ap bio unit 3

3.1 Enzymes (1)

Enzymes are macromolecules.

• Enzymes are biological catalysts that speed up biochemical reactions.

• Most enzymes are proteins.

  • Tertiary shape must be maintained for functionality

  • Have a region called an active site

The active site interacts with the substrate.

• A molecule that can interact with an enzyme is called a substrate

• Enzymes have an active site, specifically interacts with substrate

  • Has a unique shape and size

  • Can have chemical charges or not

  • Physical and chemical properties of the substrate must be compatible

  • Slight changes can occur to align with substrate

• Enzymes name often indicate the substrate or chemical reaction involved

  • Not chemically changed by the reaction

  • Cells typically maintain a specific enzyme concentration

• Enzymes can facilitate synthesis or digestion reactions

Key takeaways

1. enzymes speed up biochemical reactions by lowering activation energy requirements

2. The structural characteristics of an enzyme make the enzyme very reaction specific

3. The shape and change of the substrate must be compatible with the active site of the enzyme for a reaction to occur

4. Enzymes are not consumed by the reactions. Enzymes are reused.

3.1 Enzymes (2) 

Enzymes are biological catalysts

• Enzymes are biological catalyst, typically proteins, that speed up biochemical reactions

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

• Enzymes can facilitate synthesis or digestion reactions

Enzymes affect the rate of biological reactions

• All biochemical reactions require initial starting energy, called activation energy

• Some reactions result in a net release of energy and some reactions result in a net absorption of energy

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

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

Key Takeaways:

1. Enzymes are biological catalysts that facilitate chemical reactions in the cells by lowering activation energy requirements.

2. Activation energy is the initial energy required for a reaction to occur

3.1 Enymes (3) 

Experimental procedures should align with the testable question.

• A controlled experiment is a scientific investigation

• There are two types of tests set up in a controlled experiment

  • Control test (group)

    • Generates data under conditions with no treatment / no manipulation

    • Generates data under normal/unchanged conditions

    • Considered Baseline data

  • Experimental Test (group)

    • Generates data under abnormal/unknown conditions

    • Generates data under treated/manipulated conditions

    • Test results often compared with control test results to help determine possible impacts of a treatment/manipulation

A control group is used as a standard for comparison

• Negative control 

  • Not exposed to the experimental treatment or any treatment known to have an effect

• Positive Control 

  • Exposed to a treatment that has a known effect

  • Not exposed to the experimental treatment

• Both types of controls can be used to validate experimental procedures

A control group is not the same as a controlled variable

• Controlled variables are aspects of an experiment that would be changed but are intentionally not changed

• Controlled variables are important to help isolate and identify the impact of an intentional change/treatment

• Only variable known to have an impact should be considered as possible control variables

• Control variables are also known as constants. 

Key Takeaways:

1. The two types of control groups are negative and positive control groups

2. Positive control groups are mainly used to confirm a known effect. Negative control groups are mainly used to confirm results in the options of any kind of treatment. Results from control tests are used as baseline data. 

3. Controlled variables or aspects of an experiment left unchanged across all tests to avoid additional impacts on results

3.2 Environmental Impacts on Enzyme Function 

Changes  in the molecular structure of an enzyme may result in loss of enzyme function.

• Enzymes have unique functional 3D shapes; known as a conformational shape or tertiary structure.

• Changes in the conformational shape of the enzyme = denaturation

  • Changes in environment temperature can lead to denaturation

  • Changes in an environmental pH can lead to denaturation

  • And I'm denaturation is typically irreversible, and the catalytic ability of the enzyme is lost or severely decreased

  • In some cases, enzyme denaturation is reversible, allowing the enzyme to regain catalytic activity

Environmental temperature can alter the efficiency of enzyme activity

• Optimum temperatures

  • Range in which enzyme mediated reactions occur the fastest 

  • reaction rates change when optimal temperatures aren't maintained

• Environmental increases in temperature

  • Initially increases reaction rate

    • Increase speed of molecular movement

    • Increase frequency of enzyme substrate collisions

  • Temperature increases outside of optimum range result and enzyme denaturation

• Environmental decrease in temperature

  • Generally slows down reaction rate

    • Decrease frequency of enzyme substrate collisions

    • Does not disrupt as instructor, no denaturation 

Environmental pH can alter the efficiency of enzyme activity. 

