Microbiology Chapter 7

Metabolism

The sum of the chemical reactions in an organism. This includes reactions to build and break down things.

Catabolism

Provides energy and building blocks for anabolism. Uses hydrolysis reactions to break down molecules. This is an exergonic reaction, meaning energy is released when we break things down. 

Anabolism

Uses energy and building blocks to build large molecules. Uses dehydration reactions to build molecules. This is an endergonic reaction, meaning energy must be put in for the reaction to occur.

Endergonic reaction

The reactants contain little energy in the beginning, but energy is absorbed from the surroundings and stored in the covalent bonds of the products. EX. Photosynthesis - plants use sunlight to build glucose

Exergonic reaction

Energy is released from the covalent bonds of the reactants. This means the products will have less energy than the reactants. EX. Burning wood releases the energy in glucose, producing heat, light, carbon dioxide, and water

Metabolic pathway

A series of enzymatically catalyzed reactions that store and release energy in organic molecules. Metabolic pathways are determined by enzymes(proteins). Enzymes are encoded by genes.

Metabolic pathway patterns

Linear: A→B→C. EX. Starch hydrolysis

Branched: A→B or C EX. Oxidation vs Fermentation

Circular:  A→B→C→A. EX. Kreb Cycle

If a chemical bond is formed, does this release or store energy?

Energy is released when a chemical bond is formed. 

Does an exergonic or an endergonic reaction require a high amount of potential energy for the reaction to occur? Why?

Exergonic reactions require a high amount of potential energy because it has energy stored in their bonds. When it is broken down, that energy gets released, and the products have less energy than the reactants.

Why are some organisms able to do some metabolic processes and other organisms cannot do those processes?

This is due to enzymes.

Advantage of organisms performing metabolism

Organisms that perform metabolism can control the storage and release of energy.

Which class of macromolecule provides most of the energy in the cell?

Oxidation of carbohydrates provides most of the cellular energy (although energy yield is greatest with metabolism of fats). Glucose is the most common carbohydrate used.

Adenosine triphosphate (ATP)

Stores energy in the bond between its phosphate groups. Structure is a 5-carbon sugar, with a triphosphate group and a base attached to it. This structure is similar to RNA. The phosphate groups carry a negative charge, so they repel each other. So energy had to be put in to keep the phosphate groups together. Energy is released when the bond between the 2nd and 3rd phosphate group is broken.

Is ATP stored long-term?

No ATP is not stored long-term. Instead, cells store energy-rich molecules such as glycogen, starch, and fats. 

When is ATP energy released?

Released when ATP is hydrolyzed. Water is used to break the bond between the 2nd and 3rd phosphate group in the ATP molecule. This releases the 3rd phosphate, since phosphate is inorganic, it is transferred to another molecule. When the bond is broken between the 2nd and 3rd phosphate, energy is released and Adenosine Diphosphate (ADP) is created.

Collision theory

Molecules or atoms must make physical contact for a chemical reaction to occur.

Activation energy

The amount of energy required to get a reaction started. 

Reaction rate

The frequency of collisions containing sufficient energy to bring about a reaction. (how fast the reaction occurs).

What are the ways that a reaction rate can be increased?

Reaction rate can be increased by adding heat (not to much because it can lead to protein denaturation and all chemical reactions speeding up), stirring the tube, increasing the pressure (molecules collide more often), higher concentration of reactants (more concentrated) because the distance between the molecules decreases (more likely to collide), or adding an enzyme

Enzymes

Three-dimensional globular proteins. They catalyze chemical reactions by lowering activation energy. Active sites are specific to the substrate. Each one catalyzes only one reaction.

What type of macromolecule are enzymes usually?

Enzymes are usually proteins.

Do specific enzymes usually catalyze only one reaction or many reactions?

Each enzyme catalyses only one reaction. 

Catalysts

Substances that can retain their original chemical composition while bringing about a change in a substrate. EX. Enzyme

Denaturation

The bonds that maintain the normal characteristics of the enzyme are broken. This change can distort the enzymes shape and prevent the substrate from attaching to the active site. This makes the enzyme nonfunctional. Usually due to heat, chemicals, or pH.

Apoenzyme

The protein portion of the enzyme. By itself, it is inactive.

