Study guide for test 2

Energy and Metabolism

• Energy is the capacity to do work and exists in two states

○ Kinetic energy: the energy of motion (moving objects)

○ Potential energy: Stored energy (objects not moving but with the potential to)

• Other Forms of energy

○ mechanical energy, heat, sounds, light, electric current, and radioactivity

○ Heat is common way of measuring energy (all forms of energy can be converted to heat)

Thermodynamics: study of energy transformations

Units of Energy

• Kilocalorie (kcal)

○ 1 cal = 1000 calories (used to measure food energy)

Sun

• Sunlight powers ecosystems by providing energy

• Estimated energy from sunlight reaching earth = 1.3 x 10^24 calories per year

• Plants, algae, and certain bacteria convert light into photosynthesis

Redox reaction transfer electrons

• Oxidation : loss of electron

• Reduction: gain of electron

○ Reaction transfer electron that hold potential energy

○ Electrons move, they change the energy states if molecules involved

The First Law of Thermodynamics

• Energy cannot be created or destroyed

• It can only change form (from potential to kinetic energy)

• Chemical energy is stored in molecules and can be shifted to different forms (light energy to chemical energy in photosynthesis)

• Heat is the forms of energy that disperses into the environment and increases disorder (Entropy)

• Entropy: is the measure of disorder; heat is often the result of energy being released as it moves through systems

Second Law of Thermodynamics

• Energy transformation increases disorder (Entropy)

  • Entropy: measure of disorder or randomness in a system

• Energy naturally moves from more order (lower entropy) to more disorder (higher entropy) states

  • Ex: ICE water

    • Ice is low energy

    • Water is higher energy

    • As ice melts, disorder increases

Energy and chemical Reactions

• Free energy (G) = energy available to do work

  • G=H-TS

    • H : enthalpy (total energy in molecule)

    • T:  temperature

    • S: entropy

• Free Energy (G) helps predict if a chemical reaction will occur spontaneously:

  • Exergonic reactions (G<0) energy is released and the reaction is spontaneous

    • Catabolic: breaks down molecules (releases energy)

  • Endergonic reactions (G>0) energy is absorbed and the reaction is non spontaneous

    • Anabolic: build molecules (requires energy)

Activation energy: the energy needed to break chemical bonds to start a reaction

• Even exergonic reaction need activation energy to get started

Catalysts: lower the activation energy required to start a reaction

• Catalysts speed up reaction without being consumed in the process

• How do catalysts work

  • Catalysts do not change the direction of a reaction but help it proceed more easily by lowering the activation energy

  • They stabilize the transition state making the reaction occur faster

 Cells store and release energy in the bonds of ATP

• ATP is used to provide energy in cells

• The bonds holding the phosphate in ATP store energy when these bonds break (by hydrolysis) energy is released

• ATP is often referred to as the "Energy currency" of the cell because is powers many processes inside the cell

Structure of ATP

• ATP is made of three components

  • Ribose: 5 carbon sugar

  • Adenine: An organic molecule made of Carbon and Nitrogen

  • Phosphate Groups: a chain of three phosphate groups attached to ribose

    • Highly negatively changed and repel each other, storing energy

How Energy is Stored

• The energy in ATP is stored in the Phosphate bonds

  • These bonds are unstable and easy to break, releasing large amounts of energy when hydrolyzed (broken by H20)

• High energy bonds: bonds are between the last two phosphate groups in ATP

ATP Hydrolysis Drives endergonic Processes

• Endergonic : required energy to proceed

  • ATP is used to provide energy to drive these reaction

  • ATP is hydrolyzed (broken down) releasing energy used for the processes

ATP Cycle

• ATP cycle constantly recycles in cells

• Cells doesn't store large amount of ATP; they are constantly broken down and rebuild it

• ATP cycle: ATP is synthesized from ADP(adenosine diphosphate) and  an inorganic phosphate (P) by energy from exergonic reactions

Energy from ATP

• When ATP is hydrolyzed it releases 7.3 kcal/mol of energy which issued for cellular processes

 Cells store and release energy in the bonds of ATP

• ATP is used to provide energy in cells

• The bonds holding the phosphate in ATP store energy when these bonds break (by hydrolysis) energy is released

• ATP is often referred to as the "Energy currency" of the cell because is powers many processes inside the cell

Structure of ATP

• ATP is made of three components

○ Ribose: 5 carbon sugar

○ Adenine: An organic molecule made of Carbon and Nitrogen

○ Phosphate Groups: a chain of three phosphate groups attached to ribose

§ Highly negatively changed and repel each other, storing energy

How Energy is Stored

• The energy in ATP is stored in the Phosphate bonds

○ These bonds are unstable and easy to break, releasing large amounts of energy when hydrolyzed (broken by H20)

• High energy bonds: bonds are between the last two phosphate groups in ATP

ATP Hydrolysis Drives endergonic Processes

• Endergonic : required energy to proceed

○ ATP is used to provide energy to drive these reaction

○ ATP is hydrolyzed (broken down) releasing energy used for the processes

ATP Cycle

• ATP cycle constantly recycles in cells

• Cells doesn't store large amount of ATP; they are constantly broken down and rebuild it

• ATP cycle: ATP is synthesized from ADP(adenosine diphosphate) and an inorganic phosphate (P) by energy from exergonic reactions

Energy from ATP

• When ATP is hydrolyzed it releases 7.3 kcal/mol of energy which issued for cellular processes

Enzymes lower the activation energy of reaction (they are catalysts)

• Enzymes are proteins that help speed up chemical reaction

• Enzymes are proteins that help speed up chemical reaction by lowering the activation energy needed

• The reactant in an enzyme-catalyzed reaction is called a substrate

• Activation energy is the energy required to start a reaction

• Enzymes work by binding to substates (reactant molecules) and stressing bonds, making it easier for reactions to happen

Activation sites of enzymes

• Enzymes have active sites where substates bind

• The enzyme binds the substate and forms an enzyme-substate complex which lower the activation energy and allows reaction to proceed

• The enzyme then releases the products and is free to bind with other substrates

• Induced Fit: when substrate binds, it slightly changed to shape of the enzyme improving the fit between the two

Enzymes occur in Many Forms

• Multienzyme complexes: some enzymes work together as complexes to carry out a series of reactions, increasing efficiency

• Non protein enzymes: some enzymes are made of RNA rather than proteins; these are called Ribozymes and can catalyze reactions like proteins

Factor Influenced Enzymes

• Temperature: enzymes activity increases with temperature increase up to an optimal point (to high of temperature will denature the enzyme)

• PH: each enzyme has an optimal point (most between 6-8 )

• Inhibitor/Activators

○ Inhibitor: substances that block enzymes from activating

○ Activators: Substances that increase enzyme activation

Enzyme Cofactors

• Some enzyme need additional molecules called cofactors to work properly

• Often metal ions that assist in catalysis

*Human enzymes typically work best at 35-30 degree Celsius and pH 6-8

Competitive inhibition: an inhibitor that competes with substrates for the enzyme's active site

Noncompetitive: an inhibitor binds elsewhere on the enzyme changing its shape and preventing substrate binding

Metabolism consist of chemical reaction that happen in pathways

• Anabolic: builds molecule (requires energy-requires energy)

• Catabolic: breaks down molecule (releases energy)

Feedback Inhibition

• The final product of a pathway can stop a pathway by binding to an allosteric site on the first enzyme in the pathway

Reparation

• Organisms can be classified based on how they obtain energy:

Autotrophs (producers)

• Able to produce their own organic molecules through photosynthesis

Heterotrophs (consumers)

• Live on organic compounds produced by other organisms

All organisms use cellular respiration toe extract energy from organic molecules

Cellular respiration

• Cellular respiration is a series of reactions

• Oxidized: loss of electrons

• Reduction: gain of electron

Dehydrogenation: lost electrons are accompanied by protons

• A hydrogen atom is lost (1 electron, 1 proton)

Redox reactions

• During redox reactions, electron carry energy from molecule to another

Nikethamide adenosine dinucleotide (NAD+)

• An electron carrier and enzymatic cofactor

• NAD+ accepts 2 electron and 1 proton to become NADH

• Reaction is reversible

Energy Harvest and Redox reactions

In overall cellular energy harvest

• Dozens of redox reactions take place

• Number of electron acceptors including NAD+

In the end, high energy electron from initial chemical bonds have lost much of their energy

Transferred to a final electron acceptor

Final electron acceptors

• Aerobic Respiration

○ Most efficient way to make energy (ATP)

○ Final electron acceptor: Oxygen (O-2)

§ Example: human cells use this to make the most ATP for energy

• Anaerobic Respiration

○ Helps organisms survive without oxygen

○ Final electron acceptor: an inorganic molecule (not oxygen, example sulfate nitrate of sulfur)

§ Example: some bacteria and archaea use this in places with no oxygen, like deep-sea vents

• Fermentation

○ Provides a backup way to make ATP when no oxygen is available

○ An organic molecule( like pyruvate and acetaldehyde)

§ Example: human muscles use lactic acid fermentation during exercise: yeast uses alcohol fermentation to produce ethanol and CO_2Electron Carriers

Many types of carriers used

• Soluble, membrane-bound, move within membrane like in the mitochondria

All carrier can be reversibly oxidizes and reduced (NAD+)

Some carry just electrons, some electrons and protons

Acquires two electrons and a proton to become NADH

Cells use ATP to drive endergonic reactions

• Delta G (free energy) of hydrolyzing terminal phosphate = -7.3 kcal/mol

Two mechanisms for synthesis

1. Substate level phosphorylation

a. Transfer phosphate group directly to ADP

b. During glycolysis

2. Oxidative Phosphorylation

a. ATP synthase uses energy from a proton gradient

○ After the PEP loses a phosphate it becomes pyruvate

Oxidation of Glucose

The complete oxidation of glucose proceeds in stages

1. Glycolysis: breaks sugar is half

2. Pyruvate oxidation: prepares halves for energy extraction

3. Citric acid cycle: extraction energy from the halves

4. Electron transport chain: Converts stored energy into ATP

Glycolysis

• Converts 1 glucose C_6H_12O_6 (6carbons) to 2 pyruvate (3 carbon)

• 10 step biochemical pathway

• Occurs in the cytoplasm

• Net production of 2 ATP molecules by substrate-level phosphorylation (2 ATP use up in the reaction and ended up with 2 ATP)

• 2NADH produced by the reduction of NAH+

Priming phase

• Process starts off with one glucose molecule (6-carbon sugar)

• The cell spend 2 ATP to attach two phosphate groups to glucose (this makes glucose molecule unstable and more reactive

• Now the glucose molecule has two phosphate groups attached now becomes (6-carbon sugar diphosphate )

• This prepares glucose to be split in the next step (cells invest ATP to get more energy later)

Cleavage Phase

• The modified 6-carbon glucose splits into two 3- carbon molecules

• These 3- carbon molecules are called glyceraldehyde-3- phosphate (G3P)

• Each of these molecules still has a phosphate group attach

Energy payoff Phase

• Each 3-carbon sugar phosphate (from the previous stage) receives an additional Pi (inorganic phosphate) from the cytoplasm (stores energy temporality to be used for ATP)

• NAD+ picks up electron from the oxidation reaction and in converted into HADH

• The high energy phosphate groups (Pi) are transferred from the 3- carbon molecule to ADP forming ATP

• The ATP is produced the remaining 3-carbon molecule is not called pyruvate

• The final products of glycolysis

○ 2 Pyruvate molecules (one from each pathway)

○ 2 NADH molecules (one from each pathways)

○ Net gain of 2 ATP (4 are made but 2 were used in the first phase of glycolysis)

Steps of Glycolysis

1. involves enzyme hexokinase which traps the glucose

2. Glucose- 6- phosphate is rearranged into fructose - 6- phosphate then another ATP adds a phosphate

a. Enzyme involved Phosphoglucose isomerase into phosphofructokinase

b. This ensure glucose is fully committed to glycolysis

3. Fructose1, 6 bisphosphate is split into two 3 carbon molecule

a. Dihydroxyacetone phosphate (DHAP)

b. Gyceraldehyde-3-phosphate (G3P)

c. Enzyme involved aldose

d. G3P continues in glycolysis, while DHAP is converted into G3P

4. Oxidation Followed by phosphorylation produces 2 NADH molecules

5. G3p is oxidized (loses electrons) and NAD+ is reduced to NADH

a. Enzyme involved in glyceraldehyde-3- phosphate dehydrogenase

b. NADH stores high-energy electron for later ATP production

6. The high-energy phosphate groups from the 3-carbon molecules are transferred to ADP forming 2 ATP

a. Enzyme involved is phosphoglycerate kinase

b. This is the first ATP production step in glycolysis!

7. The molecules are rearranged and water in removed to create Phosphoenolpyruvate (PEP) a highly reactive molecule

a. Enzyme involved: Enolase

b. PEP is now ready to transfer its phosphate to ADP in the final step

8. PEP donates its phosphate to ADP, forming two more ATP molecules and two pyruvate molecules

a. Enzyme involved pyruvate kinase

b. This final step completes glycolysis and produces the molecules needed for the next phase of respiration (ends with 2 pyruvate and 2 ATP)

NAD+ must be regenerated

For glycolysis to continue, NADH must be recycled to NAD+ by either

1. Aerobic reparation

a. Oxygen is available as the final electron acceptor

b. Produces significant amount of ATP

2. Fermentation

a. Occurs when oxygen is not available

b. Organic molecules is the final electron acceptor

a. Examples: in muscle cells pyruvate is converted into lactic acid in yeast pyruvate is converted into ethanol

Fate of pyruvate (depends on oxygen availability)

• When oxygen is present, pyruvate is oxidized to acetyl coenzyme A (acetyl-CoA) which enters the citric acid cycle/ Krebs cycle

○ Aerobic respiration

• Without oxygen, pyruvate is reduces in order to oxidize NADH back to NAD+

○ Fermentation

Pyruvate oxidation

In the presence of oxygen, pyruvate is oxidized

• Occurs in the mitochondria in eukaryotes

○ Multienzyme complex called pyruvate dehydrogenase catalyzes the reaction

• It occurs at the plasma membrane in prokaryotes

Products of Pyruvate oxidation

• From each 3- carbon pyruvate molecule

○ 1CO_2

§ Decarboxylation by pyruvate dehydrogenase

○ 1 NADH (will be used later in the Electron Transport Chain for ATP

○ 1 acetyl-CoA which consists of 2 carbons from pyruvate attached to coenzyme A

§ Acetyl-CoA proceeds to the citric acid / Krebs cycle

Pyruvate oxidation of pyruvate

• Glycolysis produces 2 pyruvate molecules in the cytoplasm

• Pyruvate moves into the mitochondrial matrix where pyruvate oxidation takes place

Pyruvate oxidation : the reaction

Once inside the mitochondria each pyruvate 3- carbons undergoes oxidation

1. Step one CO_2 is released

One carbon is from pyruvate is removed as CO_2(decarboxylation

CO_2 is a waste product that’s exhaled

2. NADH is produced

a. Electrons are transferred from pyruvate to NAD+

b. NADH carried theses electron to the Electron Transport Chain to make ATP later

3. Acetyl-CoA is formed

a. The remaining 2-carbon molecule attaches to Coenzyme A (CoA) to form Acetyl-CoA

b. Acetyl- CoA is the molecule that enters the Citric acid Cyle for further production of ATP

Citric Acid Cycle

• Oxidizes the acetyl group from pyruvate

• Occurs in the matrix of the mitochondria

• Biochemical pathway of nine steps in three segments

1. Acetyl-CoA+ oxaloacetate into citrate

2. Citrate rearrangement and decarboxylation

3. Regeneration of oxaloacetate

• Citrin acid cycle yield

• Rela=ease 2 molecules of CO_2

• Reduces 3 NAD+ to 3 NADH

• Reduces 1 Fad (electron carrier to FADH_2)

Produces 1 ATP

• Regenerate oxaloacetate

Citric acid cycle

² Int he mitochondria

1. Condensation

² Acetyl-CoA(2c) + Oxaloacetate (4C) into Citrate (6C)

² This reaction is catalyzed by the enzyme Citrate Synthase

² CoA is released (CoA-SH) after the reaction (SH=sulfhydryl group)

○ Once the acetyl-CoA enters the cycle it's irreversible and must go through the cycle

2/3. Isomerization

² Itrate (6C) into Isocitrate (6C)

² The enzyme aconitase helps rearrange citrate into its isomer, isocitrate

○ This prepares the molecules for oxidation and is now in the right shape for the first energy extraction

4. The first oxidation

² Isocitrate (6C) is oxidized by the enzyme Isocitrate Dehydrogenase

² NAD+ gains electrons and is converted to NADH

² One carbon is lost as CO_2 forming alpha-Ketoglutarate (5C)

○ First energy yielding step of the citric acid cycle and NADH carried electron into the ETC

5. The second oxidation

² Alpha-Ketoglutarate (5C) is oxidized, losing one carbon as CO_2

² NAD+ picks up electrons forming NADH

² Coenzyme A (CoA) attached, forming Succinyl-CoA(4C)

6. Substrate-Level phosphorylation

² Succinyl-CoA (4C) releases CoA, forming Succinate (4C)

² The energy from this reaction drives the phosphorylation of GDP(guanosine diphosphate) into GTP (guanosine triphosphate)

² GTP can transfer a phosphate to ADP generation ATP

○ Prepares succinate for further oxidation and prepares immediate energy from the GDP to ATP

7. The third oxidation

² Succinate (4C) is oxidized to Fumarate (4C) by the enzyme succinate dehydrogenase

² Instead of NAD+, FAD is used as the electron acceptor for FADH_2

² FADH_2 carries electrons to the ETC (electron transport chain) for the ATP production

○ Links the citric acid cycle to the electron transport chain and prepares fumarate for the final steps of the cycle

8/9. Regeneration of Oxaloacetate

8. A water molecule is added to fumarate converting it into malate (4C)

9. Malate is oxidized to pxalp0acetate (4C0

² NAD+ picks up electron forming NADH

² Oxaloacetate is regenerated allowing the cycle to restart

Produces

² 4 CO_2 carbon dioxide release

² 6NAH carries high energy electron to the ETC

² 2(FADH_2) another electron carrier that contributes to

Electron transport chain

² NADH and FADH_2 donate electrons to the ETC

² Electrons pass through protein complexes in the inner mitochondrial membrane

² Protons (H+) are pumped into the intermembrane space, creating a proton gradient

² Oxygen (O_2) is the final electron acceptor forming water (H_2O)

Chemiosmosis

² Protons (H+) flow back into the mitochondrial matric through ATP synthase

² The movement of protons spins ATP synthase powering ATP production

² ADP + Pi (inorganic phosphate) into ATP(oxidative phosphorylation)

ATP Synthase

² ATP synthesis carried out by a tiny rotary motor driven by proton gradient

○ Two sub portions of ATP synthase complex

○ F_0 membrane bound complex

○ F_1 complex (stalk and know) has enzymatic activity

○ Protons travel through F_0 channel, which causes F_0 to rotate mechanical energy changes confirmation of catalytic domain in F_1

In total ATP produced

² 30 ATP per glucose for eukaryotes

² 32 ATP per glucose for bacteria

² P/O ration (phosphate to oxygen ration ) is the amount of ATP synthesized per O_2 molecule

² Theoretical and direct calculation of P/O has been contentious and has changed over time

Regulation of reparation examples of feedback inhibition

² Two key control points:

1. In glycolysis

² Phosphofructokinase is allosterically inhibited by ATP and/or citrate

2. In pyruvate oxidation/ citric acid cycle

² Pyruvate dehydrogenase inhibited by high level of NADH is stops the pyruvate

² Citrate synthase inhibited by high levels of ATP stops the citrate

Oxidation without O-2

1. Anaerobic respiration

² Use of inorganic molecules (other than O_2) as final electron acceptor

² Many prokaryotes use sulfur, nitrate, carbon dioxide, or even inorganic metals

○ Allows

2. Fermentation

² Use of organic molecules as final electron acceptor

Anaerobic respiration

Methanogens

² CO_2 is reduced to CH_4 methane

² Found in diverse organisms including cows

Sulfur prokaryotes

² Inorganic sulfate (SO_4) is reduced to hydrogen sulfide (H_2S)

² Early sulfate reduces set the stage for evolution of photosynthesis

Fermentation

² Reduces organic molecules in order to regenerate NAD+

1. Ethanol fermentation occurs in yeast

² CO_2 ethanol and NAD+ are produced

2. Latic acid fermentation

² occurs in animal cells (especially muscles )

Electrons are transferred from NADH to pyruvate to produce lactic acid