- Synthesis of complex molecules from simpler ones. - Require input of energy (often from ATP generated in catabolism).

9 Flashcards by MARIANNE JOYCE TAYAG

Series of interconnected biochemical reactions that occur within a cell, allowing organisms to convert nutrients into energy and building blocks for cellular processes.

Microbial Metabolism

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Series of enzyme-catalyzed reactions converting
substrates → products.

Metabolic pathways

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2 main types of metabolic pathways

Catabolic pathways
Anabolic pathways

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Breakdown of complex molecules → simpler
ones.
Thermal energy stored in chemical bonds is
released through catabolic routes and stored
in a manner that enables ATP generation.

Catabolic pathways

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Anabolic pathways

Synthesis of complex molecules from
simpler ones.
Require input of energy (often from ATP
generated in catabolism).

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5 catabolic pathways

Glycolysis
Krebs cycle
Electron transport chain (ETC)
Beta-oxidation (fatty acid oxidation)
Protein catabolism

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Converts glucose → 2 pyruvate.

Glycolysis

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Glycolysis produces

ATP and NADH

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Initial step in aerobic & anaerobic respiration.
Provides intermediates for other pathways.

Glycolysis

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Oxidizes acetyl-CoA.

Krebs cycle

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Krebs cycle produces

NADH, FADH₂, ATP, and releases CO₂

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Central to aerobic respiration.
Provides high-energy electrons for the electron
transport chain.

Krebs cycle

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Produces ATP through transfer of electrons from NADH and FADH₂ to oxygen.

Electron Transport Chain (ETC)

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ETC produces

ATP through transfer of electrons from
NADH and FADH₂ to oxygen

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Major ATP source in aerobic organisms.
Crucial for energy production.

Electron Transport Chain (ETC)

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Breaks down fatty acids → acetyl-CoA units for energy production.

Beta-Oxidation (Fatty Acid Oxidation)

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Provides an important source of energy from fats, especially during prolonged exercise or fasting.

Beta-Oxidation (Fatty Acid Oxidation)

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Degrades proteins → amino acids

Protein catabolism

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Allows proteins to be used for energy.
Integrates amino acids into central metabolic
pathways.

protein catabolism

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Anaerobic process that converts sugars → acids,
gases, or alcohol.
Allows ATP production without oxygen.

Fermentation

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Examples of fermentation

Lactic acid fermentation, alcoholic fermentation

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Mechanisms that control the rate of metabolic
pathways.

Metabolic regulation

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Metabolic regulation includes

Feedback inhibition
Allosteric regulation

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end product of a pathway inhibits an earlier step

Feedback inhibition

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molecules bind to enzymes to alter activity

Allosteric regulation

Metabolic Pathways by Energy Source:

Autotrophic metabolism Heterotrophic metabolism

1. Organisms (e.g., plants, some bacteria) use inorganic substances like CO₂ as carbon source and light/chemical energy to drive metabolism. 2. Photosynthesis - converts light energy into chemical energy stored in glucose. 3. Chemosynthesis - converts inorganic molecules into organic molecules using chemical energy

Autotrophic metabolism

converts light energy into chemical energy stored in glucose.

Photosynthesis

converts inorganic molecules into organic molecules using chemical energy.

Chemosynthesis

1. Organisms obtain energy and carbon from organic compounds. 2. Respiration - aerobic (with oxygen) or anaerobic (without oxygen). 3. Fermentation.

Heterotrophic Metabolism

aerobic (with oxygen) or anaerobic (without oxygen).

Respiration

Function both catabolically and anabolically.

Amphibolic pathway

Name 2 major amphibolic pathways

Glycolytic pathway Tricarboxylic acid (TCA) cycle

Metabolic diversity Respiration (energy-generating metabolism)

Aerobic Anaerobic

metabolic process in which cells convert biochemical energy from nutrients into ATP (adenosine triphosphate), using oxygen as the final electron acceptor.

aerobic respiration

type of cellular respiration that occurs without oxygen; instead of oxygen, other molecules like sulfate, nitrate, or carbon dioxide act as the final electron acceptors.

anaerobic respiration

Types of Prokaryotic Energy Production Processes

Fermentation Anaerobic respiration Aerobic respiration Lithotrophy Photoheterotrophy Anoxygenic photosynthesis Methanogenesis

- Protein catalysts that speed up and direct chemical reactions. - Have great specificity for the reaction catalyzed and the molecules acted on.

