Biology Chapter on Cellular Respiration

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Questions and Answers

What processes start with glycolysis?

Cellular respiration and fermentation

What is the net yield of ATP from glycolysis?

0 ATP

6 ATP

4 ATP

2 ATP (correct)

Glycolysis occurs in the mitochondria.

False

What are the products of the Krebs cycle?

NADH, FADH2, GTP, and CO2 Signup and view all the answers

What type of phosphorylation occurs during glycolysis?

Substrate-level phosphorylation Signup and view all the answers

What is the final electron acceptor in aerobic respiration?

Oxygen Signup and view all the answers

Which of the following is produced during fermentation?

All of the above Signup and view all the answers

Anaerobic respiration yields more ATP than aerobic respiration.

False Signup and view all the answers

What lipids are broken down into for energy supply?

Glycerol and fatty acids Signup and view all the answers

Match the fermentation type with its product:

Lactic acid fermentation = Lactic acid Alcohol fermentation = Ethanol and CO2 Signup and view all the answers

The ________ cycle fixes carbon dioxide into organic molecules.

Calvin Signup and view all the answers

What are the two photosystems used in photosynthesis?

Photosystem I (PSI) and Photosystem II (PSII) Signup and view all the answers

What do organic molecules primarily contain?

Carbon Signup and view all the answers

Inorganic molecules contain carbon atoms.

False Signup and view all the answers

What is the role of carbon in organic molecules?

Forms four covalent bonds. Signup and view all the answers

The simplest organic compound is _____ .

methane Signup and view all the answers

Which type of isomers have the same molecular formula but different structural arrangements?

Structural isomers Signup and view all the answers

What are macromolecules?

Large biomolecules formed by linking monomers. Signup and view all the answers

The empirical formula for carbohydrates is _____ .

(CH2O)n Signup and view all the answers

Which of the following is a type of fatty acid?

Saturated fatty acids Signup and view all the answers

What is the function of proteins?

Catalysts, transporters, and structural components. Signup and view all the answers

What is ATP an abbreviation for?

Adenosine triphosphate Signup and view all the answers

Catabolism builds complex molecules.

False Signup and view all the answers

What do autotrophs do?

Convert inorganic CO2 into organic compounds. Signup and view all the answers

In enzymatic reactions, the substrate fits into the _____ of the enzyme.

active site Signup and view all the answers

What happens to enzymes at extreme temperatures?

Denature Signup and view all the answers

Feedback inhibition prevents overproduction of substances.

True Signup and view all the answers

What is the primary function of glycolysis?

Breakdown of carbohydrates to release energy. Signup and view all the answers

What do organic molecules contain?

carbon Signup and view all the answers

What are the four main macromolecules?

Carbohydrates, proteins, lipids, nucleic acids Signup and view all the answers

Inorganic molecules do not contain carbon.

True Signup and view all the answers

What is the simplest organic compound known?

Methane Signup and view all the answers

The empirical formula of carbohydrates is (CH2O)n, where n represents the number of __________ units.

repeated Signup and view all the answers

What type of bond forms between hydroxyl groups during dehydration synthesis in carbohydrates?

glycosidic bond Signup and view all the answers

Which of the following is a disaccharide?

Maltose Signup and view all the answers

What are lipids primarily composed of?

carbon and hydrogen Signup and view all the answers

What type of fatty acids contain only single bonds?

Saturated fatty acids Signup and view all the answers

Proteins are made up solely of amino acids.

False Signup and view all the answers

What is ATP an abbreviation for?

adenosine triphosphate Signup and view all the answers

What is the process called that builds complex molecules from simpler ones?

Anabolism Signup and view all the answers

What do enzymes do?

speed up chemical reactions Signup and view all the answers

The __________ reaction is important in metabolism for transferring electrons between molecules.

REDOX Signup and view all the answers

What classification describes organisms that convert inorganic CO2 into organic compounds?

Autotrophs Signup and view all the answers

What is the primary process that starts glucose catabolism?

Glycolysis Signup and view all the answers

Which of the following is a type of glycolytic pathway?

Pentose phosphate pathway Signup and view all the answers

What happens during the energy investment phase of glycolysis?

Two ATP are used and a 6-carbon glucose is split into two phosphorylated 3-carbon molecules. Signup and view all the answers

What is produced in the energy payoff phase of glycolysis?

All of the above Signup and view all the answers

Glycolysis requires oxygen to occur.

False Signup and view all the answers

What is the result of the transition (bridge) reaction after glycolysis?

Pyruvate is converted to acetyl CoA. Signup and view all the answers

Which cycle generates the most NADH?

Krebs cycle Signup and view all the answers

What is the final electron acceptor in aerobic respiration?

Oxygen Signup and view all the answers

Anaerobic respiration yields more ATP than aerobic respiration.

False Signup and view all the answers

What is produced during lactic acid fermentation?

Lactic acid Signup and view all the answers

What is a common product of alcohol fermentation?

Ethanol Signup and view all the answers

Photosynthesis occurs in the mitochondria of plant cells.

False Signup and view all the answers

What is the role of RuBisCO in the Calvin cycle?

It catalyzes the addition of CO2 to RuBP. Signup and view all the answers

The process of converting light energy into chemical energy in plants is called ______.

photosynthesis Signup and view all the answers

What is the process of glucose catabolism that starts with glycolysis?

Cellular respiration and fermentation Signup and view all the answers

Glycolysis requires oxygen to proceed.

False Signup and view all the answers

What are the three types of glycolytic pathways?

Entner-Doudoroff pathway Signup and view all the answers

Glycolysis is an anaerobic process that occurs in the __________.

cytoplasm Signup and view all the answers

What is the net yield of ATP from glycolysis?

2 ATP Signup and view all the answers

The Krebs cycle occurs in the cytoplasm of both prokaryotes and eukaryotes.

False Signup and view all the answers

What are the main products of the Krebs cycle?

FADH2 Signup and view all the answers

What is the final electron acceptor in aerobic respiration?

Oxygen Signup and view all the answers

Anaerobic respiration yields more ATP than aerobic respiration.

False Signup and view all the answers

What is produced during lactic acid fermentation?

Lactic acid Signup and view all the answers

What type of fermentation produces ethanol and CO2?

Alcohol fermentation Signup and view all the answers

What are the products of lipid catabolism?

Glycerol Signup and view all the answers

Photosynthesis occurs in the __________ of eukaryotic cells.

chloroplasts Signup and view all the answers

What is the function of photosynthetic pigments?

To absorb solar energy Signup and view all the answers

What type of photosynthesis produces oxygen?

Oxygenic photosynthesis Signup and view all the answers

Match each fermentation type with its product:

Lactic acid fermentation = Produces lactic acid Alcohol fermentation = Produces ethanol and CO2 Heterolactic fermentation = Produces lactic acid and other compounds Homolactic fermentation = Produces only lactic acid Signup and view all the answers

What are organic molecules primarily composed of?

carbon Signup and view all the answers

What is the simplest organic compound?

methane (CH4) Signup and view all the answers

Which of the following groups are considered macromolecules?

All of the above Signup and view all the answers

What is the empirical formula for carbohydrates?

(CH2O)n Signup and view all the answers

What type of reaction occurs during dehydration synthesis?