• PH measures the concentration of hydrogen ions in solution

  • Measured on a logarithmic scale

  • Small changes in PH values equate to large shifts and hydrogen ion concentrations

  • Example: ph6 has 10x more hydrogen ions in solution compared to pH 7

• Optimum pH

  • Range in which enzyme mediated reactions occur the fastest

  • Changing the pH outside of this range will slow or stop and some activity

  • Enzyme denaturation can a car as result of increases and decreases outside the optimum

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

Concentrations of substrates and products affect reaction rate 

• Initial increases in substrate concentration increase reaction rate.

  • More substrates mean more opportunity to collide with enzyme

• Substrate saturation will eventually occur

  • Results in no further increase in rate of reaction

  • Reaction rate will remain constant of saturation levels are maintained

Increase concentrations of products decrease opportunity for addition of substrate

• Matter takes up space

• More products in the area means lower chance of enzyme substrate collisions

• Slow reaction rates

Enzyme concentration impacts reaction rate

• 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

Competitive Inhibitors can bind to the active site

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

  • Competes with the normal substrate for the enzymes active site

  • If inhibitor concentrations exceed substrate concentrations reactions are slowed

  • If inhibitor concentrations are considerably lower than substrate concentration reactions can proceed normally

  • If inhibitor binding is irreversible enzyme functions will be prevented

  • If inhibitor binds reversibly enzyme can regain Function, One inhibitor detaches

Non competitive Inhibitors bind to enzyme and change enzyme activity

• Enzymes can have regions other than the active site to which molecules can bind, called the allosteric site

• Non-competitive inhibitors

  • Do not bind to the active site

  • Bind the allosteric site

  • Finding causes confirmational cheap change

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

  • Reaction rate decreases. 

• Increasing substrate cannot prevent effects of non-competitive inhibitor binding

Key Takeaways:

1. Denaturation of an enzyme occurs when the confirmation protein structure is disrupted, eliminating the ability to catalyze reactions

2. Changes in PH outside of the optimum pH rate, is either direction, will result in decreased enzyme activity and eventually enzyme denaturation

3. Increasing temperature, outside of optimum temperature and call Will initially cause an increased reaction rate will continue to increase resulting in denaturation. Decreasing temperature outside optimum range will result in slow reaction rates but not denaturing of the enzyme. 

4. Increase since my concentration increased reaction rate. Decrease in some combination will decrease reaction rate

5. Increasing substrate concentration will initially increase reaction rate period sepsis saturation will not result in a continued increase in reaction rate period reaction rate will remain constant if substrate saturation levels are maintained.

6. Competitive inhibitors can bind reversibly/irreversibly to active sites, potentially altering reaction rate. 

7. Noncompetitive inhibitors can bind allosteric sites, decreasing the catalytic compatibility of enzymes. 

3.3 Cellular Energy 

All living systems require constant input of energy. 

• Sunlight is the main energy input for living systems

• Autotrophs capture energy from physical sources, like sunlight, or chemical sources and transform that energy into energy sources usable by all cells. 

• During every energy transformation process, some energy is unusable, often lost as heat. 

Life requires a highly ordered system and does not violate the second law of thermodynamics. 

• Every energy transfer increase the disorder of the universe

• Living cells are not at equilibrium; there is a constant flow of materials in and out of the cell. 

• Cells manage energy resources by energy coupling. Energy -releasing processes drive energy-storing processes. 

Pathways in biological systems are sequential. 

• Within a chemical pathway, the product of one reaction can serve as a reactant in a subsequence reaction 

• The sequential reactions allow for more controlled and efficient transfer of energy. 

The second law of thermodynamics = every energy transfer increases the entropy (disorder) of the universe

Key Takeaways:

1. Living things use the chemical energy stored in molecular bonds of macromolecules and ATP to perform necessary life functions. 