Enzymes

is a substance that increases the rate of a chemical reaction without being permanently altered itself.

Catalyst

reacting molecules

Substrates

substances formed

Products

Naming of Enzymes

Most are named by adding "-ase" to the substrate

Enzymes that are named by adding "-ase" to the substrate:

- Lipids → Lipase - DNA → DNase - Proteins → Protease - Removes a hydrogen → Dehydrogenase - Removes a phosphate → Phosphatase

Enzymes grouped based on type of reaction catalyzed:

1. Oxidoreductases - oxidation & reduction 2. Hydrolases - hydrolysis

Enzyme Structure and Functions

Structure: protein or ribozyme (ribosome) Characteristic functions: - Active site - Specificity - Modified forms: inactive / active Coenzyme / cofactor involvement (-ase)

Enzymes catalyze reactions by?

lowering the activation energy

Without enzymes, reactions would still occur but?

at a very slow rate

reduce the activation energy of a reaction.

Enzymes

Lock-and-key theory:

E + S → ES → E + P

enzyme adjusts to fit the substrate

Induced-fit model

Apoenzyme includes

Protein Allosteric site

Cofactor includes

Metal ions: CU, ZN, MG, FE, CA, CO, MN

Coenzyme includes

Vitamins COA, NAD, NADP, FAD, FMN

Protein part/portion, inactive by itself

Apoenzyme

Non-protein part, usually a metal ion, turns the apoenzyme on

Cofactor

organic cofactor (vitamins, e.g., NAD, NADP, FAD, CoA, FMN)

Coenzyme

binding site that changes enzyme activity

Allosteric site

apoenzyme + cofactor (whole active enzyme)

Holoenzyme

form a bridge between enzyme and substrate.

Metal ion cofactors

can be metal ions (Cu, Zn, Mg, Fe, Ca, Co, Mn) or vitamins.

Cofactors

is inactive without a cofactor

Enzyme

Coenzymes

1. Niacin → NAD (nicotinamide adenine dinucleotide) 2. Riboflavin → FAD (flavin adenine dinucleotide) 3. Pantothenic acid → Coenzyme A

Niacin → ___________________________ (Identify the coenzyme derived from this vitamin.)

NAD (nicotinamide adenine dinucleotide)

Riboflavin → ___________________________ (Identify the coenzyme derived from this vitamin.)

FAD (flavin adenine dinucleotide)

Pantothenic acid → ___________________________ (Identify the coenzyme derived from this vitamin.)

Coenzyme A

2 Most important coenzymes:

• NAD⁺ - carries electrons in catabolic reactions • NADP⁺ - carries electrons in anabolic reactions

NAD+ and NADP+ are both derived from

Vitamin B (nicotinic acid)

NAD+ stands for

nicotinamide adenine dinucleotide

NADP+ stands for

nicotinamide adenine dinucleotide phosphate

Electron Carriers (NAD)

NAD⁺ as coenzyme NADH as coenzyme

Reactions of NAD as electron carrier

NAD⁺ + ED → EDOX + NADH NADH + EA → EARED + NAD⁺ Overall: ED + EA → EDOX + EARED

Factors Affecting Enzymes

Temperature pH Acids/bases UV light Substrate concentration (saturation) Inhibitors

↑ Temperature =

↑ Reaction rate (until denaturation).

Enzymes have an __________ __________, temp at which the enzyme catalyzes the reaction at its maximum.

Optimal temperature

Above the optimal temperature, enzymes become ____________

Denatured

Unfolded, enzyme no longer fits substrate, cannot catalyze the reaction

Denatured

Denaturation of Active Proteins - Enzymes are __________ that only function when propely __________

Enzymes are polypeptides that only function when properly folded.

Changes in temperature, pH, or salt concentration can disrupt _____ _____ _____

Amino acid interactions

When the amino acid interactions were disrupted due to changes in temperature, pH, or salt concentration, what happens next?

unfolding (denaturation)

Enzymes have an _____ pH that favors correct folding.

Optimal pH

pH that is too acidic or too basic will

Denature enzyme

↑ Substrate concentration =

↑ Reaction rate (until saturation).

Each enzyme has a maximum turnover number =

Top speed for converting substrate into product

At saturation, all active sites are full →

the enzyme works at maximum speed

True or False Adding more substrate beyond saturation will increase the reaction rate.

False

2 types of inhibitors

Competitive inhibitors Non competitive inhibitors

- Bind at active site - Similar shape to substrate - Binding can be reversible or irreversible

Competitive inhibitors

- Bind at allosteric site - Change enzyme shape - Binding can be reversible or irreversible

Non competitive inhibitors

Enzyme Inhibition Summary

• Inhibitors bind enzymes in 2 main ways: o Competitive inhibition → binding to active site o Allosteric (non-competitive) inhibition → binds elsewhere, changes shape • Inhibitors may be reversible (can detach) or irreversible (e.g., poisons).

Compete for the active site.

Competitive inhibitors

2 examples of competitive inhibitors

Penicillin Sulfanilamide (sulfa drugs)

Competes for the active site on the enzyme involved in synthesis of the pentaglycine crossbridge.

Penicillin

o Competes for the active site on the enzyme that converts PABA into folic acid. o Folic acid is required for the synthesis of DNA and RNA.

Sulfanilamide

Required for the synthesis of DNA and RNA

Folic acid

• Attach to an allosteric site. • Change the enzyme shape and prevent activity.

Non competitive inhibitors

- The end-products of metabolic pathways are important reversible enzyme inhibitors - inhibit 1st enzyme in pathway, turning the pathway "off"

feedback inhibition

2 Energy Production

Oxidation Reduction

Refers to the loss of hydrogens and/or electrons.

Oxidation

Refers to the gain of hydrogens and/or electrons.

Reduction

1. Microorganisms oxidize carbohydrates as their primary energy source. 2. Glucose is the most common energy source. 3. Energy is obtained from glucose by: A. Respiration B. Fermentation

Carbohydrate catabolism

most common energy source (in carbohydrate catabolism)

Glucose

In carbohydrate catabolism, energy is obtained from glucose by:

Respiration Fermentation

ATP-generating process in which molecules are oxidized and the final electron acceptor is almost always an inorganic molecule.

Respiration

Metabolic process by which Bacterial cells generate ATP by oxidizing organic molecules through biochemical reactions.

Respiration

2 types of reparation

Aerobic respiration Anaerobic respiration

final electron acceptor is oxygen.

aerobic respiration

final electron acceptor is different (exogenous), usually inorganic (e.g., NO₃⁻, SO₄²⁻, CO₂, Fe³⁺, SeO₄²⁻, fumarate)

Anaerobic respiration

Fermentation came from this latin word

fermentare = to rise of ferment

Energy substrate is oxidized and degraded without external electron acceptor.

Fermentation

Anaerobic catabolism where organic compounds both donate and accept electrons, and redox balance is achieved without external electron acceptors.

Fermentation

3 ways in which microorganisms degrade sugars to pyruvate

1. Glycolysis 2. Pentose phosphate pathway 3. Entner-Doudoroff pathway

Carbohydrates and other nutrients serve 2 functions in heterotrophic microorganisms:

1. Oxidized to release energy. 2. Supply carbon/building blocks for new cell constituents

4 subpathways of aerobic cellular respiration

1. Glycolysis 2. Transition reaction 3. Krebs cycle 4. Electron transport system

3 types of phosphorylation

Substrate-level phosphorylation Oxidative phosphorylation Photophosphorylation

direct transfer of phosphate to ADP (e.g., glycolysis, Krebs cycle).

Substrate-level phosphorylation

- electrons move through ETC, releasing energy [this energy is used to pump protons (H+ ions) across the membrane, creating a protion gradient (PMF)] - chemiosmosis

Oxidative phosphorylation

light energy converted to chemical energy (photosynthesis)

Photophosphorylation

ATP is formed through a series of sunlight-driven reactions

Photophosphorylation

Part of the light-dependent reactions of photosynthesis where light energy excites electrons, and they move through protein complexes in the photosynthetic electron transport chain

Photophosphorylation

is central to the cell's energy cycle (heterotrophs, photosynthetic organisms, chemoautotrophs).

