisms to regulate body temperature

Electrons from organic compounds are transferred to the ETC by an electron carrier, NAD⁺, in its reduced form, NADH

ATP regeneration can be accomplished in cells via substrate-level phosphorylation or oxidative phosphorylation

Glycolysis and the Citric Acid Cycle make a small amount of ATP using substrate-level phosphorylation 

Glycolysis is an ancestral, universal process that occurs in the cytosol

Glycolysis is the splitting of glucose into two pyruvate molecules, producing ATP and NADH

pyruvate is transported from the cytosol to the mitochondrion

• pyruvate is actively transported through mitochondrial membranes into the matrix

• pyruvate is oxidized and a product of pyruvate oxidation enters the Krebs Cycle

Following the oxidation of glucose, pyruvate is further oxidized into a more reactive compound, Acetyl-CoA

The acetyl-CoA is processed in an enzymatically-mediated cycle called the Citric Acid Cycle or Krebs Cycle

• The citric acid cycle has eight steps, each catalyzed by a specific enzyme

• in Krebs cycle, carbon dioxide is released from organic intermediates

• the Krebs cycle is a pathway involving many key reactions

  • carbon dioxide is released from intermediate reactions

  • high energy electrons are transferred to NADH and FADH2

  • ADP is phosphorylated forming ATP

The NADH and FADH₂produced by the cycle relay electrons extracted from food to the electron transport chain

The NADH and FADH₂ produced in glycolysis, pyruvate oxidation and the Citric Acid Cycle are oxidized by the proteins of the mitochondrial ETC

• NADH created in glycolysis, and NADH and FADH2 created in the Krebs cycle, donate electrons to the ETC

• electrons are transferred between membrane proteins of the ETC

• ETC establishes an electrochemical gradient of protons (hydrogen ions) across the inner mitochondrial membrane

The mitochondrial ETC is on the highly folded inner membrane

Electrons are passed from one protein complex to the next, until they are accepted by an oxygen atom, the final electron acceptor

As the protein complexes pass electrons, protons are pumped into the intermembrane space

The proton gradient and low pH of the intermembrane space will power chemiosmosis and the production of ATP in large quantities

Fermentation enables cells to produce ATP without the use of oxygen 

• Without oxygen as the final electron acceptor, the ETC would fail to operate

In the case that oxygen is unavailable, glycolysis couples with fermentation or anaerobic respiration to produce ATP

• Anaerobic respiration uses a different final electron acceptor such as sulfate

• Anaerobic respiration is a prokaryotic process - ETC protein complexes are embedded in the cell membrane because prokaryotes lack mitochondria

Fermentation includes glycolysis, plus reactions that regenerate NAD⁺ so that glycolysis can occur again

Two common types of fermentation are alcohol fermentation and lactic acid fermentation

• Alcohol fermentation by yeast is used making wine, beer and bread

• In lactic acid fermentation, pyruvate is reduced to NADH, forming lactate as an end product without the release of CO₂

• Human muscle cells use lactic acid fermentation when oxygen is scarce

• fermentation allows glycolysis to proceed in the absence of oxygen

  • ethanol and lactic acid are byproducts of fermentation

the conversion of ATP to ADP releases energy

• energy is released when chemical bonds are broken

• ATP is converted to ADP when the bond between the 2nd and 3rd phosphate is broken

• energy released from ATP hydrolysis can be used to power many metabolic processes

Photosynthesis is the process that converts solar energy into chemical energy

• evidence supports the claim that prokaryotic photosynthesis by organisms, such as cyanobacteria, was responsible for the production of oxygen in the atmosphere

• photosynthetic pathways are the foundation of eukaryotic photosynthesis

Autotrophs sustain themselves without eating anything derived from other organisms

• Autotrophs are the producers of the biosphere, producing organic molecules from CO₂ and other inorganic molecules

• Photosynthesis occurs in plants, algae, certain other protists, and some prokaryotes

Heterotrophs obtain their organic material from other organisms and are the consumers of the biosphere

Almost all heterotrophs, including humans, depend on photoautotrophs for food and O₂

Leaves are the major locations of photosynthesis

Their green color is from chlorophyll, the green pigment within chloroplasts

• CO₂ enters and O₂ exits the leaf through microscopic pores called stomata

• The chlorophyll is in the membranes of thylakoids (connected sacs in the chloroplast)

• Thylakoids may be stacked in columns called grana

Chloroplasts also contain stroma, a dense interior fluid

Chloroplasts split H₂O into hydrogen and oxygen; the electrons from the hydrogen power the production of sugar molecules, and oxygen is released as a by-product

• In photosynthesis, electrons flow from water to glucose

Photosynthesis is an endergonic process; the energy boost is provided by light

6 CO₂ + 12 H₂O + Light energy → C₆H₁₂O₆ + 6 O₂ + 6 H₂O

Photosynthesis consists of two stages:

1. The Light Reactions (the photo- part)

   1. light-dependent reactions capture light energy by using light-absorbing molecules called pigments

2. The Calvin Cycle (the -synthesis part)

The light reactions, in the thylakoids

• Split H₂O in a process called photolysis

• Release O₂

  • oxygen is produced as a result of water hydrolysis

• Reduce NADP⁺ to NADPH

  • chemical energy is temporarily stored in the chemical bonds of carrier molecules aka NADPH