2. Pathways in biological systems are sequential to allow for a more controlled and efficient transfer of energy. 

3.4 Photosynthesis 

Organisms capture and store energy for use in biological processes. 

• Photosynthesis is the biological process that captures energy from the SUN and produces sugars

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

• Photosynthesis pathways are the foundation of eukaryotic photosynthesis. 

Light-depended reactions of photosynthesis in eukaryotes involve a series of pathways.

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

• Pigments help transform light energy into chemical energy. 

• Chemical energy is temporarily stored in the chemical bonds of carrier molecules, called NADPH. 

• 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. 

• Oxygen is produced as a result of water hydrolysis. 

Key Takeaways:

1. Plants and other autotrophs use pigments to trap light energy to make organic molecules 

2. The pigments used in the light-depended reactions help transform light energy into chemical energy. The chemical energy is temporarily stored in the chemical bonds of carrier molecules, called NADPH. 

3. The products of the light dependent reactions are ATRP and NADPH. 

4. ATP and NADPH are products that will be used in the Calvin cycle to produce carbohydrates. 

3.4 Photosynthesis (2) 

During photosynthesis, chlorophylls absorb energy from light 

• Chlorophylls capture energy from sunlight and convert it to high energy electrons. 

• Chlorophyll electrons will be energized when light absorption occurs. The energy from the electrons will be used to establish a proton gradient and reduce NADP+ to NADPH

Photosystems I and II are embedded in the internal membrane of chloroplasts. 

• Photosystems are light capturing units in the chloroplast thylakoid membrane. 

• WHY is the hydrolysis of water necessary as it is related to PSII and the light dependent reactions? 

  • The hydrogen molecules from the splitting of water are released into the thylakoid space and used to create an electrochemical/protein gradient. 

When electrons are transferred between molecules in a reaction, they pass through the electron transport chain. 

• How are PSII and PSI functionally related to the electron transport chain (ETC)?

• - PSII and PSI pass high energy elections on the the EYC

• What is an electrochemical/proton gradient?

  • It is a difference in concentration of protons (hydrogen ions) across a membrane. 

The formation of the proton gradient is linked to the synthesis of ATP. 

• Photosynthesis used a form of passive transport to generate ATP from ADP. 

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

Energy captured in the light powers the production of carbohydrates in the Calvin CYcle. 

• The calvin cycle uses ATP, NADPH, and Co1 and produces carbohydrates. 

• What is the ultimate goal of the Calin cycle reactions?

  • 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. 

Key TakeawaysL

1. Chlorophyll captures energy from sunlight and excites electrons

2. As the electrons pass through the electron transport chain, protons are actively transported across a membrane, establishing a gradient. Protons diffuse through ATP synthase, powering ATP synthesis. 

3. ATP, nADPH, and CO2 are used during the Calvin cycle to produce carbohydrates through a series of reactions. 

3.5 Cellular Respiration 

Fermentation and cellular respiration are processes that allow organisms to use energy stored in biological macromolecules 

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

• Cellular respiration and fermentation release chemical energy from organic molecules, like glucose. 

• Oxygen is not used during the process of fermentation  but is used during the process of cellular respiration. 

• Fermentation and anaerobic respiration are not the same process. 

Cellular respiration in eukaryotes involves a series of coordinated polymer catalyzed reactions that capture energy from biological macromolecules. 

• Cellular respiration involves the release of chemical energy through the break down of glucose and created an energy-storing molecule called ATP

• ARP is used by all cells to do biological work

• Cellular respiration involves multiple metabolic pathways

  • Glolysis - occurs in the cytoplasm

  • Pyruvate oxidation - occurs in mitochondria 

  • Kerbs cycle (The CItric Avid CYcle) - occurs in the mitochondria

  • Electron transport - occurs in the mitochondria

The electron transposed chain transfers energy from electrons in a series of couples reactions. 

• Electron transport chain reactions occur in the membrane of chloroplast and mitochondria, and in the cell membranes of prokaryotes. 

• And electron transport chain (STC) facilitates a series of couples reactions used during cellular respiration 

• The electron transport chain allows for a more controlled and efficient transfer of energy. 