ATP (metabolic role)

Expenditure of ____ powers all processes in cellular work.

ATP (metabolic role)

Series of reactions (Krebs cycle, respiratory chain) that converts glucose → CO₂, produces H₂O, and uses O₂ as final electron acceptor.

aerobic respiration

Generates large amounts of ATP.

Aerobic respiration

Aerobic respiration is found in

Bacteria, fungi, protozoa, animals

Primary central pathway for all living organisms.

Glycolysis (Embden-Meyerhof-Parnas Pathway)

starts from 6-carbon (glucose) and ends up producing 3-carbon (pyruvate)

Glycolysis

glycolysis occurs where

Cytoplasm of prokaryotes and eukaryotes

Do glycolysis require oxygen

End product of glycolysis

Pyruvate (3C) - utilized for 3 different destinations

Net yield of glycolysis

2 ATP, 2 NADH per glucose

Other name for glycolysis

Embden-Meyerhof-Parnas Pathway

Oxidation of glucose into 2 molecules of pyruvic acid

Glycolysis

ATP synthesis via substrate-level phosphorylation

Glycolysis

In the six-carbon stage of glycolysis, how many ATP molecules are used, and what compound is formed?

2 ATPs are used to form fructose 1,6-bisphosphate

For each molecule of glyceraldehyde 3-phosphate (G3P) transformed into pyruvate, what is produced?

1 NADH and 2 ATP are formed

How many molecules of glyceraldehyde 3-phosphate (G3P) are generated from one glucose molecule? → ___________________________ (Clue: Consider the role of dihydroxyacetone phosphate.)

Two G3P molecules

Because two G3P molecules are formed per glucose, how many ATP and NADH molecules are produced in the three-carbon stage? → ___________________________ (Clue: Multiply the output per G3P by two.)

4 ATPs and 2 NADHs per glucose

Subtracting the ATP used in the six-carbon stage from the ATP produced in the three-carbon stage gives what net ATP yield per glucose molecule?

2 ATPs per glucose

Pentose Phosphate Pathway (PPP) is also called

phosphoketolase or hexose monophosphate pathway

It can operate either aerobically or anaerobically and is important in biosynthesis as well as in catabolism

Pentose Phosphate Pathway (PPP)

Pentose Phosphate Pathway (PPP) provides

o NADPH as electron source o 4-carbon sugar for aromatic amino acid synthesis o 5-carbon sugar for nucleic acid synthesis o CO₂ acceptor

a second pathway that may be used at the same time as the glycolyticpathway or Entner Duodoroff sequence

Pentose Phosphate Pathway (PPP)

Entner Doudoroff Pathway occurs where

Cytoplasm

Anaerobic pathway that uses different enzymes

Entner Doudoroff Pathway

Entner Duodoroff Pathway is found in these microorganisms

Pseudomonas, Zymomonas, Enterococcus.

End products of Entner Duodoroff Pathway

1 ATP, 1 NADPH, 1 NADH, 2 pyruvate, H₂O.

The Entner-Doudoroff pathway begins with the formation of two key intermediates that are also found in the pentose phosphate pathway. Name them.

Glucose 6-phosphate and 6-phosphogluconate

Name 3 bacterial genus that utilizes the Entner-Doudoroff pathway.

Pseudomonas, Rhizobium, Agrobacterium.

Instead of being further oxidized, 6-phosphogluconate is dehydrated to form this key intermediate of Entner-Doudoroff Pathway

2-keto-3-deoxy-6-phosphogluconate (KDPG)

The enzyme that cleaves KDPG into pyruvate and glyceraldehyde 3-phosphate (G3P) is called:

KDPG aldolase

in the bottom portion of the glycolytic pathway, the glyceraldehyde 3-phosphate is converted to

Pyruvate

What are the final products (energy yield) of the ED pathway per glucose molecule degraded?

1 ATP, 1 NADPH, and 1 NADH per glucose

- Oxidizes pyruvate → CO₂. - aerobic (use O2 as e- acceptor) - Provides carbon skeletons for biosynthesis.

Krebs Cycle (TCA/Tricarboxylic acid, Citric Acid Cycle)

Products of krebs cycle per Acetyl-CoA

• 2 CO₂ • 3 NADH • 1 FADH₂ • 1 ATP (from GTP)

Krebs cycle regenerates

CoA and oxaloacetic acid

Overall products of krebs cycle

• 2 ATP • 6 NADH • 2 FADH₂ • 4 CO₂

Location of krebs cycle

• Eukaryotes - mitochondria • Prokaryotes - cytoplasm

the respiratory chain

Electron Transport Chain (ETC)

Sequence of carriers transferring electrons from donors NADH & FADH₂ to receiver O₂.

Electron Transport Chain (ETC)

ETC generates a proton motive force (PMF) which leads to formation of

ATP (thus, referred electron transport phosphorylation)

Location of ETC

- Inner mitochondrial membrane (eukaryotes) - Plasma membrane (prokaryotes)

Electron donors of ETC

NADH (3 ATPs) FADH (2 ATPs)

Anaerobic Processes • Lactic acid - • Mixed acid - • Butanediol - • Butyric acid - • Butanol-acetone - • Propionic acid -

• Lactic acid - Lactobacillus • Mixed acid - Enterobacteriaceae • Butanediol - Klebsiella, Enterobacter • Butyric acid - Clostridia • Butanol-acetone - Clostridia • Propionic acid - Corynebacteria

• Anaerobic, cytoplasmic. • Partial oxidation, small ATP yield (substrate-level phosphorylation). • Organic intermediaries = final electron acceptors.

Fermentation

End products of fermentation

o Acids: lactic acid, acetic acid, butyric acid, acetone o Alcohols: ethanol, isopropyl o Gases: CO₂, H₂ o contaminants

Fermentation end-products depend on:

1. Type of organism 2. Original substrate 3. Enzymes present and active

o Yield: 2 ATP o End product: lactic acid o Uses: yogurt, pickles, sauerkraut, milk fermentation o Genera: Streptococcus, Lactobacillus o Groups: ▪ Homolactic fermenters - use glycolysis, reduce pyruvate → lactate ▪ Heterolactic fermenters - produce lactate, ethanol, CO₂ (phosphoketolase pathway)

Lactic acid fermentation

ATP yield of Lactic acid fermentation

2 ATP

End product of lactic acid fermentation

Lactic acid

2 genera of bacteria commonly involved in lactic acid fermentation.

Streptococcus and Lactobacillus

Give 6 examples of food produced by lactic acid fermentation.

Yogurt Pickles Sauerkraut Milk Cucumber Cabbage

End products of alcohol fermentation

Alcohol and CO₂

used in alcoholic beverages, bread dough to rise

alcohol fermentation

What microorganism is responsible for alcohol fermentation

Saccharomyces cerevisiae (yeast)

2 GROUPS OF LACTIC ACID FERMENTERS

HOMOLACTIC FERMENTERS HETEROLACTIC FERMENTERS

Use the glycolytic pathway and directly reduce almost all their pyruvate to lactate with the enzyme lactate dehydrogenase

Homolactic fermenters

Form substantial amounts of products other than lactate

heterolactic fermenters

What are produced by way of the phosphoketolase pathway

Lactate, ethanol, co2

Important for identification of Enterobacteriaceae.

Formic acid fermentation

2 types of formic acid fermentation

Mixed acid fermentation Butanediol fermentation

ATP yield of propionic acid fermentation

2 ATP

End products of propionic acid fermentation

propionic acid and CO₂

Organism that utilizes propionic acid fermentation

Propionibacterium sp.

End product of Butylene-Glycol Fermentation (2,3-Butanediol)

2,3-butanediol

Organisms that utilize Butylene-Glycol Fermentation (2,3-Butanediol)

Pseudomonas, Enterobacter, Serratia, Erwinia, Bacillus

ATP yield of mixed acid fermentation

2 ATP

End products of mixed acid fermentation

acetic, lactic, succinic, formic acids + ethyl alcohol

Organisms that utilize mixed acid fermentation

E. coli, Salmonella, Proteus, Enterobacter

Pyruvate is converted to acetoin, which is then reduced to 2,3-butanediol (via NADH)

butanediol fermentation

End products of butanediol fermentation

ethanol + small amounts of acids found in mixed acid fermentation

Organisms that utilize butanediol fermentation

Enterobacter, Serratia, Erwinia, Bacillus

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