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AP Biology > Unit 3 - Enzymes + Photosynthesis + Cellular Respiration > Flashcards

Unit 3 - Enzymes + Photosynthesis + Cellular Respiration Flashcards

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1
Q

enzyme

A
  • A protein made of amino acids
  • The shape/structure of the active site makes each enzyme different
  • Enzymes increase the rate of chemical reactions by decreased the energy required for the reaction to perform (activation energy)
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2
Q

how is each enzyme differentiated from each other?

A

Specific amino acids and their R groups have different properties which affects the shape of the protein and how it folds, leading to a different enzyme being formed. This created different active sites too.

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3
Q

what is saturation point?

A

when enzyme number is constant and there is a maximum number of enzymes interacting with substrates.

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4
Q

How do you increase the rate of reaction at the saturation point?

A

If you wanted to increase the rate of reaction at the saturation point you would need to add enzymes. However, if all the substrates have been turned into products then adding enzymes would do nothing.

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5
Q

How does temperature affect the rate of reaction?

A

Increasing temperature initially affects enzyme activity because this initial increase causes more enzyme activity because molecules are moving around faster so it increases the chances of enzyme and substrate collisions. The enzyme goes through denaturation if temperature is increased too high from the optimum temperature. Lowering the temperature generally decreases enzyme activity because molecular movement slows down, resulting in fewer collisions between enzymes and substrates.

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6
Q

How does pH affect the rate of reaction?

A

Each enzyme has an optimal pH at where the reaction rate is the highest. Changing from this optimal pH too much can lead to denaturation, where the enzyme’s structure breaks down, reducing or entirely halting its activity. Maintaining the optimal pH range is crucial for ensuring the highest efficiency in enzyme reactions, while too high or too low pH values can significantly slow the reaction or stop it altogether. Larger numbers of H+ & OH- ions distort the active site.

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7
Q

Lipase

A

catalyzes digests triglycerides into glycerol and fatty acids

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8
Q

Pepsin

A

catalyzes digests large polypeptides into smaller polypeptides and amino acids. In the stomach. Optimum temp is 37 degrees celsius or 98.6 degrees fahrenheit which is the normal human body temp.

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9
Q

Amylase

A

catalyzes digests of carbohydrates into simple sugars

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10
Q

Induced Fit Model

A

Shows the enzyme structure as more flexible and is complementary to the substrate only after the substrate is bound.

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11
Q

Competitive Inhibitor

A

attaches to an enzyme’s active site but it produces no reaction. Competes with the substrate to bind to the active site. Effects reduced when substrate concentration increases

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12
Q

Noncompetitive Inhibitor

A

Also called allosteric. Allosteric inhibitor molecules are described as noncompetitive because it doesn’t bind to the active site of the substrate. Can reduce the function of the enzyme/no reaction takes place because the enzyme changes shape.

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13
Q

Endergonic reaction

A

requires an input of energy

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14
Q

Exergonic reaction

A

energy is released

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15
Q

what happens to energy when bonds are formed and when bonds are broken?

A

All bonds require energy to break
Energy is released when bonds are formed
Energy is absorbed when bonds are broken

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16
Q

Anabolic reactions

A

bonds are being synthesized between substrates, requires input of energy (endergonic)
coupled with catabolic

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17
Q

Catabolic reactions

A

bonds are being hydrolyzed, releases energy (exergonic)
coupled with anabolic

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18
Q

what is adenine triphosphate and how is it used in cells?

A

Adenosine triphosphate (ATP) is used as “energy currency” in cells, Used for coupling exergonic and endergonic reactions

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19
Q

hydrolysis of ATP

A

The hydrolysis of ATP results in net output of energy because you break the phosphate off of the ATP so it is a catabolic reaction, and catabolic reactions are exergonic reactions. Exergonic reactions are when energy is released. This energy is used for cellular processes that require energy like active transport, cell movements, anabolism

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20
Q

why does the hydrolysis of ATP release energy even though bonds are being broken?

A

During ATP hydrolysis, the bond between the terminal phosphate and the rest of the molecule is broken, producing ADP (adenosine diphosphate) and an inorganic phosphate (Pi). Breaking this bond does require energy input.