• Electron transport chains used electron energy to establish electrochemical/proton gradients across membranes. 

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

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

Key Takeaways

1. All living things use fermentation and cellular respiration to produce ATP

2. Eukaryotes coordinate cellular respiration in three metabolic stages which are glycolysis, pyruvate oxidation and Krebs cycle, and oxidative phosphorylation. 

3. NADH and FADH2 deliver electrons to the ETC which uses the electron energy to create an electrochemical gradient of protons. 

3.5 Cellular Respirator (2)

Electron transport chain reactions occur in chloroplast, mitochondria, and in the plasma membrane of some cells. 

• The highly complex organization of living cells and living systems relies on a constant input of energy. 

• Electron transport chain (ETC) reactions are conserved process

• In eukaryotic cells, electrons transport chains are located in the inner mitochondrial membrane and internal membrane of chloroplast. 

• In prokaryotic cells, electron transport chains are located in the plasma membrane. 

The electron transport chain transfers energy from electrons. 

• Membrane proteins make up the electron transport chain (ETC)

• Electron transport chain proteins facilitate a series of couples reactions using the energy from electrons. 

• High energy electrons are donated by electron carries, NADH2 and FADH2

• Active transport of protons (hydrogen ions occur during ATC reactions .

• Active transport of proteins establishes an electrochemical gradient across the membranes. 

• Electrochemical gradients are maintained as a result of biological membrane impermeability of the charge molecules/ions. 

The flow of protons by chemiosmosis through ATP synthase drive ATP synthesis

• The Process of making ATP using the stored energy of a proton gradient is referred to as oxidative phosphorylation

  • 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 gradients (diffusion),through ATP synthase, power ATP synthesis. 

In cell respiration, decoupling oxidative phosphorylation from electron transport generates heat

• 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.

Key takeaways:

1. Do you like the transfer train that allows for the efficient transfer of energy from electrons to a proton gradient?

2. NADHA and FADH2 donate high energy electrons to the electron transport chain. 

3. The electrochemical gradient provides stored energy that is transformed into the energy of chemiosmosis used by ATP synthase to synthesize ATP. 

4. Oxidative phosphorylation is the pathway utilizing electron transport chains, chemiosmosis and ATP synthase to make ATP.

5. When decoupling occurs during cell respiration, he is released and can be used for thermoregulation. . 

3.5 Cellular respiration (3) 

Glycolysis is a body chemical pathway that releases energy stored in glucose. 

• Glycolysis results in the production of pyruvate NADH and ATP

Pyruvate is transported from the cytosol to the mitochondrion. 

• Pyruvate is actively transported through mitochondrial memories into the matrix. 

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

In the crab cycle (citric acid cycle), carbon dioxide is released from organic intermediates.

• The Krebs cycle is a pathway involving many key interactions. 

• Carbon dioxide is released from intermediate interactions. 

• High transfer electrons are transferred from NADH and FADH2 

• ADP is phosphorylated forming ATP

Electrons extracted and glycolysis and Krebs cycle reactions are transferred to the electron transport chain.

• Nadh created in the classes and NADH and FADH2 created in Krebs cycle donate electrons to the ETC

• Electrons are transferred between membrane proteins of the ETC

• The ETC establishes an electrochemical gradient of protons, hydrogen ions, across the inner mitochondrial membrane.

Fermentation allows glycolysis to proceed in the absence of oxygen.

• ethanol lactic acids are byproduct 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 second and third phosphate is broken. 

• Energy between the ADP hydrolysis can be used to power many metabolic processes.

Key takeaways. 

1. Glycolysis releases energy and glucose to form ATP and nadh. 

2. Pyruvate is transported to the mitochondria where it is oxidized. 

3. During the Krebs cycle, the citric acid cycle, carbon dioxide is released, ATP is synthesized, and NADH and FADH2 are produced. 

4. The electrons extracted in glycolysis and the Krebs cycle are transferred by NADHand FADH2 to the ETC. 

5. Fermentation allows glycolysis to occur without oxygen and produces ethanol or lactic acid period energy is released when the third phosphate is broken off to ATP resulting in ADP.