Microbial Metabolism

Catabolism

Breaks down complex molecules and releases energy (exergonic)

Exergonic

Releases more energy than they use (catabolic)

Endergonic

Uses more energy than they release (anabolic)

Anabolism

Uses energy and building blocks (monomers) to build complex molecules (endergonic)

Main difference between catabolism and anabolism

Catabolism provides energy and building blocks for anabolism by breaking down complex molecules

How does ATP couple catabolic and anabolic reactions

ATP is the product of catabolic reactions

It is used as energy for anabolic reactions in the process of making more complex molecules.

ATP is what helps balance both reactions

Fun fact

If a cell loses its ability to make ATP, it will die. ATP is more abundant in lipids than carbohydrates

ATP-ADP cycle

ADP uses energy from catabolic reactions to make ATP (phosphorylation)

ATP is broken down into ADP by anabolic reactions (dephosphorylation)

Enzymes

Protein catalysts that help chemical reactions occur under cellular conditions

General characteristics of enzymes

• Biological catalysts

• Effective in small amounts

• Act on specific substrates to generate specific products

• Increase the rate of reaction

• Provide a route from reactants to products w/lower activation energy

• Not consumed/permanently changed

• Some require cofactors to activate

• Genetically determined

What do enzymes increase

Reaction rate (speed at which reaction occurs)

How are enzymes named

They are named after their substrate and/or the type of reaction it performs

• Their name often ends in “ase”

• - Oxidoreductase: Assist in oxidation-reduction reactions

• - Transferase: Transfer of functional groups

• - Hydrolase: Hydrolysis

• - Lyase: Removal of atoms w/o hydrolysis

• - Isomerase: Rearrangement of atoms

• - Ligase: Joining of molecules, uses ATP

How do enzymes catalyze reactions

1. The substrate contacts the enzyme’s active site to form an “enzyme-substrate complex”

2. The substrate is transformed into products, which are then released from the enzyme

3. The enzyme is unchanged and interacts w/other substrates

Coenzymes

ORGANIC nonprotein cofactors that range from free molecules that can move about to factors anchored to the enzyme they assist

Cofactors

Non-protein components used by enzymes

• Can be inorganic (metal ions like zinc and iron) or organic (coenzymes like vitamins)

Apoenzyme

Enzyme without its necessary cofactor (inactive form)

Holoenzyme

Enzyme w/its necessary cofactor (active form)

3 important coenzymes

NAD

NADP

FAD

CoA

What is denaturation of a protein (an enzyme)

Loss of their 3D structure due to temperatures above the optimal temperature or extreme changes in pH

• Can be reversible or irreversible

What is the site where substrate and enzyme interact to generate a chemical reaction

An enzyme’s active site

Temperature

Lower temperatures cause cells to grow more slowly

Higher temperatures cause enzymes to grow faster, but too high a temperature can cause denaturation of the enzyme

pH

pH above or below the optimal can reduce the reaction rate or the speed at which a reaction occurs

• pH alters H+ (acid) and OH-(base), affecting hydrogen and ionic bonds supporting the 3D structure of protein

• E.g. Amylase (enzyme in human saliva) denatures when it reaches the lower pH levels (acidic) in the stomach

Competitive inhibitor

Slows reaction due to inhibitor competing against substrates for the target enzyme’s active site

Noncompetitive inhibitor

Slows reaction due to a noncompetitive inhibitor binding to the allosteric site of the target enzyme in a process called allosteric inhibition

How do competitive and noncompetitive inhibitors affect the works of an enzyme

Noncompetitive: Decreases enzyme activity when binding to the enzyme at a site other than the active site

Competitive: Decreases enzyme activity when binding to the active site of the enzyme

Competitive inhibitor example

Sulfa drugs compete against PABA, the enzyme’s normal substrate, for the active site

• If they bind to the active site, folic acid production decreases, and the bacteria soon stop growing and die

• Safe for humans bc we obtain folic acid from our diet, and unlike bacterial cells, our cells do not make it

Noncompetitive inhibitor example

Enzyme poisons (e.g. mercury) and Cyanide

• Cyanide inhibits enzymes in the electron transport chain, the pathway that makes ATP

• Lead and mercury are generalized and do not bind to a specific allosteric site, causing heavy metal poisoning

Noncompetitive reversible ones are important in allosteric inhibition

Ribozyme

Made w/nucleic acid RNA

• Not made w/protein

• Limited range of substrates

• Only act on other RNA molecules

Redox reactions

Term used for oxidation and reduction reactions as they always occur as partners

Oxidation

A molecule loses an electron.

• Oxidizing agents carry out oxidation reactions

  • E.g. Oxygen

Reduction

A molecule gains an electron

• Reducing agents carry out reduction reactions

  • E.g. Hydrogen

How do cells recharge ADP to ATP

Cells use oxidation and reduction reactions to extract energy from nutrients to recharge ADP to ATP

What is “oil” and “rig”

OIL → Oxidation Is Loss of electrons

RIG → Reduction is Gain of electrons

What role do coenzymes (NAD and FAD) play in oxidation/reduction

These coenzymes act as electron sponges

• FADH₂ = reduced form of FAD

• NADH = reduced form of NAD+

Hydrogen is a reducing agent, so when they bind to these coenzymes, they actually gain an electron in the form of a hydrogen

Phosphorylation

Process of adding a phosphoryl group or phosphate group to a molecule.

Can be used for the ATP-ADP cycle:

• Direct (substrate-level)

• Electron transport chain (oxidative phosphorylation, photophosphorylation)

• Enzyme regulation

Photophosphorylation

Only in light-trapping photosynthetic cells

Light energy is used to activate electrons and is converted to ATP when electrons (oxidation) are transferred from chlorophyll through a system of carrier cells

3 ways to generate ATP from ADP

• Substrate-level phosphorylation

• Oxidative phosphorylation

• Photophosphorylation

Substrate-level phosphorylation

An enzyme transfers a high-energy phosphoryl group (PO4-) from a donor substrate directly to ADP to make ATP

Oxidative phosphorylation

When a collection of redox reactions strip electrons from food and hand them off to the electron transport chain on a membrane to release energy and generate ATP

Glycolysis

Oxidation of glucose to pyruvic acid produces ATP and NADH

1. 2 ATPs are used to split glucose into 2 glyceraldehyde 3-phosphate (G3P)

2. The two G3P are oxidized by NAD and converted to 2 pyruvic acids

3. 4 ATPs and 2 NADHs are produced

End product of glycolysis

2 pyruvic acids, 4 ATPs, 2 NADHs, and 2H gained

• The overall net gain was of 2 ATP for each molecule of glucose oxidized

How many ATP are invested in the glycolysis process

2 in the beginning

Is glycolysis an oxidation or a reduction process?

It is an oxidation process as it takes out electrons throughout its process.

NAD coenzymes come in and take the electrons out of G3P and convert it to pyruvic acid, while NAD converts to its reduced version, NADH

Decarboxylation of pyruvic acid

It is the process used in cellular respiration to make acetyl-CoA by removing Carbon Dioxide (CO2) from a molecule

1. Pyruvic acid is taken from glycolysis

2. CO2 is removed from pyruvic acid

3. 2-carbon acetyl groups are formed

4. Acetyl groups bond to coenzyme A

5. Acetyl-CoA is formed and delivered to Krebs cycle

Starting materials for Krebs cycle

Acetyl-CoA and Oxaloacetic acid (form Citric Acid) and NADH

First intermediate product of Krebs cycle

After Acetyl-CoA and Oxaloacetic acid form citric acid, they are oxidized and produce

2. NADH (4)

3. FADH2 (2)

4. ATP (2)

5. CO2 (4)

What products are formed for each acetyl-CoA that enters the Krebs cycle

CO2, NADH, FADH2, ATP

Where does Krebs Cycle occur

Prokaryotes: Cytoplasm

Eukaryotes: Matrix of mitochondria

Importance of Kreb’s Cycle

Its mass production of reduced cofactors NADH and FADH2, which are then delivered to the electron transport chain

Electron transport chain

A series of carrier molecules that have collected electrons are oxidized and reduced as electrons are passed down the chain.

Energy released is used to produce ATP by chemiosmosis

What 2 mechanisms does electron transport chain drive

Oxidative phosphorylation and photophosphorylation

Chemiosmosis (oxidative phosphorylation)

Electrons from NADH pass through the transport chain while protons are pumped out (a proton gradient is established)

Protons diffuse through ATP synthase

What does ATP synthase do

Releases energy to synthesize ATP (recharge ADP)

Where does chemiosmosis take place

Bacteria: Plasma membrane
Eukaryotic cell: Inner mitochondrial membrane

Last electron acceptor for aerobic cellular respiration

Oxygen is the last electron acceptor

• Each NADH can be oxidized (made positive) in the ETC to produce 3 molecules of ATP

• DDEach FADH produces 2 molecules of ATP

Last electron acceptor for anaerobic respiratory chains

Inorganic substance other than oxygen is the final electron acceptor

• Yields less energy than aerobic respiration

How many ATP molecules are formed from

1 NADH? 3 molecules of ATP

what about 1 FADH2? 2 molecules of ATP

Final electron acceptors for anaerobic respiration

NO3, SO4, CO3

How many ATP are formed from the complete oxidation of glucose in bacteria

34 from the ETC, 2 from krebs, and 2 from glycolysis= 38 ATPs per 1 glucose in bacteria

Fermentation

Releases energy from oxidation of organic molecules

How is fermentation different from cellular respiration?

• Does not need oxygen

• No use of Krebs cycle or ETC

• Uses organic molecules as final electron acceptors

• Produces small amount of ATP

How is lactic acid fermentation different from alcohol fermentation?

4 fermentation products and the organisms that produced these products

What is beta oxidation?

With beta oxidation, lipids generate more energy than carbohydrates

Why is this the case? Explain?

Chemoheterotrophs

Chemoautotrophs

Photoautotrophs

Bacteria that carry out photosynthesis

Photoautotrophs. Explain.