After the bond is broken, new bonds form in the products: the ADP molecule, the free phosphate ion (Pi), and the water molecules involved. The formation of these new bonds releases more energy than was required to break the original ATP bond.

The combination of bond-breaking and bond-forming results in a significant net release of energy.

Note: we don’t necessarily have to know this for the test, this is just for understanding of why ATP hydrolysis releases energy instead of absorbs energy

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21
Q

Phosphorylation

A

addition of phosphate onto ADP to form ATP. Endergonic because phosphate is added onto ADP which requires energy

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22
Q

substrate-level phosphorylation

A

Direct transfer of a phosphate group to ADP. Happens in the cytoplasm during Glycolysis and in the mitochondrial matrix during the Krebs Cycle.

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23
Q

electron transfer (oxidative phosphorylation)

A

Energy from the movement of electrons from one molecule to another, via electron carriers like NAD+ and FAD, is used to synthesize ATP. Most cellular ATP is synthesized by electron transfer in the mitochondria.

24
Q

Oxidation

A

A molecule loses electrons (and often hydrogen atoms)
LEO - Loss of Electrons is Oxidation

25
Q

Reduction

A

Reduction: A molecule gains electrons (and often hydrogen atoms)
GER - Gain of Electrons is Reduction

26
Q

Redox Reactions

A

Oxidation and reduction are coupled with each other. Electrons are passed from one substance to another - as one substance loses electrons, the other gains electrons. Can think of it in gain or loss of hydrogen atoms
Transfers of hydrogen atoms involve transfers of electrons (H = H+ + e–)
When a molecule loses a hydrogen atom, it becomes oxidized.
Use NAD+ and FAD to transport electrons (and hydrogen)

27
Q

How does hydrogens indicate stored energy?

A

The more reduced a molecule is (has electrons/hydrogen), the more stored energy it has. This is because when NAD+ or FAD take hydrogen from a molecule, it releases energy. Reduced molecules, such as glucose or fatty acids, have many electrons that can be transferred to electron carriers like NAD⁺ and FAD. As electrons move through these carriers, energy is released and used for processes like ATP synthesis.

28
Q

Hydrogen Acceptors

A

NAD+ and FAD: job is to take hydrogens from organic molecules and hold on to them ​to be used in later reactions (electron transfer phosphorylation/oxidative phosphorylation)
NAD → accepts electrons and becomes NADH.
FAD → accepts electrons and becomes FADH₂

29
Q

Reduction of NAD+ and FAD

A

highly endergonic. electrons do not remain with NADH or FADH2

NAD⁺ + 2H⁺ + 2e⁻ → NADH + H⁺

FAD + 2H⁺ + 2e⁻ → FADH₂
FAD, in its oxidized state, accepts two electrons (2e⁻) and two protons (2H⁺) to form FADH₂

30
Q

Oxidation of NADH and FADH2

A

Exergonic. Due to oxygen’s high electronegativity, it readily accepts electrons from the reduced NADH or FADH2 molecule. Oxidation of NADH or FADH2 releases more energy than hydrolysis of ATP. Oxidation of NADH releases more energy than the oxidation of FADH2 so in terms of energy release, (oxidation of NADH > oxidation of FADH2 > ATP hydrolysis)

Oxidation:
NADH + H+ + ½ O2 —> NAD+ + H2O

31
Q

reaction specificity

A

The ability of an enzyme to selectively catalyze a particular chemical reaction among many possible reactions that a substrate molecule could undergo

This goes beyond substrate recognition. Once bound to a substrate, the enzyme ensures that only a specific reaction occurs, even if the substrate could theoretically undergo several different transformations. Reaction specificity is due to the precise arrangement of amino acids in the enzyme’s active site, which creates a unique environment that favors only one reaction pathway.

Ex: the enzyme hexokinase specifically catalyzes the phosphorylation of glucose, even though glucose could participate in other types of reactions.

32
Q

Cellular Respiration: Glycolysis

A
  • occurs in the cytoplasm
  • Partially oxidizes glucose (6C) to 2 pyruvates (3C)
  • Takes energy to break glucose apart (2 ATP) to make pyruvate but glycolysis makes 4 ATP so net gain is 2 ATP
  • Also makes 2H2O
  • NAD+ recycling is essential for glycolysis to continue
  • Does not require oxygen (anaerobic)
  • Glycolysis is catabolic (hydrolyzes bonds) and exergonic (net release of energy)
33
Q

Cellular Respiration: Link Reaction

A
  • occurs in mitochondrial matrix
  • Pyruvate (3C) is oxidized to form Acetyl CoA (2C)
  • Simultaneously, pyruvate goes through decarboxylation (chemical reaction that removes a carboxyl group and releases carbon dioxide (CO₂))
  • Coenzyme A is added to the oxidized and decarboxylated pyruvate molecule (acetic acid) to form Acetyl CoA
  • Pyruvate dehydrogenase complex catalyzes the reaction
  • Acetyl CoA enters the Krebs Cycle
  • No ATP made
  • Products per pyruvate:
    - 1 CO₂
    - 1 NADH+
    - 1 Acetyl CoA
  • Inputs per pyruvate:
    - 1 NADH
    - 1 pyruvate
  • Remember that since 2 pyruvate molecules are produced from each glucose during glycolysis, the reaction occurs twice per glucose
34
Q

Cellular Respiration: Krebs Cycle

A
  • Occurs in mitochondrial matrix
  • The Acetyl CoA enters and will be completely oxidized (all additional H’s removed)
  • Acetyl CoA + oxaloacetate —> Citrate —> many rxns —> CO2 + NADH + FADH2 released
  • Net gain of: 2 ATP (produced by substrate-level phosphorylation) 6 NADH, 2 FADH2 (electron carriers)
  • 6 NADH are generated (3 per Acetyl CoA that enters)
  • 2 FADH2 is generated (1 per Acetyl CoA that enters)
  • 2 ATP are generated (1 per Acetyl CoA that enters)
  • 4 CO2 are released (2 per Acetyl CoA that enters)
  • Remember 1 CO2 was pulled off each pyruvate to make the Acetyl CoA before it entered so we have a total of 6
  • Supplies high-energy electron carriers (NADH, FADH₂) for oxidative phosphorylation.
  • catabolic and exergonic
35
Q

Cellular Respiration: Oxidative Phosphorylation

A
  • occurs in the inner mitochondrial membrane
  • Also known as the electron transport chain

Step 1: NADH+ and FADH₂ from previous steps carry electrons to the electron transport chain. NADH donates electrons to Complex I (proton pump). FADH₂ donates electrons to Complex II (peripheral protein). Complex I pumps H+ into the intermembrane space (between outer and inner membrane) to create proton gradient.

Step 2: Electrons get transported to Complex III (proton pump) where they go to cytochrome c. Complex III pumps H+ into the intermembrane space (between outer and inner membrane) to create proton gradient.

Step 3: Cytochrome c transfer electrons to Complex IV (proton pump). Complex IV transfers electrons to oxygen inside the inner membrane. Oxygen is the final electron acceptor, forming water (H₂O). Each electron carrier gets more electronegative as the electrons move through the chain. Oxygen is very electronegative so it is the “magnet” that is pulling the electrons through the chain.

Step 4: the proton gradient (aka electrochemical gradient) formed from the proton pumps (I, III, IV) powers the enzyme ATP synthase. H+ can travel from high concentration to low concentration without the use of energy (simple diffusion). This process is called chemiosmosis. High concentration of H+ in intermembrane space and low concentration in mitochondrial matrix (inside inner membrane). ATP synthase combines ADP and Pi to form ATP in the MATRIX.
Final net gain: 34 ATP, 6 H₂O

36
Q

Uncoupling

A
  • If the H+ gradient is destroyed by the presence of a membrane channel that is always open to protons, ATP cannot be made
  • Oxidation of NADH still happens and O2 is still reduced, releasing considerable energy. This forms HEAT instead of being used to make ATP.
37
Q

Fermentation

A
  • Keep glycolysis going by regenerating NAD+
  • Occurs in cytosol
  • No oxygen needed (anaerobic)
  • Produces ethanol (+ CO2) or lactate
  • 2 ATP (from glycolysis)
  • Performed by obligate anaerobes and facultative anaerobes
  • Much lower ATP yield compared to aerobic respiration
38
Q

