Cellular Respiration and Metabolism

Cellular Respiration

• Electrons flow from reduced coenzymes (FADH2 and NADH) to electron acceptors in the electron transport chain (ETC).
• Aerobic respiration uses O2 as the final electron acceptor.

Glycolysis

• Occurs in the cytosol.
• Glucose (6C) is oxidized into 2 pyruvate molecules (3C).
• NAD+ is reduced to NADH.
• Glycolysis is a 10-step process.
• Produces a net total of 2 ATP molecules.

Aerobic vs. Anaerobic Metabolism

• In the absence of oxygen, anaerobic metabolism occurs, producing lactate or ethanol instead of Acetyl CoA.
• Fermentation is anaerobic ATP production via glycolysis, but it is not as efficient as aerobic respiration.
• NADH is reoxidized by pyruvate, converting it into ethanol or lactate.
• The Cori Cycle involves glucose fermentation in muscles followed by gluconeogenesis in the liver.

Mitochondria

• The number of mitochondria per cell varies from hundreds to thousands.
• It is the second largest organelle.

Outer Membrane

• Permeable to ions and small molecules.

Intermembrane Space

• Continuous with the cytosol.
• Contains some confined enzymes.

Inner Membrane

• Impermeable to most solutes.
• Sometimes touches the outer membrane.
• Contains little cholesterol.
• Rich in unsaturated fatty acids.
• Cristae increase the surface area.
• Proteins accumulate in intracristal spaces.

Intramembrane Complex

• Protein complexes embedded within the inner membrane include F0F1 and ATP Synthase.

Matrix

• The interior of the mitochondria contains enzymes, DNA, and ribosomes.

Bacteria

• Lack organelles.
• Consist of a plasma membrane, cytosol, inner mitochondrial membrane, and matrix.

Pyruvate Oxidation

• Coenzyme A is acetylated.
• NAD+ is reduced to NADH.
• Acetyl CoA is produced.
• Dietary fatty acids with even numbers are degraded into Acetyl CoA, two carbons at a time.

The Krebs Cycle

• Begins with acetyl CoA.
• Produces 1 ATP, 3 NADH, 1 FADH2, and 2 CO2 in eight steps.
• Approximately 90% of glucose-free energy is conserved in 12 molecules of NADH and FADH2.

The Electron Transport Chain

Complexes and Coenzyme Q

• Flavoproteins contain FAD prosthetic groups.
• Iron-sulfur proteins have iron complexed with a sulfur cystol residue.
• Cytochromes have a heme prosthetic group.
• Coenzyme Q (quinone) undergoes redox reactions to transfer electrons.
• Molecules accept and release electrons based on their redox potentials.
• Complexes I, II, III, IV, and ATP Synthase build up and use an H+ gradient to produce ATP.

Standard Redox Potential

• Pairs with the most negative E○ have the weakest affinity for electrons and readily give them up.
• As E○ becomes more positive, molecules prefer to accept electrons rather than donate them.
• The ETC operates forward because the E○ increases from complex I to IV and ATP Synthase.

ATP Synthase

• Electrochemical potential links electron transport and ATP synthase.
• H+ travels through the intermembrane space via complexes.
• The matrix is depleted of H+, making it more basic, a process called chemiosmotic coupling.
• ATP Synthase acts as a channel, allowing H+ to return to the matrix and creating ATP.
• ATP Synthase consists of two parts: Fo (13 subunits) and F1 (9 subunits).

The Endomembrane System

• Consists of the ER, Golgi apparatus, endosomes, and lysosomes.
• Transport vesicles move lipids and proteins, endocytosed material, and waste.
• Endosomes carry and sort material brought into the cell.

Rough ER

• Made up of flattened sheets
• The lumen is continuous with the smooth ER and nuclear membrane.
• Ribosomes are on the side facing the cytosol, used in the endomembrane system.
• Proteins from the cytosol travel through to the lumen or stay inside the ER membrane.
• Regions help shuttle lipids and proteins to the Golgi apparatus using vesicles.
• Folds polypeptides and assembles multimeric proteins.
• Adds carbohydrates to create glycoproteins and removes misfolded proteins.

Smooth ER

• More tubular than flat.
• Continuous with the rough ER.
• Primary source of membrane lipids, especially phospholipids and cholesterol.

Drug Detoxification

• Cytochrome P450 adds hydroxyl groups to hydrophobic drugs to increase solubility.
• Induces enzymes that affect drug tolerance, response, and toxicity.

Carbohydrate Metabolism

• Glycogen granules are closely associated with smooth ER in liver cells.