Water is formed Signup and view all the answers

What is a glycosidic bond?

covalent bond formed between hydroxyl groups of carbohydrates Signup and view all the answers

What type of lipids consist of a glycerol molecule and two fatty acids?

Complex lipids Signup and view all the answers

Saturated fatty acids contain at least one double bond.

False Signup and view all the answers

What is ATP commonly known as?

energy currency of the cell Signup and view all the answers

Which type of metabolism involves the breakdown of complex molecules?

Catabolism Signup and view all the answers

What do autotrophs convert CO2 into?

organic compounds Signup and view all the answers

Which of the following is NOT a type of electron carrier?

ATP Signup and view all the answers

Denaturation of a protein results in its active form.

False Signup and view all the answers

Study Notes

Organic vs Inorganic Molecules

Organic molecules contain carbon and are essential for biological and chemical processes.
Inorganic molecules lack carbon (except for carbonates and carbon oxides).
Organic molecules are larger and more complex than inorganic molecules.
Most of the carbon in organic molecules originates from inorganic carbon captured in the process of carbon fixation.

Carbon

Carbon bonds with other atoms through four covalent bonds due to its four valence electrons.
The simplest organic compound is methane (CH4).
Carbon atoms can form straight, branched, or ring-shaped carbon skeletons.

Isomers

Isomers are molecules with the same formula but different arrangements of atoms.
Structural isomers differ in their structural formulas.
Stereoisomers differ in the arrangement of atoms in space.
Enantiomers are non-superimposable mirror images.
Optical isomers rotate the plane of polarized light:
- d-form rotates light clockwise.
- l-form rotates light counterclockwise.

Functional Groups

Specific groups of atoms (in addition to carbon) that determine a molecule's chemical reactivity and properties.
Important functional groups include: hydroxyl, amino, and carboxylic acid groups.

Macromolecules

Large biomolecules formed by monomers (building blocks) linked together to form polymers.
Dehydration synthesis links monomers, releasing water as a byproduct.
Four main macromolecules: carbohydrates, proteins, lipids, and nucleic acids.

Carbohydrates

Most abundant biomolecules containing carbon, hydrogen, and oxygen.
Empirical formula is (CH2O)n, where n represents the number of repeated units.
Have a 1:2:1 ratio of carbon to hydrogen to oxygen.
Can also contain nitrogen, phosphorus, and sulfur.
Important functions:
- Food source in ecosystems.
- Part of DNA and RNA.
- Structural components (cellulose and chitin).
- Primary source of energy storage (starch and glycogen).

Monosaccharides

Simple sugars that are monomers for complex carbohydrate synthesis.
Classified based on their number of carbon atoms:
- Triose (3 carbons)
- Tetrose (4 carbons)
- Pentose (5 carbons)
- Hexose (6 carbons)
Hexoses include glucose, galactose, and fructose.
Pentoses include ribose and deoxyribose.
Molecules with four or more carbon atoms are more stable in a ring structure.

Disaccharides

Composed of two monosaccharides linked by glycosidic bonds.
Examples:
- Maltose (two glucose molecules, grain sugar).
- Lactose (galactose and glucose, milk sugar).
- Sucrose (glucose and fructose, table sugar).

Polysaccharides

Composed of hundreds of monosaccharides linked by glycosidic bonds.
Not soluble in water.
Can have linear or branched configurations due to the orientation of glycosidic linkages.
Examples:
- Cellulose (linear chains of glucose, cell walls in plants).
- Starch and glycogen (branched polymers of glucose, energy storage).
Modified polysaccharides:
- N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) are found in bacterial cell wall peptidoglycan.
- Polymers of NAG form chitin (found in fungal cell walls).

Lipids

Composed primarily of carbon and hydrogen (also may contain nitrogen, oxygen, phosphorus, and sulfur).
Diverse structures and functions:
- Source of nutrients.
- Energy storage.
- Structural components for membranes and hormones.
Chemically distinct groups:
- Fatty acids and triglycerides.
- Phospholipids and biological membranes.
- Isoprenoids and sterols.

Fatty Acids

Long hydrocarbon chains with a terminal carboxylic acid group.
Hydrophobic.
Types:
- Saturated fatty acids (contain only single bonds, straight, solid at room temperature).
- Unsaturated fatty acids (contain at least one double bond, have kinks in the carbon skeleton making them liquid at room temperature).

Triglycerides

Three fatty acids linked to a glycerol molecule (simple lipids).
Components of adipose tissue (body fat).
Energy storage molecules.

Complex Lipids

Composed of:
- Glycerol molecule.
- Two fatty acids (saturated and/or unsaturated).
- An additional component (phospholipid/glycolipid).
Amphipathic:
- Hydrophilic heads.
- Hydrophobic tails.
Form unique structures in aqueous environments:
- Micelles (spherical particles, interior is hydrophobic tails, exterior is hydrophilic heads).
- Unit membranes (lipid bilayer sheets, forming vesicles/liposomes).

Isoprenoids

Branched lipids formed by modification of isoprene.
Technological applications.

Steroids

Complex ringed structures.
Found in cell membranes, some function as hormones.
Most common are sterols.
- Cholesterol (most common in animal tissues, strengthens cell membranes in eukaryotes and bacteria lacking cell walls).
- Hopanoids (similar to cholesterol, found in prokaryotes to strengthen bacterial membranes).
- Ergosterol (similar compound to cholesterol, found in fungi and some protozoa).

Proteins

Composed of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur.
Essential for cell structure and function:
- Enzymes catalyze chemical reactions.
- Transporter proteins move molecules across membranes.
- Flagella aid in movement.
- Some bacterial toxins and cell structures.
Composed of amino acids.
Each amino acid has an alpha-carbon bonded to:
- Hydrogen.
- Carboxyl group.
- Amino group.
- Side chain (R-group).

Peptide Bonds

Chemical bond formed between two amino acids.
Created by dehydration synthesis between the carboxyl group of one amino acid and the amino group of another.
Products:
- Peptides (<50 amino acids).
- Proteins (very large number of amino acids or multiple polypeptide chains).

Levels of Protein Structure

Primary structure: sequence of amino acids in a polypeptide chain.
- Flexible structure due to peptide bonds.
Secondary structure: hydrogen bonding between amine and carboxyl groups within the peptide backbone.
- α-helix (amino acids every four residues apart, helical shape).
- β-pleated sheets (amino acids are farther apart, pleated sheet structure).
Tertiary structure: 3D shape of a polypeptide chain, essential for function (all proteins have a tertiary structure).
- Bonds between amino acid residues that are far apart in the chain (example: disulfide bridges, hydrogen bonds, and ionic bonds).
- Protein folding: the process where a polypeptide chain assumes its tertiary structure.
- Native structure: folded proteins that are fully functional.
- Denatured proteins: unfolded proteins that are no longer functional (loss of secondary, tertiary, and quaternary structure, typically irreversible).
Quaternary structure: present only in proteins consisting of multiple polypeptide chains.
- All subunits must be present and properly arranged for functional activity.
- Stabilized by weak interactions.
- Examples: hemoglobin (four globular protein units, 2 alpha and 2 beta polypeptides, heme group contains iron).

Conjugated Proteins

Consist of both protein and non-protein components:
- Glycoprotein (carbohydrate component).
- Lipoprotein (lipid component).
- Nucleoprotein (RNA component).
Important component of gram-negative cell membranes.