Obligate Anaerobes

A
  • Organisms that cannot survive in the presence of oxygen
  • They rely exclusively on anaerobic processes, such as fermentation or anaerobic respiration, to generate ATP.
  • Oxygen is toxic to obligate anaerobes because they lack the enzymes (e.g., catalase or superoxide dismutase) needed to neutralize reactive oxygen species (ROS).
39
Q

Facultative Anaerobes

A
  • Organisms that can survive in both the presence and absence of oxygen.
  • they can use aerobic or anaerobic respiration
  • Ex: Yeast and some bacteria
40
Q

Obligate Aerobes

A
  • Obligate aerobes are organisms that require oxygen for survival and energy production
  • They cannot grow or sustain life without oxygen because they depend entirely on aerobic respiration to generate ATP.
  • Ex: Humans!
41
Q

Lactic Acid Fermentation

A
  • Type of anaerobic respiration
  • happens in cytoplasm
  • Undergoes glycolysis
  • Without oxygen, NAD⁺ cannot be regenerated via the electron transport chain. Fermentation solves this problem by recycling NADH back into NAD⁺.
  • The regenerated NAD⁺ is reused in glycolysis to allow continued ATP production.
  • Pyruvate —> Lactate
  • Ex. fungi, bacteria, human muscle cells
  • Used to make cheese, yogurt, acetone, methanol
  • Once oxygen is available, lactate is converted back to pyruvate by the liver
  • Outputs: 2 Lactic Acid molecules (end product), 2 NAD⁺ (recycled for glycolysis), 2 ATP (from glycolysis only; no additional ATP in fermentation).
  • During intense exercise, when oxygen delivery to muscles is insufficient, muscle cells switch to lactic acid fermentation.
  • This results in lactic acid buildup, contributing to muscle fatigue and soreness.
42
Q

Alcohol Fermentation

A
  • Type of anaerobic respiration
  • happens in cytoplasm

Step 1: Glycolysis
- undergoes glycolysis
- Inputs: 1 Glucose (C₆H₁₂O₆), 2 NAD⁺, 2 ADP + 2 Pi
- Outputs: 2 Pyruvate, 2 NADH, 2 ATP.

Step 2: Decarboxylation of Pyruvate
- next, pyruvate is decarboxylated
- Each pyruvate (C₃H₄O₃) loses one carbon atom as carbon dioxide (CO₂) in a reaction called decarboxylation.
- The remaining two-carbon molecule forms acetaldehyde (C₂H₄O).
- Pyruvate decarboxylase catalyzes this step.
- Inputs: 2 pyruvate
- Outputs: 2 Acetaldehyde, 2 CO₂.

Step 3: Reduction of Acetaldehyde to Ethanol
- Each acetaldehyde molecule is reduced to ethanol (C₂H₆O) by accepting electrons from NADH.
- This regenerates NAD⁺, which is essential for glycolysis to continue.
- Alcohol dehydrogenase catalyzes this step.
- All ATP comes from glycolysis; no additional ATP is generated during fermentation itself.
- Inputs: 2 Acetaldehyde, 2 NADH
- Outputs: 2 Ethanol, 2 NAD⁺
- Regeneration of NAD⁺ is critical for glycolysis to continue under anaerobic conditions.
- The CO₂ produced causes bread to rise and carbonates beverages
- Ethanol produced by fermentation is used as a renewable energy source
- Over time, the ethanol that is produced by this process kills the yeast and bacteria that do it

43
Q

How does a plant increase its biomass?

A

Plant increases its biomass through the formation of new organic molecules in the stroma.

44
Q

Thylakoids

A

Flat green “pancakes” that store chlorophyll and collect sun energy for the first part of photosynthesis. light reactions are carried out here. Light reactions transform light energy to chemical energy. Light energy drives the formation of ATP molecules from ADP and NADPH molecules from NADP+. Water molecules are split and oxygen is formed.

45
Q

Grana

A

Stacks of thylakoids - helps to increase surface area

46
Q

Stroma

A

The fluid that surrounds the thylakoids. Site where the second half of photosynthesis occurs. It also contains ribosomes and chloroplast DNA. Calvin cycle happens here. Use the chemical energy of ATP and NADPH to combine carbon dioxide from the air with organic molecules to form new molecules. ADP and NADP+ are recycled.