Calcium Storage

• Muscle cells specialize in this function, with significant C+2 binding in the lumen.
• ATP-dependent C+2-ATPases pump C+2 into the ER.
• C+2 is released by neurotransmitters.

Steroid Biosynthesis

• Many pathway enzymes are P450s that hydroxylize steroids.
• Smooth ER is abundant in the ovary, liver, Leydig cells, and adrenal cells, where steroids are made.

Golgi Complex

• Linked with the ER.
• Consists of flattened, stacked sacks called cisternae.
• Surrounded by transport vesicles.
• ER glycoproteins and membrane lipids are sorted and packaged for transport.

Golgi Structure

• CGN (cis-Golgi network): Transition vesicles from the ER fuse with this side.
• TGN (trans-Golgi network): Transition vesicles bud and leave from this side.

Models of Movement of Lipids and Proteins

• Stationary cisternae model: Compartments are stable, and molecules bud and move to the next cisterna (cis → trans).
• Cisternal maturation model: Cisternae are transient, moving instead of buds (cis → trans).
• The models may depend on cell type and molecules processed, possibly a combination.

Trafficking Lipids and Proteins in the ES

• Glycosylation: Adding carbohydrates to proteins, lipids, or polysaccharides.

Protein Sorting

• Early stages occur in the ER, CGN, and medial cisternae (protein processing and glycosylation).
• Later sorting occurs in the TGN (packing into vesicles).
• Some proteins remain in the ER and undergo retrograde transport from the GCN to the ER.

Intracellular Protein Sorting

• Post-Translational import: Occurs with free ribosomes in the cytosol. (cytosol, nucleus, mitochondria, chloroplasts, or peroxisomes).
• Co-Translational import: Occurs with ribosomes attached to the ER membrane. (endomembrane system or outside the cell).

Exocytosis

• Eukaryotic only.
• Vesicles fuse with the plasma membrane, releasing the vesicle contents to the outside.

Endocytosis

• Uptake of extracellular material.
• The plasma membrane folds in and pinches off an endocytic vesicle.
• Used to ingest nutrients and defend against microorganisms.
• Endocytic vesicles form early endosomes, fuse with the TGN, and mature into lysosomes.

Phagocytosis

• Ingestion of large particles such as cell parts or microorganisms.
• Major nutrient intake for unicellular eukaryotes.
• In humans, neutrophils and macrophages ingest foreign particles.
• Phagocytic vacuoles (phagosomes) fuse with late endosomes or mature into lysosomes.

Receptor-Mediated Endocytosis

• Eukaryotic, clathrin-dependent.
• Important for hormone and enzyme uptake.
• Receptor proteins on the cell membrane bind specific ligands.
• Receptor-ligand complexes diffuse along the membrane, internalized with adaptor proteins, clathrin, and dynamin.

Lysosomes

• Found in most animal cells.
• Use hydrolytic enzymes to digest extracellular and intracellular material.
• Mature from phagocytic or endocytic vacuoles.
• Digestion products return to the cytosol or are used as nutrients.

Lysosomal Storage Disease

• Harmful accumulation of polysaccharides or lipids.
• Caused by defective digestive enzymes or transport mechanisms.

Peroxisomes

• Single membrane vesicle with enzymes dependent on cell type.

Functions

• Hydrogen peroxide metabolism: Oxidases catalyze, catalases degrade H2O2.
• Detoxification: Toxins serve as substrates for catalase and become oxidized.
• Fatty acid oxidation: 25%-50% in animals and 100% in plants and yeast.

Peroxisomal Disorder

• Problems arise when fatty acids or enzymes fail to transport to peroxisomes.
• Biogenesis occurs by division of pre-existing peroxisomes or vesicle fusion.

Different Types of Animal Tissues

• Cells vary in size, shape, and function.
• Cells of the same function make up tissue.
• Apical cells differ from basal cells attached to the basal lamina.

Major Cell Attachment Types in Epithelial Cells

• Impermeable seals between cells.
• Direct chemical and electrical communications between cells.
• Attaches the basal surface to the basal lamina, anchored to intermediate filaments.

Important Transmembrane Proteins

• Cell-to-cell adhesion in animal cells.
• Adhesion receptors are dynamic and coordinate assembly and disassembly.

Adhesion Protein Classes

• Immunoglobulins, cadherins, selectins, integrins.

Cadherins

• Found at sites of cell-to-cell adhesion.
• E-cadherin (best studied) works in pairs, acting as homodimers.
• Interacts with structure proteins in neighboring cells while being outside the cell.