Cofactor

Non-protein portion of the enzyme. May be inorganic (minerals) or an organic coenzyme (vitamins)

Holoenzyme

Apoenzyme + cofactor = whole, active enzyme

Active site

Location where substrate binds on the enzyme

Allosteric site

Space on the enzyme that can be used for regulation. (“other space”)

Trace elements

Microorganisms use these as coenzymes. EX. Iron, copper, magnesium, zinc, cobalt, etc. They participate in precise functions between the enzyme and substrate, by helping bring the active site and substrate close together, or they participate directly in chemical reactions with the enzyme-substrate complex

Important coenzymes

1. NAD+

2. NADP+

3. FAD

4. CoA

NAD+

Nicotinamide adenine dinucleotide. An electron carrier that is derived from the B vitamin, niacin. Important for cellular respiration. 

NADP+

Nicotinamide adenine dinucleotide phosphate. An electron carrier that is derived from the B vitamin, niacin. Important for photosynthesis.

FAD

Flavin adenine dinucleotide.  An electron carrier that is derived from the B vitamin, riboflavin. Used in the electron transport chain during cellular respiration.

CoA

Coenzyme A. Derived from the B vitamin, pantothenic acid. Plays an important role in the synthesis and breakdown of fats and the Krebs cycle.

Mechnism of enzymatic action

1. The substrate comes into contact with the active site and binds to it. 

2. A temporary enzyme-substrate complex forms.

3. A substrate is transformed into the products.

4. The products are released, and the enzyme remains unchanged and available. 

Induced fit

When the substrate binds to the active site. This means the enzyme changes shape to accommodate the substrate. This results in a tighter binding site.

Factors that influence enzyme activity

1. Temperature

2. pH

3. Substrate concentration

4. Inhibitors

Temperature

Bacteria that can withstand high temperatures have many covalent bonds, which means they have more cysteine amino acids. The sequence of the amino acids determines the temperatures an enzyme can withstand.

pH

Different enzymes in our body have different optimal pHs. 

Substrate concentration

Increasing substrate concentration increases the reaction rate, until saturation is reached. Once saturation is reached, adding more substrate no longer increases the reaction rate. 

Inhibitors

Molecules that inhibit the enzymes. Types: Competitive, noncompetitive, and feedback.

Competitive inhibition

Where the inhibitor has a structure similar to the substrate. The inhibitor will compete with the substrate for the active site. When it binds to the active site, it will block the substrate from binding to the active site, preventing a reaction from occurring. This can be reversed by increasing the concentration of the substrate. 

Non-competitive inhibitors

Do not compete with the substrate for the enzyme’s active site. Instead, they bind to a different location on the enzyme known as the allosteric site. When the inhibitor binds to this site, it causes a change in the enzyme’s shape, including the shape of the active site. As a result, the substrate can no longer bind effectively to the active site, and the enzyme cannot function. Unlike competitive inhibition, this cannot be reversed by adding more substrate.

Feedback inhibition

A product of a particular pathway can turn off an earlier step in the pathway. This is caused by excess amounts of the end product binding to the allosteric site on the first enzyme and deforming it. When the enzyme is deformed the pathway shuts down short-term. The active site will reform and activity will resume.

How does sulfanilamide inhibit the synthesis of folic acid? Why is this important?

Sulfanilamide is a competitive inhibitor that interferes with the synthesis of folic acid by competing with PABA (para-aminobenzoic acid), an essential nutrient used in the folic acid pathway. By blocking the use of PABA, sulfanilamide prevents bacteria from producing folic acid, which is essential for the synthesis of nucleic acids. This inhibits bacterial growth.

Endoenzymes

Found inside the cell and are normally essential for metabolism. The substrates are usually smaller. 

Exoenzymes

Secreted outside the cell and are normally used to metabolize unusual food sources or larger food or used to neutralize harmful chemicals. The substrates are usually larger. They will get broken down and transported into the cell.

Constitutive enzymes

Always present and always produced. These enzymes are essential to metabolism. 

Induced enzymes

Only produced when the substrate is present. They are used to conserve energy.

Riboenzymes

RNA-based enzymes that cut and splice RNA. These enzymes are found in the nucleus, which means they are only in eukaryotic cells

Reduction

The gain of electrons to a substance.

Oxidation

The loss of electrons from a substance.

Redox reaction

An oxidation reaction paired with a reduction reaction. Two components: Oxidation, which is the removal (loss) of electrons from one substance, and reduction, which is the addition (gain) of electrons to a substance. This is the redistribution of electrons. 

Reactants of cellular respiration

The reactants are glucose and oxygen.

Products of cellular respiration

The products are carbon dioxide, water, and energy (ATP). 

Cellular respiration

One big redox reaction. Glucose and oxygen are the reactants. Glucose is broken down to the inorganic carbon dioxide. When these bonds are broken, electrons are released. This causes glucose to become oxidized (loses hydrogen) and oxygen is reduced (gains hydrogen). By doing this process energy is produced. 

Aerobic respiration

Number of ATP produced: 30-32 ATPs per glucose

Oxygen required: Yes

Final electron acceptor: Oxygen

Organic or inorganic products: Inorganic products

Anaerobic respiration

Number of ATP produced: 3-29 ATPs per glucose

Oxygen required: No

Final electron acceptor: Inorganic molecules that are not oxygen

Organic or inorganic products: Inorganic products

Fermentation

Number of ATP produced: 2 ATPs per glucose

Oxygen required: No

Final electron acceptor: Organic molecules

Organic or inorganic products: Organic products

Coenzymes

The electron carriers in cellular respiration. Reduced molecules are energy-rich (has hydrogen). Oxidized molecules are energy-poor(lose hydrogen).

Aerobic respiration steps

1. Glycolysis

2. Transition

3. Krebs cycle

4. Electron transport chain

Glycolysis

Glucose, a polar 6-carbon sugar, is transported into the cell via a glucose transporter, since it cannot cross the cell membrane on its own. Once inside the cell, glucose is broken down into two 3-carbon pyruvate molecules in the cytosol. This process requires the input of 2 ATP molecules, which are then converted to ADP. As glucose is broken down, the electrons are transferred to NAD⁺, forming NADH. Results in a net gain of 2 ATP molecules through phosphorylation, and also produces 2 molecules of water as byproducts.

Glycolysis

Input: A polar 6-carbon sugar and 2 ATP molecules

Output: Two 3-carbon pyruvate molecules, 2 water molecules, 2 ATP, and 2 NADH

Occurs: Cytosol

Transition

The remaining 2 3-carbon pyruvate molecules are transported into the mitochondria via transport proteins in eukaryotic cells. This step just occurs in the cytosol of prokaryotic cells. The molecules are broken down further into 2 carbon dioxide molecules. 2 NADH and 2 acetyl-CoA are also produced. 

Transition

Input: Two 3-carbon pyruvate molecules

Output: 2 carbon dioxide molecules, 2 NADH, and 2 acetyl-CoA.

Occurs: Cytosol

Krebs cycle

Takes place in the mitochondria’s matrix in eukaryotic cells. Takes place in the cytosol of prokaryotes. The 2 acetyl-CoA are broken down completely into 4 carbon dioxide molecules. 6 NADH, 2 FADH₂ (electron carrier), and 2 ATP molecules are also produced. The ATP molecules are produced through substrate-level phosphorylation. 

Krebs cycle

Input: 2 acetyl-CoA

Output: 4 carbon dioxide molecules, 6 NADH, 2 FADH₂ (electron carrier), and 2 ATP molecules.

Occurs: Cytosol of prokaryotes and the matrix of the mitochondria of eukaryotes

Electron Transport Chain

Occurs in the cristae of the mitochondria of eukaryotic cells. Embedded in the membrane are large multiprotein complexes. For prokaryotic cells, this process happens in the cell membrane. NADH(becomes oxidized) will drop off electrons at the first electron carrier of the ETC and turn back into NAD+. The first electron carrier will pass it off to the second electron carrier, then to the third, and so on. As this happens, the carriers alternate between reduced and oxidized states as they accept and donate electrons. The electrons move down the ETC due to electronegativity. When the electrons reach the end of the chain, they are transferred onto oxygen(aerobic), and the oxygen will be reduced to water. As the electrons move down the chain, they give off a little energy. This energy is used to pump hydrogen ions against the concentration gradient. The hydrogens will then move down the concentration gradient through channels in ATP synthase, which causes ATP synthase to rotate. This causes mechanical motion, and this motion produces ATP from ADP through oxidative phosphorylation.

Electron Transport Chain

Input: NADH, FAD₂, O₂, ADP, and inorgaic phosphate

Output: NAD+, FAD, H₂O, and 26-28 ATP molecules.

Occurs: Cell membrane of prokaryotes and the cristae of the mitochondria of eukaryotes

Glycolysis and the Krebs cycle produce very little ATP compared to the electron transport chain. What is the important product produced during those steps, and why is that product important?

Glycolysis and the Krebs cycle produce NADH and FADH₂, which are used to carry electrons to the electron transport chain. Without these electron carriers, the electron transport chain would not have enough energy to function.

What activates ATP synthase to produce ATP?

The hydrogens will move down the concentration gradient, which causes ATP synthase to rotate. This causes mechanical motion, and this motion produces ATP (oxidative phosphorylation).

Phosphorylation mechanisms (used to make ATP from ADP): 

1. Substrate level phosphorylation

2. Oxidative phosphorylation

3. Photophosphorylation

Substrate level phosphorylation

Transferring a phosphate from a substrate onto the ADP using an enzyme. Used in glycolysis and the krebs cycle.

Oxidative phosphorylation

A series of redox reactions using electron carriers to form ATP.  EX. Electron Transport Chain, which generates the majority of ATP.

Photophosphorylation

Uses light energy to form ATP and NADPH(electron carrier). These two products will then be used in photosynthesis.

Phosphorylation

The addition of a phosphate group to ADP, turning it into ATP. 

Mitochondria

The site of cellular respiration in eukaryotic cells. A double-membrane system. It has a smooth outer membrane and a highly folded inner membrane (also called the cristae). The space between these two membranes is called the intermembrane space. The folds of the membrane increase the surface area, allowing for a higher ATP yield. The matrix is the space inside the inner membrane. Have their own DNA.

Electron carriers

Begin with NAD+, which is empty. NAD+ will pick up electrons from glucose. NAD+ accepts electrons from a hydrogen atom and picks up another hydrogen atom to form NADH. This loads up NADH. NADH will then drop the electrons off at the electron transport chain and release the hydrogen ion. This causes the NADH to oxidize and return to its original form, NAD+. 

Oxidative phosphorylation

The energy stored in a H+ gradient across a membrane couples the redox reactions of the electron transport chain to ATP synthesis.

Anaerobic respiration

Does not use oxygen as the final electron acceptor. Instead, it uses inorganic molecules such as nitrate, sulfate, etc as the final electron acceptor. Glycolysis and the transition step are the same as aerobic respiration. The Krebs cycle and electron transport chain are different. This enter process yields about 3-29 ATP per glucose.

Anaerobic respiration vs fermentation

They both go through glycolysis in the same way. But anaerobic respiration produces acetyl-CoA while fermentation produces pyruvic acid. Anaerobic respiration then continues on with cellular respiration, but fermentation goes on to produce fermentation end products.

Fermentation

An anaerobic process, but it is not anaerobic respiration. Uses organic molecules as the final electron acceptor and produces organic products. 2 ATP molecules are produced in glycolysis. Also, NAD+ is regenerated, so glycolysis can keep happening. Incomplete oxidation of glucose occurs in this process.

Fermentation steps

1. Glycolysis breaks down one molecule of glucose into 2 pyruvate molecules, producing a net gain of 2 ATP and 2 NADH. This process occurs in the absence or presence of oxygen.

2. If there is no oxygen present, cells undergo fermentation. 

3. Pyruvate acts as the final electron acceptor, or it is converted to acetaldehyde to act as the final electron acceptor. 

4. If pyruvate is used, lactic acid fermentation occurs. Where each pyruvate molecule is reduced by NADH, forming lactic acid. In this process, NADH is oxidized back to NAD⁺, which is recycled into glycolysis. Products: 2 lactic acid, 2 NAD⁺, and 2 ATP (from glycolysis).

5. Or pyruvate is converted into acetaldehyde and releases carbon dioxide. Then, acetaldehyde is reduced by NADH to form ethanol, and NADH is oxidized back to NAD⁺. Products: 2 ethanol, 2 CO₂, 2 NAD⁺, and 2 ATP (from glycolysis).

Fermentation products

Lactic acid fermentation: 2 lactic acid, 2 NAD⁺, and 2 ATP (from glycolysis).

Alcohol fermentation: 2 ethanol, 2 CO₂, 2 NAD⁺, and 2 ATP (from glycolysis).

Lactic acid fermentation

Pyruvate is used as the final electron acceptor. In this process, pyruvate is reduced by NADH to form lactic acid. As a result, NADH is oxidized back to NAD⁺, which is recycled into glycolysis. Products: 2 lactic acid, 2 NAD⁺, and 2 ATP (from glycolysis). This occurs in animal cells and some bacteria. EX. Lactobacillus 

Alcohol fermentation

Pyruvate is converted into acetaldehyde, and carbon dioxide is also released. Acetaldehyde acts as the final electron acceptor by accepting electrons from NADH. This causes NADH to be oxidized back to NAD+, and the acetaldehyde is reduced to form ethanol. Products: 2 ethanol, 2 CO₂, 2 NAD⁺, and 2 ATP (from glycolysis). This occurs in yeast cells.