47
Q

Mesophyll

A

The middle of a leaf, chloroplasts are mainly found in these cells of leaf

48
Q

Stomata

A

pores in leaf (CO2 enter/O2 exits)

49
Q

Vascular bundles

A

Transportation of organic molecules produced in its leaf cells through the plumbing system called vascular bundles.

50
Q

Photoautotrophs

A

organisms that use light energy to make organic molecules

51
Q

Chemoautotrophs

A

use chemicals in the environment to make organic molecules

52
Q

Photosynthesis: Light Dependent Reactions

A
  • occurs in the thylakoid membrane
  • Light photons are absorbed by chlorophyll molecules in Photosystem II (PSII).
  • This energy excites electrons in the chlorophyll to a higher energy state.
  • The energized electrons are passed to the electron carriers (NADP+)
  • Water splits and releases electrons, which replaces those lost at photosystem 2. The waste product of this is oxygen. The other products are protons/H+ ions which get moved to the inside of the thylakoid (lumen)
  • The excited electrons move to the cytochrome complex. Electron carriers receive the electrons and move them to photosystem 1. Electrons lost most of the energy they got from light in photosystem 2.
  • Photons of light hit photosystem 1 and excite the electrons again. Electrons are passed to the electron carrier.
  • These electrons are either recycled or interact with an enzyme and NADP+ the final electron acceptor of the light reactions to form NADPH.
  • Some of the energy released from the electrons is used to make a proton gradient across the thylakoid membrane.
  • Protons that accumulated in the lumen diffuse into the stroma though the enzyme ATP synthase to form ATP from ADP and Pi. ATP and NADPH now have stored energy from the light reactions. This can be used in the calvin cycle.
53
Q

Light Independent Reactions

A
  • also known as the calvin cycle
  • occurs in stroma
  • is C3 photosynthesis because its end product is a 3 carbon molecule (G3P). 75% of plants do this

Step 1: Carbon Fixation
- Carbon dioxide is “fixed” into a carbohydrate by the enzyme Rubisco.
- Each CO2 attaches to a molecule of RuBP
- This forms 6 3-PGA
- RuBisCo catalizes the reaction

Step 2: Reduction
- ATP and NADPH are used to make G3P (also known as PGAL) molecules.
- ADP and NADP go back to the light reactions to be reused and re-energized
- 6 3-PGA -> 6 G3P
- 1 G3P leaves the cycle

Step 3: Regeneration
- the other 5 G3P are used to regenerate RuBP so that another carbon dioxide can be “fixed” into a carbohydrate (makes it a cycle)
- Glyceraldehyde-3-phosphate is the end product of Calvin cycle. It is an energy-rich 3 carbon sugar
- Important intermediate to other molecules: G3P → glucose → carbohydrates
→ lipids
→ amino acids
→ nucleic acids

To summarize:
- Inputs: 3 CO2, 9 ATP, 6 NADPH
- Outputs: 1 G3P, 9 ADP, 6 NADH+

54
Q

Photorespiration

A
  • On hot, dry days, plants partially close their stomata to try to conserve water
  • This also reduces their intake of carbon dioxide
  • In response, Rubisco binds oxygen instead of carbon dioxide leading to photorespiration, which does not produce sugar
55
Q

C4

A
  • Some plants, called C4 plants, avoid photorespiration by making a 4 carbon molecule (rather than 3)
  • Ex. corn, sugarcane, grass
  • Reactions are separated; Calvin Cycle occurs in bundle sheath cells around veins
  • Hot, dry days → stomata close
  • ↓photorespiration ↑sugar production
  • Advantage in hot, sunny areas
56
Q

Crassulacean acid metabolism (CAM)

A

NIGHT: stomata open → CO2 enters → converts to organic acid, stored in mesophyll cells
still makes 4 carbon sugar
DAY: stomata closed → light reactions supply ATP, NADPH; CO2 released from organic acids for Calvin cycle
Ex. cacti, pineapples, succulent (H2O-storing) plants
WHY? Advantage in arid conditions

AP Biology (5 decks)

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