• Generate ATP from ADP by photophosphorylation

  • light-dependent reactions help facilitate ATP synthesis

  • ATP and NADPH transfer stored chemical energy to power the production of organic molecules in another pathway, called the Calvin cycle

The Calvin cycle, in the stroma

• Affixes atmospheric CO₂ to an organic compound, during Carbon Fixation, using the ATP and NADPH formed during the light reactions

The light reactions convert solar energy to the energy of ATP and NADPH

• Light is a type of electromagnetic radiation that occurs in waves

Wavelength determines the type of electromagnetic energy

Pigments are substances that absorb visible light

• Different pigments absorb different wavelengths

• Wavelengths that are not absorbed are reflected or transmitted

Leaves appear green because chlorophyll reflects and transmits green light

• capture energy from sunlight and convert it to high-energy electrons

• chlorophyll electrons will be energized

  • the energy from the electrons will be used to establish a proton gradient and reduce NADP+ to NADPH

An absorption spectrum is a graph plotting a pigment’s light absorption versus wavelength

The absorption spectrum of chlorophyll a suggests that violet-blue and red light work best for photosynthesis

An action spectrum profiles the relative effectiveness of different wavelengths of radiation in driving a process

• Chlorophyll a is the main photosynthetic pigment

• When a pigment absorbs light energy, its electrons go from ground state to excited state

• As electrons return to the ground state, energy is lost in the form of heat and light

A photosystem consists of a reaction-center complex (a type of protein complex) surrounded by light-harvesting complexes

• The light-harvesting complexes (pigment molecules bound to proteins) transfer the energy of photons to the reaction center

  • light-capturing unit in a chloroplast’s thylakoid membrane

• referred to as PSII and PSI

  • the hydrogen molecules from the splitting of water (hydrolysis) are released into the thylakoid space and used to create an electrochemical/proton gradient (which is important for PSII)

    • electrochemical/proton gradient - a difference in concentration of protons (hydrogen ions) across a membrane

• A primary electron acceptor in the reaction center accepts excited electrons and is reduced as a result

Solar-powered transfer of an electron from a chlorophyll a molecule to the primary electron acceptor is the first step of the light reactions

Excited electrons are passed from protein to protein, through the thylakoid membrane, until they reach NADP⁺, reducing it to NADPH

NADP⁺ is an electron carrier, a type of molecule responsible for transporting electrons from one cellular chemical reaction to another

1. PSII (P680) is a very strong oxidizing agent, causing photolysis to occur; removing water’s electrons. Oxygen is released and the electrons in PSII are excited by light.

2. Excited electrons are shuttled through an Electron Transport Chain (similar to the ETC in cellular respiration but different location).

• PSII and PSI pass high-energy electrons to the ETC (explains how they are functionally related)

3. Electrons reach PSI and are re-excited by light, where they eventually pass to NADP⁺ and H⁺, forming NADPH

NADP⁺ is the final electron acceptor

The NADPH formed will be used to make carbohydrates in the Calvin Cycle

4. While electrons flow through the ETC, protons are pumped from the stroma to the thylakoid space

5. The high proton concentration (and low pH) in the thylakoid space, creates proton motive force, which is required for ATP synthesis

• photosynthesis uses a from of passive transport to generate ATP from ADP

6. The enzyme, ATP Synthase, rapidly produces ATP as protons diffuse through it - this process is known as Chemiosmosis

• ATP synthase - an enzyme that creates ATP when protons pass through the enzyme

7. The ATP produced will be used in the Calvin cycle

Photophosphorylation is the regeneration of ATP from ADP using the energy of light

The Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO₂ to sugar

• (Calvin cycle uses ATP, NADPH, and CO2 and produces carbohydrates)

• goal - make organic products that plants need using the products from the light reactions of photosynthesis

• plants and other organisms mainly get their carbon dioxide from the environment

The cycle regenerates its starting materials after molecules re-enter and leave the cycle

The cycle builds sugar from smaller molecules by using ATP and the reducing power of electrons carried by NADPH

Carbon enters the cycle as CO₂ and leaves as a sugar named glyceraldehyde 3-phosphate (G3P)

The Calvin cycle has three phases

1. Carbon fixation (catalyzed by rubisco)

2. Reduction

Regeneration of the CO₂ acceptor (RuBP)

Organisms have genetic variation allowing them to respond to environmental stimuli 

• variation can be evident on a cellular and molecular lever

  • includes differences in…

    • molecular structure

    • molecular types, proteins, carbohydrates, lipids, etc.

    • the number of molecules present

• Individuals possessing variations that allow them to survive and reproduce have a higher level of fitness

  • individual fitness…

    • refers to an individual organism’s being able to survive and reproduce

    • contributes to species fitness

    • not every individual within a species need show fitness for the species to continue generationally

    • the more variation within individual organisms in a population, the better chance a species can demonstrate fitness generationally under changing environmental conditions

Fitness is a measure of an individual’s reproductive success - organisms that are more fit reproduce more often and pass their genes onto the next generation in greater frequency

• A variation that improves reproductive success is also known as an adaptation

Some soil insects can alter the composition of their cell membranes and in cold temperatures to increase the number of phospholipids with unsaturated fatty acids tails

• Unsaturated fatty acids enhance membrane fluidity and help prevent the cell from freezing in cold temperatures

Chloroplasts contain multiple types of photosynthetic pigments

• This expands the wavelengths of light that the chloroplast can capture and use to produce sugar