Microbial Metabolism

The sum of all chemical reactions within a cell.
Reactions provide energy and create substances that sustain life.
Many microbial metabolic pathways are beneficial rather than pathogenic.

Catabolism

Breaks down complex molecules into simpler ones.
Exergonic (releases energy).
Example: breakdown of glucose into CO2 and H2O.

Anabolism

Builds complex molecules from simpler ones.
Endergonic (requires energy).
Example: building proteins from amino acids.

ATP

Adenosine triphosphate, the energy currency of the cell.
Stores energy released from catabolism.
Releases energy to drive anabolic reactions.

Classification of Organisms by Carbon and Energy Source

Carbon source:
- Autotrophs: convert inorganic CO2 into organic compounds.
- Heterotrophs: use organic compounds as nutrients.
Energy source:
- Phototrophs: obtain electrons from light.
- Chemotrophs: obtain electrons from chemicals.
  - Organotrophs: electrons from organic compounds.
  - Lithotrophs: electrons from inorganic compounds (unique to microbes).

REDOX Reactions

Electron transfer between molecules, crucial for energy transfer.
Oxidation: loss of electrons (OIL).
Reduction: gain of electrons (RIG).

Energy Carriers

Energy released from catabolism can be stored:
- By reducing electron carriers.
- In the bonds of ATP.
Electron carriers:
- Bind and carry high-energy electrons.
- Easily reduced or oxidized.
- Examples: NAD, NADP, FAD.
ATP as an energy carrier:
- Adenosine triphosphate (ATP) is the primary energy currency of the cell, storing and releasing energy as needed.
- Adenine molecule bonded to ribose molecule and three phosphate groups.
- Phosphorylation: adding an inorganic phosphate group (Pi) to ADP, storing energy.
- Dephosphorylation: breaking high-energy phosphate bonds, releasing energy.

Enzymes

Biological catalysts that speed up chemical reactions without being altered.
Lower the activation energy (Ea) required for reactions.
Substrates: reactants to which an enzyme binds.
Active site: location on the enzyme where the substrate binds.
Enzymes have specificity for particular substrates.
Some enzymes are entirely protein-based, while others consist of a protein component (apoenzyme) and a non-protein component (cofactor or coenzyme).
- Cofactor: inorganic ions like Fe2+ and Mg2+.
- Coenzyme: organic molecules that assist enzymes in electron transfer (derived from vitamins).
- Holoenzyme = apoenzyme + cofactor (active enzyme).

Environmental Factors Affecting Enzyme Activity

Temperature:
- Higher temperature increases reaction rate.
- Optimum temperature: maximum reaction rate.
- Denaturation: loss of tertiary protein structure (irreversible) at high temperatures.
pH:
- Optimal pH: when the enzyme is most active.
- Reduced activity above or below the optimum pH.
Substrate Concentration:
- High substrate concentration leads to enzyme saturation (active site always occupied).
- Further substrate increase does not affect rate.

Enzyme Inhibition

Competitive inhibitors: bind to the enzyme's active site and compete with the substrate.
Noncompetitive inhibitors: interact with the allosteric site (not the active site), changing the shape of the active site.
Allosteric activators: bind to the allosteric site, increasing enzyme activity.

Feedback Inhibition

The end product of a reaction allosterically inhibits enzymes from earlier in the pathway.
Biochemical control mechanism that prevents overproduction of substances.

Carbohydrate Catabolism

Breakdown of carbohydrates to release energy.
Involves enzymatic hydrolysis of glycosidic bonds in polysaccharides to form monomers.
- Hydrolysis: splitting with the addition of water (opposite of dehydration synthesis).
Glucose is the most common carbohydrate.
Glucose is a highly reduced compound, storing significant energy.

Glucose Catabolism

Processes of glucose catabolism:
- Start with glycolysis
- Cellular respiration
- Fermentation

Glycolysis (Sugar lysis)

Single 6 carbon glucose molecule is split into 2 molecules of pyruvate (3 carbon sugar)
Most common pathway for glucose catabolism in prokaryotes and eukaryotes
Occurs in cytoplasm (10 enzymatic steps)
Anaerobic - does not require O2
Types of glycolytic pathways:
- Embden-Meyerhof- Parnas (EMP) pathway: found in animals and most common in microbes
- Entner-doudoroff (ED) pathway
- Pentose phosphate pathway (PPP)

Glycolysis EMP Pathway

Energy investment phase:
- 2 ATP used
- 6 carbon sugar (Glucose) split into two phosphorylated 3 carbon molecules, (G3P)
Energy payoff phase:
- Two G3P molecules are oxidized to 2 pyruvate molecules
- 4 ATP formed by SLP (substrate-level phosphorylation)
  - Net yield ATP = 4 - 2 = 2 ATP
- 2 NADH are produced
- Substrate level phosphorylation (SLP): a phosphate group is removed from an organic molecule and is directly transferred to an available ADP molecule, producing ATP

Transition Reaction (Bridge Reaction)

Pyruvate from glycolysis can be further oxidized in the Krebs cycle, producing more energy
Steps:
- Decarboxylation (loss of CO2): pyruvate (3 carbon) is oxidized to acetyl group (2 carbon)
  - NAD+ is reduced to NADH
- Acetyl group attaches to coenzyme A (CoA) forming acetyl CoA
- Occurs: in cytoplasm (prokaryotes) and mitochondrial matrix (eukaryotes)
- For every molecule of glucose:
  - 2 acetyl CoA
  - 2 NADH are formed
- Acetyl CoA enters the Krebs cycle

Krebs Cycle (Citric Acid Cycle)

Transfers remaining electrons present in the acetyl group
Occurs: in cytoplasm (prokaryotes) and mitochondrial matrix (eukaryotes)
Closed loop, 8 step cycle
Steps:
- Acetyl CoA loses the CoA, acetyl combines with oxaloacetate to form citric acid
- Oxidation of each acetyl group produces:
  - 3 NADH
  - 1 FADH2
  - 1 GTP by substrate level phosphorylation (equivalent to 1 ATP)
  - Releases 2 CO2
Most important products of Krebs cycle: NADH and FADH2
- Contain most of the energy that was originally present in the glucose
Intermediates in Krebs cycle: useful for many biosynthetic pathways (amino acids, fatty acids, nucleotides, etc.)