Effects of Cadherins on Cell Adhesion

• Different types of cadherins on specific tissues.
• As an example: E-cadherin-expressing cells segregate from those expressing P-cadherin.
• P-cadherin was first described in the placenta.
• Cancer cells lose E-cadherin expression.
• Regulates adhesion in embryonic development; organization of tissue.
• Depletion of mRNA for EP-cadherin causes abnormal organization.

Cadherin Domains

• Extracellular, outside of cell.
• Cytosolic: Connected to the cytoskeleton via β-catenin and other proteins.
• β-catenin also binds to α catenin, which recruits actin.
• p120 catenins are also important to endocytosis.

Desmosomes

• Resist stress.
• Important in tissues used in the heart, skin, uterus.
• Shaped like a button, the core is filled with special cadherins.
• Core binds the cytoskeleton to tonofilaments.
• Tonofilaments are intermediate filaments made of keratin.
• Help provide mechanical strength to epithelial sheets like skin.

Leukocyte Adhesion and Selectins

• A group of lectins, which bind to sugars, that are cell adhesion molecules.
• They are glycoproteins on the cell surface.
• Selectins mediate the attachment of leukocytes to carbohydrates on endothelial cells.
• Each cell type has its own type of selectin.
• Leukocytes have L-selectin.

Different Extracellular Matrix

• Materials outside of tissue that interact with the cells.
• Shape tissues and organs.
• In cartilage, cells are embedded in a flexible matrix that contains large amounts of proteoglycans.
• In connective tissues, fibroblasts are surrounded by an ECM that contains lots of collagen fibers.

Three Molecule Classes

• Structural proteins, proteoglycans, and adhesive glycoproteins.

Structural Proteins

Collagens

• Most abundant in animals.
• 25% to 30% of total body protein.
• High tensile strength fibers secreted by various cells such as fibroblasts.
• Has 3 polypeptide chains, a triple helix, and unusual amino acid composition.
• H-Bond crosslinks within and between fibrils.

Elastins

• Flexible.
• Has glycine and proline (amino acids) but is not hydroxylated.
• Covalent bond crosslinks via lysines.
• Relaxed conformation is disordered; under tension, it takes an extended molecular conformation.

Proteoglycans

• In cartilage, many proteoglycans associate with a hyaluronate backbone to form a complex.
• Gel-like network containing collagen and elastin.
• Many glycosaminoglycans (GAGs) attached to a protein.
• GAGs are made up of repeating disaccharides and amino sugars.
• A proteoglycan is a GAG with an attached protein.

Adhesive Glycoproteins

• Fibronectins: glycoproteins that occur in soluble form in blood and as insoluble fibrils in ECM.
• Lamins: major adhesive glycoproteins present in the basal lamina.
• Reinforce the links between the extracellular matrix and the plasma membrane.

Fibronectin Structure

• Made up of 2 nearly identical polypeptide chains joined by 2 disulfide bonds near the carboxyl ends.
• Chains split into different domains that bind to distinct and specific proteins.
• Various forms and functions such as blood clotting and cell migration.

Laminins

• Located mainly in the basal lamina.
• A highly organized ECM that binds the basal surfaces of epithelial cells.
• Consist of 3 polypeptides held into a cross-linked structure by S-S bonds.
• Domains on ends of the α chain are recognized by cell surface receptors.
• Domains at the other 2 (β and 𝛾) arm ends of the cross bind collagen.

The Basal Lamina

• A thin sheet that separates an epithelial cell layer from underlying connective tissue.
• A permeability barrier, glomerular filtration, allows small molecules but not proteins.
• Made up of collagen, proteoglycans, laminins, and other glycoproteins.
• Laminins face overlying epithelial cells and bind them to the lamina.

Lamina Structure

• Laminin associates with other molecules or components to form a mat of ECM.
• Cells attach to the basal lamina using integrins.
• Cells regulate basal lamina thickness.
• Secrete matrix metalloproteinases (MMPs).
• MMPs are metal cofactors that degrade the ECM and allow cells to pass.

Integrin - the Fibronectin Receptor

• They are cell surface and transmembrane proteins
• Consist of 2 subunits that are glycosylated on the exterior end and associate non-covelently
• Binding site for fibronectin is on the outer surface, and for talin on the cytosolic side

Focal adhesions and hemidesmosomes

• Both types of intermeditery proteins in cytosol that link integrins to the cytoskeleton
• Migrating cells use focal adhesion, and epithelial cells use hemidesmosomes
• Integrin is also involved in cell signaling
• Anchorage-dependent growth in tissue culture, no attachment, leads to apoptosis
• