AP BIO CHAPTER 3

topics covered :

1. 3.1: Enzyme Structure

2. 3.2: Enzyme Catalysis

3. 3.3: Environmental Impacts on Enzyme Function

4. 3.4: Cellular Energy

5. 3.5: Photosynthesis

6. 3.6: Cellular Respiration

7. 3.7: Fitness

3.1 Enzyme Structure

• what are enzymes

  • enzymes are macromolecules

  • biological catalysts that speed up biochemical reactions

  • most enzymes are proteins

    • have a tertiary shape that must be maintained

  • what is an active site?

    • interacts with the substrate (a molecule that interacts with the active site of an enzyme)

    • enzymes have an active site specific to the substrate (unique shape and size + can have charges + must have specific properties that are compatible with the substrate)

  • enzyme names often indicate the chemical reactions involved

    • often end in -ase (sucrase: digests sucrose)

  • Enzymes are reusable

    • they are not chemically changed by the reaction

    • cells usually maintain a specific enzyme concentration

• Enzymes can facilitate synthesis or digestion reactions

• Enzymes speed up reactions by lowering activation energy requirements

• The structural characteristics of an enzyme make the reactions very enzyme-specific

• the shape and charge of the substrate must be compatible with the active site of the enzyme for a reaction to occur

enzymes are not consumed by a reaction; they are reused

3.2 Enzyme Catalysis

• each enzyme only facilitates one specific reaction (enzymes are really specific)

• what is activation energy?

  • the initial starting energy

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

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

  • What do enzymes do? : they lower activation energy, which accelerates the reactions

• A controlled experiment is a scientific investigation

  • there are 2 groups

  • control : they’re intentionally not changed

    • generates data under conditions with no manipulation

    • generates data under normal conditions

    • considered baseline data

      • negative control : not exposed to manipulation or any treatment

      • positive control : exposed to a treatment that has a known effect

        • not exposed to experimental effect

  • experimental group

    • generates data under abnormal/unknown conditions

    • generates data under manipulated conditions

    • often compared with the control group to determine impacts of manipulation

3.3 Environmental Impacts on Enzyme Function

• Enzymes may have unique conformational shapes : different tertiary structures

  • changes in these shapes is denaturation

• denaturation can occur to :

  • changes in temperature

  • changes in environmental pH

• denaturation is typically irreversible (catalytic ability of the enzyme is lost or significantly decreased)

  • in some cases, its reversible

• Enzymes have optimum temperatures

  • range in which their mediated reactions occur the most efficiently

  • reaction rates change when the optimum temperatures arent maintained

• When there is an environmental increase in temperature

  • the reaction rate typically increases: increased speed of molecular movement

  • temperature increases outside of the optimum temperatures, result in denaturation

• When there is an environmental decrease in temperature

  • the reaction rate is generally slowed

  • decrease the frequency of enzyme-substrate collisions

  • does not interrupt enzyme structure ; no denaturation

• pH changes can affect enzyme activity

  • pH measures the amount of hydrogen ions in a solution

  • Optimum pH

    • same thing as optimum temperature : range in which enzyme mediated reactions occur the fastest

    • changing the pH out of the range will slow or stop enzyme activity

    • enzyme denaturation can occur

• When the substrate concentration increases

  • initially, the reaction rate increases

  • more substrates means more of a chance to collide with the enzyme

  • substrate saturation will eventually occur, there will be no further increase in the rate —> the reaction rate will remain constant if the saturation levels remain the same

• changes in enzyme concentration can also change reaction rates

  • less enzymes = slower reaction rate

    • less opportunity for substrates to collide with an active site

  • more enzymes = higher reaction rate

    • more opportunity for substrates to collide with an active site

• Competetive inhibitor : molecules can bind reversibly or irreversibly to the active site of an ezyme

  • competes with normal substrate for the enzymes active site

  • if inhibitor reactions exceed substrate : the reactions are slowed

  • if inhibitor binding is irreversible, enzyme activity will be prevented and vis versa.

• Enzymes can have regions other than the active sites called the allosteric sites

  • noncompetitive inhibitors : do not bind to the active site

  • causes conformational shape change

  • binding prevents enzyme function because the active site is no longer available → reaction rate decreases

3.4 Cellular Energy

• All living systems require a constant input of energy

  • sunlight is the main source of energy

  • autotrophs capture sunlight and turn it into useable energy by all sources

  • during some energy transformations, energy is typically lost (as heat)

• Every energy transfer increases the disorder of the universe

  • living cells are not at equilibrium: there is constant flow in and out of the cell

• Cells maintain energy by energy coupling

  • energy releasing processes drive energy-storing processes

• Within cells, the product of one reaction can serve as the reactant for another

3.5 Photosynthesis

• Structure of Chloroplast

  • surrounded by double membrane

  • central fluid filled space : stroma

  • system of interconnected membranous sacs : thylakoids

  • stacks of thylakoids : grana

  • fluid filled compartment in thylakoids : lumen

• Two stages of photosynthesis

  • Light reactions (light dependent reactions)

    • convert solar energy to the chemical energy of ATP and NADPH

    • happens in thylakoid

    • noncyclic electron flow

      • linear flow of electrons

      • move in one direction from water to NADPH

      • create a concentration gradient of H+ that drives the production of ATP through ATP sythase

    • Cyclic electron flow

      • only produces ATP (no NADPH no OXYGEN)

      • makes more ATP

  • calvin cycle (light independent reactions)

    • uses energy from the light reactions to incorporate CO2 from the atmosphere into sugar

    • happens in stroma

    • Carbon fixation : carbon dioxide is attatched to RuBP

      • carbon is unstable and immediately splits in to 2 3-PGA

    • Reduction : ATP provides energy / NADPH provides power to reduce intermediates

      • 6 G3P are produced —> 1 leaves the cycle leaves the cycle to be made in glucose

    • Regeneration : rest of the G3P rearrange to regenerate the starting RuBP molecules

3.6 Cellular Respiration

OILRIG : oxidation and reduction are coupling reactions

Photosynthesis and cellular respiration are coupling reactions.

oxidation: losing electrons

reduction : gaining electrons

Cellular respiration

the process by which cells convert glucose and oxygen into energy, carbon dioxide, and water. This process can be divided into three main stages: Glycolysis, the Krebs cycle, and the Electron Transport Chain.

Cellular respiration is the catabolism of organic molecules within cells to generate energy, ATP.

equation : C6H12O6 + 6O2 —> 6CO2 + 6H2O + energy (ATP)

1) Glycolysis

happens in the cytoplasm

Glucose cannot fit into the mitochondrial matrix naturally, so it must be broken down.

• Six-carbon glucose is converted into two 3-carbon molecules of pyruvate.

• Step 1 -3 : 2 ATP are input and broken down into ADP (endergonic reactions —> require energy) ; the bonds between the 2nd and 3rd phosphates are high energy bonds, so the energy released from these bonds in the early steps of glycolysis powers the rest of the reaction

• Step 4 : the six-carbon sugar is split into two 3-carbon sugars

• step 5 -10 : the three carbon sugars are further processed through exergonic reactions, producing 4 ATP molecules and 2 NADH molecules

the net gain for glycolysis of one glucose molecule is two molecules of ATP and 2 NADH

NADH and NAD+ are intermediary molecules that transport electrons

2) Pyruvate Oxidation

Pyruvate oxidation occurs in the mitochondrial matrix.

Pyruvate oxidation links glycolysis and the citric acid cycle by oxidizing (taking away electrons) from pyruvate to form acetyl coA

Step 1 : pyruvate undergoes decarboxylation —> the two 3-carbon sugars lose 2 CO2

• —> NAD+ is released

  —> NAD+ is reduced (gains electrons) to form NADH

  —> One molecule of NADH is produced per pyruvate, resulting in 2 NADH molecules

  —> NADH is reduced to capture the high-energy electrons that are found in NAD+

  2 Acetyl CoA is produced: the main purpose is for its acetyl group to be donated to the four-carbon compound oxaloacetate to form the six-carbon molecule citrate

3) Krebs Cycle (Citric Acid Cycle)

Acetyl CoA is the starting point for the citric acid cycle; the pathway of 8 reactions oxidizes the two-carbon acetyl group to two molecules of CO2

• Step 1: Acetyl CoA

• Step 2 : oxidized: it loses 2 electrons, which are given to the 4 carbon molecule oxaloacetate to form citrate

• Step 2-3: NAD+ is reduced to form NADH, loses a CO2 (this happens 2 times so 2 carbons are lost —> forms a four-carbon molecule)

• Step 8: NAD+ is reduced again to regenerate oxaloacetate

the citric acid cycle harvests energy from the oxidation of acetyl CoA

4) Electron transport chain

a series of redox carrier proteins embedded in the inner membrane of the mitochondrion

the electron transport chain takes NADH and oxidizes it to NAD+, so the electrons and hydrogens pass through the carrier proteins to the outer mitochondrial matrix, thus setting up a concentration gradient

the H+ ions move through the final carrier protein, ATP synthase which uses the H+ gradient to synthesize ATP by chemiosmosis

chemiosmosis is when the ATP synthase receives the H+ ions, a spinning enzyme begins to rotate which causes ADP to gain phosphate and become ATP

the H+ ions are passed back to the inner mitochondrial matrix, where they are attracted to oxygen —> the oxygen is reduced to H2O to keep the concentration gradient higher on the outside so H+ keeps going through the ATP synthase

FOR EVERY GLUCOSE MOLECULE 34-38 ATP ARE CREATED UNDER AEROBIC CONDITIONS

Fermentation

under anaerobic conditions, the electron transport chain cannot operate and NADH produced by glycolysis would not be reoxidized, causing glycolysis to stop because there would be no NAD+ for step 6 of glycolysis —> to solve this problem organisms use fermentation to reoxidize the NADH

Fermentation pathways occur in the cytoplasm

only 2 ATP per glucose is made in fermentation (restricted to the amount of glucose made in glycolysis because fermentation doesn’t go further than the cytoplasm and glycolysis)

Lactic acid fermentation

• glycolysis occurs

• pyruvate serves as the electron acceptor and the product is lactate

• NADH oxidized back to NAD+

• reversible

Alcoholic fermentation

• glycolysis occurs

• pyruvate is converted to ethanol 

• NADH oxidized back to NAD+ & CO2 is a byproduct

• reversible

3.7 Fitness

• cells can vary

  • molecular shape

  • molecular types (carbohydrates, lipids)

  • variation increases fitness

• Individual fitness

  • refers to an individual organisms ability to survive and reproduce

  • individual fitness connects to species fitness

  • the more variation a species has, the more likely the species is to thrive and survive