Cellular Respiration

Begins when electrons are transferred from NADH and FADH2 (produced in glycolysis, transition reaction, and Krebs cycle)
Electron acceptor:
- Oxygen - aerobic respiration
- Non-oxygen inorganic molecules - anaerobic respiration
Occurs: in inner part of cytoplasmic membrane (prokaryotes) and inner mitochondrial membrane (eukaryotes)
Energy of electrons generates an electrochemical gradient: this is used to make ATP via oxidative phosphorylation

Electron Transport Chain (ETC)

Last component of cellular respiration
Comprised of membrane-associated protein complexes and mobile electron carriers (NADH, FADH2, etc.)
Major membrane-associated electron carriers:
- Cytochromes
- Flavoproteins
- Iron-sulfur Proteins
- Quinones

Proton Motive Force (PMF)

As electrons move down ETC, protons (H+) are pumped:
- To the outside of cytoplasmic membrane (bacteria)
- From the mitochondrial matrix across the inner mitochondrial space (eukaryotes)
Buildup of protons: establishes an electrochemical gradient
- Higher concentration of protons on one side of the membrane
- Potential energy is called Proton Motive Force (PMF):
  - Can be used to make ATP
  - Can also be used for rotation of flagella or movement of ions

Chemiosmosis: ATP synthesis using energy from PMF

Proteins cannot diffuse back into the cytoplasm due to the selectively permeable membrane
Can move back through protein channels containing ATP synthase:
- ATP synthase is a catalyst for the conversion of PMF into ATP
- Releases energy as protons move through it
- Addition of inorganic PO4 to ADP (oxidative phosphorylation)
- Forms ATP, a more readily usable form of energy
Total ATP yield: 4 from Substrate level phosphorylation, 34 from Oxidative phosphorylation
NADH makes 3 ATP, FADH makes 2 ATP

Aerobic Respiration

Final electron acceptor is Oxygen
Reduced to water by the final ETC carrier cytochrome oxidase
Sometimes aerobic respiration is not possible due to:
- Missing cytochrome oxidase
- Other missing enzymes
- Low amounts of available oxygen

Anaerobic Respiration

Final electron acceptor is NOT oxygen
- Nitrate reduced to nitrite or nitrogen gas
- Sulfate reduced to hydrogen sulfide
- Carbonate reduced to methane
Essential for nitrogen and sulfur cycles
Yields less ATP than in aerobic respiration:
- Only part of the krebs cycle operates under anaerobic conditions
- Only some ETC carriers participate
Organisms using anaerobic respiration grow slowly compared to aerobes

Fermentation

Does not use Krebs cycle or ETC, produces small amounts of ATP (only 2 ATP)
Many cells unable to carry out respiration because:
- Lack the inorganic final electron acceptor
- Lack genes for complexes and electron carriers in ETC
- Lack genes to make one or more enzymes in the Krebs cycle
NADH must be re-oxidized to NAD+ for reuse as an electron carrier for glycolysis to continue
Some use organic molecule (pyruvate) as a final electron acceptor

Lactic Acid Fermentation

Produces lactic acid from glucose
Seen in some bacteria and by animals in muscles during oxygen depletion
- Pyruvate + NADH → lactic acid + NAD+
- Only 2 ATP produced
Homolactic fermentation: produces lactic acid only
- Lactic acid bacteria example: Streptococcus and Lactobacillus
Heterolactic fermentation: produces lactic acid and other compounds
- Lactic acid fermentation can lead to food spoilage
- Can also produce yogurt, sauerkraut, pickles, etc.
The whole process can not proceed if no NAD+ to generate electrons

Alcohol Fermentation

Produces ethanol and CO2 from glucose
Steps
- Glucose is oxidized to 2 pyruvic acid
- Pyruvic acid is converted to acetaldehyde and CO2
- NADH reduces acetaldehyde to ethanol
Only 2 ATP produced
This process is carried out by many bacteria and yeasts:
- Yeast (Saccharomyces cerevisiae):
  - Baker’s yeast or brewer’s yeast
  - Beer, wine (ethanol)
  - Breads (CO2 makes bread dough rise)

Lipid Catabolism

In addition to glucose, lipids and proteins can also be broken down to supply energy
Main lipids: triglycerides and phospholipids
Broken down by hydrolytic enzymes:
- Lipases break down triglycerides (3 fatty acids and glycerol)
- Phospholipases break down phospholipids (2 fatty acids attached to glycerol)
Products generated: glycerol and fatty acids
- Glycerol is phosphorylated and converted to G3P → continues through glycolysis and Krebs cycle
- Fatty acids undergo β-oxidation to form acetyl CoA and enter the Krebs cycle

Protein Catabolism

Proteins broken down by microbial proteases
The last thing the cell wants to do is break down proteins, but if it can't use other energy sources shown above it will!
Extracellular proteases: cut proteins internally at specific amino acid sequences into smaller peptides that can be taken up by cells
Intracellular proteases (=peptidases): break down peptides further into individual amino acids after removal of functional groups, amino acids can enter the Krebs cycle
- Deamination: removal of amino group
- Decarboxylation: removal of carboxyl group

Photosynthesis

Conversion of light energy from the sun into chemical energy
Location:
- Chloroplasts within thylakoids - eukaryotes
- Thylakoids with photosynthetic membranes - prokaryotes
Light reactions:
- Conversion of light energy into chemical energy (ATP) by photosynthetic pigments
- NADPH or NADH (energy rich electron carriers) are produced
Dark reactions:
- ATP and NADPH/NADH reduce CO2 to sugar (=carbon fixation)

Photosynthetic Pigments

Molecules used to absorb solar energy
Other things besides chlorophyll can absorb energy beyond sunlight
Organized into photosystems used to generate ATP by chemiosmosis:
- Photosystem I (PSI) and Photosystem II (PSII)
  - Cyanobacteria and chloroplasts have both
  - Anoxygenic bacteria use only one

Photophosphorylation: Type of oxidative phosphorylation

Cyclic Photophosphorylation:
- Uses Photosystem I ONLY!
- Electrons released from the photosystem RETURN back!
- Preferred for a higher production of ATP
Noncyclic Photophosphorylation:
- Uses BOTH Photosystems I & II!
- Electrons released from the photosystems DO NOT return! Instead, they get incorporated into NADPH.
- Replenished by the breakdown of water.
- ATP is produced

Oxygenic Photosynthesis

Produces O2
Electron donor is H2O
Example: Plants, algae, cyanobacteria

Anoxygenic Photosynthesis

Does NOT produce O2, produces Sulfur and Sulfate (SO4)
Electron donor is H2S or S2O3
Example: Bacterial phototrophs (purple and green bacteria)

Dark Reactions of Photosynthesis

Calvin cycle: biochemical pathway for CO2 fixation
- Cytoplasm - in photosynthetic bacteria
- Stroma - in eukaryotic chloroplast
3 Stages:
- Fixation: RuBisCo catalyzes the addition of a CO2 to RuBP, producing 3-PGA
- Reduction: ATP and NADPH are used to convert 3-PGA into G3P
  - Some G3P is used to build glucose
- Regeneration: remaining G3P is used to regenerate RuBP to continue the cycle

Microbial Biochemistry

Organic Molecules contain carbon and are held together by covalent bonds.
Inorganic Molecules do not contain carbon, except for carbon oxides and carbonates.
Biomolecules are organic molecules essential for biological and chemical processes.
Carbon has four valence electrons and can form four covalent bonds.
Isomers are molecules with the same formula but different structures.
- Structural isomers differ in their structural formulas.
- Stereoisomers differ in how atoms are arranged in space.
- Enantiomers are non-superimposable mirror images.
- Optical isomers can rotate the plane of polarized light.
  - D form rotates light clockwise
  - L form rotates light counterclockwise
Functional groups are specific groups of atoms that contribute to specific chemical reactions.
- Important functional groups include hydroxyl, amino, and carboxylic acid groups.
Macromolecules are large biomolecules formed by linking together monomers (building blocks) to form polymers.
- Dehydration Synthesis is the process of monomers binding end-to-end, releasing water as a byproduct.

Carbohydrates

Carbohydrates are the most abundant biomolecules.
Function:
- Food sources in ecosystems
- Components of DNA and RNA
- Structural components (cellulose and chitin)
- Energy storage (starch and glycogen)
Monosaccharides are simple sugars.
- Classified based on number of carbon atoms:
  - Triose (3), tetrose (4), pentose (5), and hexose (6)
  - Hexoses: glucose, galactose, fructose
  - Pentoses: ribose, deoxyribose
- Carbon atoms (4 or greater) are more stable in ring structures.
Disaccharides consist of two monosaccharides.
- Maltose: two glucose molecules
- Lactose: galactose and glucose
- Sucrose: glucose and fructose
- Glycosidic bond - covalent bond formed between hydroxyl groups of carbohydrates during dehydration synthesis
Polysaccharides consist of hundreds of monosaccharides.
- Glycans can be linear or branched depending on the orientation of glycosidic linkages.
- Cellulose: linear chains of glucose (cell walls in plants).
- Starch and Glycogen: branched polymers of glucose
  - Glycogen: energy storage in animals and bacteria
  - Starch: energy storage in plants
- Modified Polysaccharides:
  - NAG and NAM: found in bacterial cell wall peptidoglycan.
  - Chitin: polymer of NAG found in fungal cell walls.

Lipids

Lipids are composed primarily of carbon and hydrogen.
Functions:
- Source of nutrients
- Energy storage
- Structural components (membranes and hormones)
Types of Lipids:
- Fatty acids: long hydrocarbon chains with a terminal carboxylic acid
  - Saturated fatty acids: contain only single bonds, saturated with hydrogen (straight and flexible).
  - Unsaturated fatty acids: contain at least one double bond, unsaturated with hydrogen (kinks in carbon skeleton, liquid at room temperature).
- Triglycerides: three fatty acids linked to a glycerol molecule.
- Complex lipids: composed of glycerol, two fatty acids, and an additional component.
  - Amphipathic: hydrophilic heads and hydrophobic tails.
  - Unique structures in aqueous environments:
    - Micelles: spherical particles with hydrophobic tails inside and hydrophilic heads outside.
    - Unit membranes: lipid bilayer sheets, forming vesicles/liposomes.
- Isoprenoids: branched lipids formed by chemical modification of isoprene.
- Steroids: complex ringed structures found in cell membranes and function as hormones.
  - Sterols:
    - Cholesterol: most common in animal tissues, strengthens cell membranes in eukaryotes and bacteria lacking cell walls (mycoplasma).
    - Hopanoids: similar compounds found in prokaryotes, strengthen bacterial membranes.
    - Ergosterol: similar compound found in fungi and some protozoa.

Proteins

Proteins are made of CHNO, sometimes S.
Functions:
- Enzymes that speed up chemical reactions.
- Transporter proteins that move across cell membranes.
- Flagella that aid in movement.
- Some bacterial toxins and cell structures.
Composed of Amino Acids:
- Each amino acid contains an alpha-carbon attached to four groups:
  - Hydrogen
  - Carboxyl group
  - Amino group
  - Side chain
Peptide bond: chemical bond formed between two amino acids during dehydration synthesis.
- Products:
  - Peptides: 50 or fewer amino acids
    - Oligopeptide: 20 amino acids
    - Polypeptides: 50 amino acids
  - Protein: very large number of amino acids or multiple polypeptides.
Protein Structure:
- Primary Structure: sequence of amino acids in the polypeptide chain.
- Secondary Structure: hydrogen bonding between amine and carboxyl groups within the peptide backbone.
  - 𝜶-helix: four amino acids apart.
  - 𝝱-pleated sheets: amino acids further separated.
- Tertiary Structure: 3D shape of the polypeptide chain, crucial for protein function.
  - Protein folding: process of assuming tertiary structure.
  - Native structure: correctly folded, fully functional protein.
  - Denatured proteins: unfolded, non-functional protein, loss of secondary, tertiary, and quaternary structures.
- Quaternary Structure: exists only in proteins consisting of several polypeptide chains.
  - All subunits must be present and configured to function.
  - Stabilized by weak interactions.
  - Example: Hemoglobin has four globular protein units (two alpha and beta polypeptides, each containing an iron-based heme).
Conjugated Proteins:
- Protein portion + non-protein portion
  - Glycoprotein: carbohydrate
  - Lipoprotein: Lipid
  - Nucleoprotein: RNA

Microbial Metabolism

Metabolism is the sum of all chemical reactions within a cell.
Functions:
- Provide energy to sustain life.
- Create substances that sustain life.
Catabolism breaks down complex molecules into simpler ones.
- Exergonic: releases energy.
Anabolism builds complex molecules from simpler ones.
- Endergonic: requires energy.
ATP (adenosine triphosphate):
- Links catabolic and anabolic reactions.
- Stores energy released from catabolism.
- Releases energy to drive anabolic reactions.
Classification by carbon and energy source:
- Carbon source:
  - Autotrophs: convert inorganic CO2 into organic compounds.
  - Heterotrophs: obtain organic compounds as nutrients.
- Energy (electrons) source:
  - Phototrophs: obtain electrons from light.
  - Chemotrophs: obtain electrons from chemicals.
    - Organotrophs: electrons from organic compounds.
    - Lithotrophs: electrons from inorganic compounds (unique to microbes).
- Chemoheterotrophs: use organic molecules as both energy and carbon sources (most organisms).
REDOX reactions: transfer of electrons between molecules.
- Oxidation: loss of electrons (OIL).
- Reduction: gain of electrons (RIG).
Energy Carriers:
- Electron carriers: bind and carry high energy electrons, easily reduced or oxidized, often derived from B vitamins:
  - NAD (NAD+/NADH)
  - NADP (NADP+/NADPH)
  - FAD (FAD/FADH2)
- ATP: stores and releases energy safely as needed.
  - Phosphorylation: addition of a phosphate group to ADP, requires energy.
  - Dephosphorylation: breakage of high-energy phosphate bonds, releasing energy.
Enzymes: biological catalysts that speed up chemical reactions.
- Activation energy: energy needed to initiate a reaction.
- Lower activation energy: enzymes accelerate reactions.
- Substrates: reactant molecules that bind to the enzyme's active site.
- Active site: region on enzyme where substrate binds.
- Specificity: enzymes are specific for certain substrates.
Enzyme structure: most enzymes are made of protein and non-protein components.
- Apoenzyme: protein component of enzyme, inactive on its own.
- Cofactor: inorganic ion that assists the enzyme (e.g., Fe2+, Mg2+).
- Coenzyme: organic molecule that assists the enzyme, often derived from vitamins (e.g., CoA, NAD+, FMN).
- Holoenzyme: apoenzyme + cofactor, the complete active enzyme.
Factors affecting enzyme activity:
- Temperature:
  - Optimum temperature: maximum reaction rate.
  - Denaturation: loss of tertiary structure, leads to loss of function.
- pH:
  - Optimum pH: maximum enzyme activity.
- Substrate concentration:
  - Saturation: all active sites are occupied, maximum reaction rate.
Enzyme Inhibition:
- Competitive inhibitors: bind to the active site and compete with the substrate.
- Noncompetitive inhibitors: bind to an allosteric site (not the active site), changing the active site's shape.
  - Allosteric inhibition: noncompetitive inhibition.
- Allosteric activators: bind to an allosteric site, increasing the enzyme's affinity for the substrate.
- Feedback inhibition: end product of a reaction inhibits enzymes earlier in the pathway, stopping excess synthesis.
Carbohydrate Catabolism: breakdown of carbohydrates to release energy.
- Hydrolysis: splitting of glycosidic bonds with the addition of water (opposite of dehydration synthesis).
- Amylase: hydrolyzes glycogen or starch into glucose monomers.
- Cellulase: hydrolyzes cellulose into glucose monomers.
- Glucose: highly reduced compound, primary source of energy.

Glucose Catabolism

Glucose catabolism encompasses processes that breakdown glucose to generate energy.
Glycolysis is the first common step in glucose catabolism.
Glycolysis is a 10-step process that splits a 6-carbon glucose molecule into two 3-carbon pyruvate molecules.
Glycolysis is an anaerobic process, meaning it does not require oxygen.
The Embden-Meyerhof-Parnas (EMP) pathway is the most common glycolytic pathway found in animals and microbes.
The Entner-doudoroff (ED) pathway and Pentose phosphate pathway (PPP) are alternative glycolytic pathways.

The EMP Pathway

Energy investment phase consumes 2 ATP molecules and splits glucose into two 3-carbon molecules.
Energy payoff phase oxidizes two 3-carbon molecules into two pyruvate molecules, generating 4 ATP (net yield of 2 ATP) and 2 NADH.
Substrate-level phosphorylation (SLP) directly transfers a phosphate group from an organic molecule to ADP, generating ATP.

Transition Reaction

Pyruvate from glycolysis is further oxidized in the Krebs cycle.
Decarboxylation (loss of CO2) occurs, converting pyruvate into an acetyl group.
The acetyl group attaches to coenzyme A (CoA), forming acetyl CoA, which enters the Krebs cycle.
This reaction generates 2 NADH and 2 acetyl CoA per glucose molecule.

Krebs Cycle

The Krebs cycle occurs in the cytoplasm (prokaryotes) or mitochondrial matrix (eukaryotes).
The cycle consists of 8 steps and oxidizes acetyl CoA, generating:
- 3 NADH
- 1 FADH2
- 1 GTP (equivalent to 1 ATP)
- 2 CO2
The main products of the Krebs cycle are NADH and FADH2, which contain most of the energy initially present in glucose.
Intermediates in the Krebs cycle are used for biosynthesis of amino acids, fatty acids, and nucleotides.

Cellular Respiration

Cellular respiration involves the transfer of electrons from NADH and FADH2 (produced in glycolysis, transition reaction, and Krebs cycle) to a final electron acceptor.
Aerobic respiration uses oxygen as the final electron acceptor.
Anaerobic respiration uses non-oxygen inorganic molecules as the final electron acceptor.
Cellular respiration occurs in the cytoplasmic membrane (prokaryotes) or inner mitochondrial membrane (eukaryotes).
The energy of electrons generates a proton gradient, which is used to produce ATP via oxidative phosphorylation.

Electron Transport Chain (ETC)

The ETC is the final component of cellular respiration.
It consists of membrane-bound protein complexes and mobile electron carriers.
Major membrane-associated electron carriers include:
- Cytochromes
- Flavoproteins
- Iron-sulfur proteins
- Quinones

Proton Motive Force (PMF)

As electrons move down the ETC, protons (H+) are pumped across the membrane, creating a proton gradient.
This gradient stores potential energy called proton motive force (PMF).
PMF can be used for ATP synthesis, flagella rotation, or ion movement.

Chemiosmosis

Chemiosmosis utilizes the PMF to generate ATP.
Protons move back across the membrane through ATP synthase, releasing energy and driving the synthesis of ATP.
The total ATP yield from glucose catabolism is 4 ATP from SLP and 34 ATP from oxidative phosphorylation (3 ATP per NADH, 2 ATP per FADH2).

Aerobic Respiration

Aerobic respiration utilizes oxygen as the final electron acceptor.
Oxygen is reduced to water by the final ETC carrier, cytochrome oxidase.

Anaerobic Respiration

Anaerobic respiration uses non-oxygen inorganic molecules as the final electron acceptor.
Common examples include:
- Nitrate (NO3-) reduced to nitrite (NO2-) or nitrogen gas (N2)
- Sulfate (SO42-) reduced to hydrogen sulfide (H2S)
- Carbonate (CO32-) reduced to methane (CH4)
Anaerobic respiration is essential for nitrogen and sulfur cycles.
It yields less ATP than aerobic respiration and involves only partial operation of the Krebs cycle and ETC.
Organisms using anaerobic respiration grow slower than aerobic organisms.

Fermentation

Fermentation does not use the Krebs cycle or ETC, producing only 2 ATP.
It occurs when cells lack an inorganic final electron acceptor, the genes for ETC components, or enzymes required for the Krebs cycle.
Fermentation regenerates NAD+ for glycolysis to continue by using an organic molecule as the final electron acceptor.

Lactic Acid Fermentation

Lactic acid fermentation produces lactic acid from pyruvate.
Occurs in some bacteria and in animal muscles during oxygen depletion.
It generates only 2 ATP.
Homolactic fermentation produces only lactic acid, while heterolactic fermentation produces lactic acid and other compounds.
Lactic acid fermentation is used in the production of yogurt, sauerkraut, and pickles.

Alcohol Fermentation

Alcohol fermentation produces ethanol and CO2 from glucose.
It is carried out by many bacteria and yeasts, including Saccharomyces cerevisiae (baker's yeast and brewer's yeast).
Used in the production of beer, wine, and bread.

Lipid Catabolism

Lipids, such as triglycerides and phospholipids, can be broken down to provide energy.
Lipases break down triglycerides into glycerol and fatty acids.
Phospholipases break down phospholipids.
Glycerol enters glycolysis, while fatty acids undergo beta-oxidation to produce acetyl CoA, which enters the Krebs cycle.

Protein Catabolism

Proteins are broken down by microbial proteases.
Extracellular proteases cut proteins into smaller peptides, which are taken up by cells.
Intracellular proteases break down peptides into amino acids.
Amino acids can enter the Krebs cycle after deamination (amino group removal) and decarboxylation (carboxyl group removal).

Photosynthesis

Photosynthesis converts light energy into chemical energy, specifically glucose.
It occurs in chloroplasts (eukaryotes) or photosynthetic membranes (prokaryotes).

Light Reactions of Photosynthesis

Photosynthetic pigments absorb light energy, generating ATP and NADPH/NADH.
These pigments are organized into photosystems (PSI and PSII) that drive the electron transport chain.

Dark Reactions of Photosynthesis

Dark reactions utilize ATP and NADPH/NADH to reduce CO2 into sugar through carbon fixation.

Calvin Cycle

The Calvin cycle is the primary pathway for carbon fixation in photosynthesis.
It involves three stages:
- Fixation: RuBisCo enzyme adds CO2 to RuBP, generating 3-PGA.
- Reduction: ATP and NADPH convert 3-PGA into G3P, with some used to build glucose.
- Regeneration: remaining G3P regenerates RuBP to continue the cycle.

Photophosphorylation

Photophosphorylation is a type of oxidative phosphorylation driven by light energy.
Cyclic photophosphorylation uses only PSI, generating ATP.
Noncyclic photophosphorylation uses both PSI and PSII, generating ATP and NADPH.

Oxygenic Photosynthesis

Oxygenic photosynthesis produces oxygen as a byproduct.
Uses water as the electron donor.
Performed by plants, algae, and cyanobacteria.

Anoxygenic Photosynthesis

Anoxygenic photosynthesis does not produce oxygen.
Uses H2S or S2O3 as the electron donor, producing sulfur or sulfate as byproducts.
Performed by bacterial phototrophs, such as purple and green bacteria.

Microbial Biochemistry

Organic molecules contain carbon and are held together by covalent bonds. They account for 20-30% of a cell's mass and include carbohydrates, lipids, and proteins.
Inorganic molecules do not contain carbon. They are linked by ionic bonds and account for only 1% of a cell's mass. Examples include water and salts.
Carbon fixation is the process by which inorganic carbon dioxide is captured to create organic molecules.
Biomolecules are organic molecules essential for biological and chemical processes.
Carbon has four valence electrons and forms four covalent bonds. Methane (CH4) is the simplest organic compound.
Isomers are molecules with the same formula but different structures. This impacts their function.
Structural isomers differ in their structural formulas, such as glucose, galactose, and fructose.
Stereoisomers differ in the arrangement of atoms in space, such as enantiomers.
Enantiomers are non-superimposable mirror images.
Optical isomers can rotate plane-polarized light. The "d" form rotates light clockwise, while the "l" form rotates light counterclockwise.
Functional groups are groups of atoms attached to a carbon skeleton that determine the molecule's chemical reactivity. Examples include hydroxyl, amino, and carboxyl groups.
Macromolecules are large biomolecules formed by linking monomers together to form polymers. These polymers are constructed through dehydration synthesis, which releases water as a byproduct.
Four main macromolecules: carbohydrates, proteins, lipids, and nucleic acids.

Carbohydrates

Carbohydrates are the most abundant biomolecules and are composed of carbon, hydrogen, and oxygen in a 1:2:1 ratio.
The empirical formula for carbohydrates is (CH2O)n, where n is the number of repeating units.
Carbohydrates function as food sources, components of DNA and RNA, building blocks for structural components, and primary energy storage molecules.
Monosaccharides are simple sugars that serve as monomers for complex carbohydrates. Examples include glucose, fructose, galactose, ribose, and deoxyribose.
Disaccharides are composed of two monosaccharides linked by a glycosidic bond. Common examples include maltose, lactose, and sucrose.
Polysaccharides are composed of hundreds of monosaccharides linked by glycosidic bonds. Examples include cellulose, starch, and glycogen. Both starch and glycogen are branched polymers of glucose that serve as energy storage molecules.

Lipids

Lipids are composed primarily of carbon and hydrogen, often containing nitrogen, oxygen, phosphorus, and sulfur.
Lipids are diverse in structure and function, serving as sources of nutrients, energy storage molecules, and key structural components for membranes and hormones.
Fatty acids are long hydrocarbon chains terminating with a carboxylic acid group.
- Saturated fatty acids contain only single bonds and are typically solid at room temperature.
- Unsaturated fatty acids contain at least one double bond and are typically liquid at room temperature.
Triglycerides are composed of three fatty acids linked to a glycerol molecule. They are the primary components of adipose tissue.
Complex lipids include phospholipids and glycolipids. These lipids are characterized by their amphipathic nature, containing both hydrophilic and hydrophobic regions.
Isoprenoids are branched lipids formed by chemical modification of isoprene.
Steroids are complex ringed structures found in cell membranes and often serve as hormones. Cholesterol is a common steroid found in animal tissues, while hopanoids and ergosterol are similar compounds found in bacteria and fungi, respectively.

Proteins

Proteins are essential for cell structure and function, playing roles in diverse processes like enzymatic catalysis, transport, and motility.
Proteins are composed of amino acids. Each amino acid contains an alpha-carbon attached to a hydrogen, carboxyl group, amino group, and a side chain.
A peptide bond is a covalent bond formed between two amino acids.
- Peptides consist of 50 or fewer amino acids, including oligopeptides (20 amino acids) and polypeptides (50 amino acids).
- Proteins are composed of very large numbers of amino acids or multiple polypeptides.
The structure of a protein is critical to its function and is determined by the length of the amino acid chain, specific amino acid sequences, and the resulting 3D shape.
- Primary Structure is the sequence of amino acids in the polypeptide chain.
- Secondary Structure arises from hydrogen bond formation between amine and carboxyl groups within the peptide backbone, resulting in 𝜶-helix or 𝝱-pleated sheet formations.
- Tertiary Structure is the 3D shape of the polypeptide chain. This structure is critical for protein function and is achieved through interactions between amino acid residues that are far apart in the chain.
  - Protein folding is the process by which a polypeptide chain assumes its tertiary structure.
  - Native structure refers to a folded protein that is fully functional.
  - Denatured proteins have lost their 3D shape and are no longer functional.
- Quaternary structure exists only in proteins composed of multiple polypeptide chains. Each subunit must be present and properly arranged for the protein to function.
Conjugated proteins are composed of a protein portion and a non-protein portion such as carbohydrates, lipids, or RNA. Examples include glycoproteins, lipoproteins, and nucleoproteins.

Microbial Metabolism

Metabolism is the sum of all chemical reactions that occur in a cell, providing energy and creating substances necessary for life.
Catabolism is the breakdown of complex molecules into simpler ones, releasing energy.
Anabolism is the biosynthesis of complex molecules from simpler ones, requiring energy input.
ATP (adenosine triphosphate) is the main energy currency of the cell. It stores energy released from catabolism and releases energy to drive anabolic reactions.
Organisms can be classified by their sources of carbon and energy (electrons).
- Autotrophs use inorganic CO2 as their carbon source.
- Heterotrophs use organic compounds as their carbon source.
- Phototrophs obtain electrons from light.
- Chemotrophs obtain electrons from chemical compounds.
  - Organotrophs use organic compounds as the electron source.
  - Lithotrophs use inorganic compounds as the electron source.
Redox reactions involve the transfer of electrons between molecules.
- Oxidation is the loss of electrons (OIL).
- Reduction is the gain of electrons (RIG).

Energy Carriers

Energy carriers bind and carry high energy electrons and are easily reduced or oxidized through a series of metabolic reactions.
- Electron carriers are often derived from B vitamins and include NAD, NADP, and FAD.
- ATP is a highly energy-rich molecule used to drive cellular processes.
Enzymes are biological catalysts that speed up chemical reactions without being altered.
- Activation energy is the energy required to initiate a chemical reaction. Enzymes lower activation energy by binding to substrate molecules.
- Substrates are the reactant molecules that bind to the enzyme's active site.
- Active site is the location on the enzyme where the substrate binds.
Enzyme activity is influenced by factors such as temperature, pH, and substrate concentration.
- Optimum temperature is the temperature at which an enzyme exhibits its maximum activity.
- Denaturation is the loss of tertiary structure due to extreme temperatures or pH changes, resulting in loss of catalytic ability.
- Optimum pH is the pH at which an enzyme exhibits its maximum activity.
- Saturation occurs when an enzyme's active site is constantly occupied by substrate, reaching its maximum rate of catalysis.

Inhibition of Enzyme Activity

Competitive inhibitors bind to the active site and compete with the substrate for binding, preventing the formation of products.
Noncompetitive inhibitors bind to an allosteric site, altering the shape of the active site and reducing the enzyme's affinity for the substrate.
Feedback inhibition is a regulatory mechanism where the end product of a reaction inhibits enzymes earlier in the pathway, preventing the overproduction of a substance.

Carbohydrate Catabolism

Carbohydrate catabolism refers to the breakdown of carbohydrates to release energy. It involves the enzymatic hydrolysis of glycosidic bonds to form monomers.
- Amylase hydrolyzes glycogen or starch into glucose monomers.
- Cellulase breaks down cellulose into glucose monomers.
Glucose is a highly reduced compound, serving as a primary energy source for many organisms.

Glucose Catabolism

Glucose catabolism is the breakdown of glucose to extract energy.
Two major pathways start with glycolysis: cellular respiration and fermentation.

Glycolysis

The breakdown of a six-carbon glucose molecule into two three-carbon pyruvate molecules.
Occurs in the cytoplasm of both prokaryotes and eukaryotes.
Requires 10 enzymatic steps and is anaerobic.

Glycolysis Pathways

Three major pathways: Embden-Meyerhof-Parnas (EMP) pathway, Entner-Doudoroff (ED) pathway, and Pentose phosphate pathway (PPP).
EMP pathway is the most common pathway, used by animals and many microbes.

EMP Pathway: Energy Investment and Payoff Phases

Energy Investment Phase: 2 ATP molecules are used to split glucose into two phosphorylated G3P molecules.
Energy Payoff Phase: Two G3P molecules are oxidized to two pyruvate molecules, producing:
- 4 ATP molecules by substrate-level phosphorylation (net yield of 2 ATP).
- 2 NADH molecules.

Transition (Bridge) Reaction

Occurs in the cytoplasm (prokaryotes) and mitochondrial matrix (eukaryotes).
Pyruvate is oxidized to an acetyl group (2 carbon) and CO2 is released.
Acetyl group forms acetyl-CoA and joins the Krebs cycle.
For each glucose molecule, two acetyl-CoA and two NADH molecules are formed.

Krebs Cycle (Citric Acid Cycle)

Occurs in the cytoplasm (prokaryotes) and mitochondrial matrix (eukaryotes).
An eight-step cycle that oxidizes the acetyl group from acetyl CoA.
Key products include:
- 3 NADH
- 1 FADH2
- 1 ATP (from GTP via substrate level phosphorylation)
- 2 CO2
Most energy is stored in the NADH and FADH2 molecules.
Intermediates in the Krebs cycle are used for biosynthetic pathways.

Cellular Respiration

Begins when electrons from NADH and FADH2 are transferred to a final electron acceptor.
Occurs in the inner part of the cytoplasmic membrane (prokaryotes) and inner mitochondrial membrane (eukaryotes).
Energy from electron movement creates an electrochemical gradient used for ATP generation via oxidative phosphorylation.

Electron Transport Chain (ETC)

Membrane-associated protein complexes and mobile electron carriers (NADH, FADH2, etc.)
Major electron carriers include cytochromes, flavoproteins, iron-sulfur proteins, and quinones.

Proton Motive Force (PMF)

As electrons move through the ETC, protons (H+) are pumped across the membrane, creating an electrochemical gradient.
Higher proton concentration on one side of the membrane stores potential energy (PMF), used for ATP production, flagella rotation, and ion movement.

Chemiosmosis

Protons move back across the membrane through ATP synthase channels, releasing energy to generate ATP via oxidative phosphorylation.

Total ATP Yield

Approximately 38 ATP molecules are produced per glucose molecule:
- 4 ATP from substrate-level phosphorylation (glycolysis and Krebs cycle).
- 34 ATP from oxidative phosphorylation (ETC and chemiosmosis).

Aerobic Respiration

Final electron acceptor is oxygen, reduced to water.
Requires cytochrome oxidase.

Anaerobic Respiration

Final electron acceptor is not oxygen, such as nitrate, sulfate, or carbonate.
Yields less ATP than aerobic respiration.
Only part of the Krebs cycle and ETC operate under anaerobic conditions.
Organisms grow more slowly than aerobes.

Fermentation

Does not use the Krebs cycle or ETC.
Produces small amounts of ATP (only 2 ATP).
Occurs in the absence of oxygen or without the specific enzymes for respiration.
NADH is re-oxidized to NAD+ for reuse in glycolysis.

Lactic Acid Fermentation

Uses pyruvate as a final electron acceptor.
Produces lactic acid from glucose.
Occurs in some bacteria and animal muscle cells during oxygen depletion.
Examples include Streptococcus and Lactobacillus.

Alcohol Fermentation

Produces ethanol and CO2 from glucose.
Pyruvate is converted to acetaldehyde and CO2.
Acetaldehyde is then reduced to ethanol by NADH.
Carried out by many bacteria and yeast.

Lipid Catabolism

Breakdown of lipids (triglycerides and phospholipids) to produce energy.
Lipases break down triglycerides into glycerol and fatty acids.
Phospholipases break down phospholipids into glycerol and fatty acids.
Glycerol is converted to G3P and enters glycolysis.
Fatty acids undergo beta-oxidation forming acetyl-CoA, which enters the Krebs cycle.

Protein Catabolism

Break down of proteins into smaller peptides and amino acids.
Extracellular proteases break down proteins into smaller peptides.
Intracellular proteases break down peptides into individual amino acids.
Amino acids can enter the Krebs cycle through deamination (removal of amino group) and decarboxylation (removal of carboxyl group).

Photosynthesis

Conversion of light energy into chemical energy.
Occurs in chloroplasts (eukaryotes) or thylakoids (prokaryotes).
Two main stages: light reactions and dark reactions.

Light Reactions

Conversion of light energy into chemical energy (ATP) and reducing power (NADPH or NADH).
Photosynthetic pigments (chlorophyll) absorb light energy.

Dark Reactions

Carbon fixation using ATP and NADPH/NADH to reduce CO2 into sugar.

Photosynthetic Pigments

Molecules that absorb light energy.
Organized into photosystems to generate ATP via chemiosmosis.
Photosystem I (PSI) and Photosystem II (PSII).

Photophosphorylation

ATP production from light energy.
Cyclic photophosphorylation: Only uses PSI, electrons return to the system, and is preferred for ATP production.
Noncyclic photophosphorylation: Uses both PSI and PSII, electrons do not return, and some electrons are incorporated into NADPH.

Oxygenic Photosynthesis

Produces oxygen.
Electron donor is water.
Occurs in plants, algae, and cyanobacteria.

Anoxygenic Photosynthesis

Does not produce oxygen.
Produces sulfur or sulfate.
Electron donor is hydrogen sulfide (H2S) or thiosulfate (S2O3).
Occurs in bacteria, such as purple and green bacteria.

Calvin Cycle

The biochemical pathway for carbon dioxide fixation.
Occurs in the cytoplasm (photosynthetic bacteria) or stroma (eukaryotic chloroplast).
Three stages:
- Fixation: RuBisCo catalyzes the addition of CO2 to RuBP, producing 3-PGA.
- Reduction: ATP and NADPH convert 3-PGA into G3P.
- Regeneration: Remaining G3P regenerates RuBP for the cycle to continue.

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Test your knowledge on key processes in cellular respiration including glycolysis, the Krebs cycle, and fermentation. Understand the roles of ATP and carbon in these biochemical pathways. This quiz covers essential concepts you need to master in biology.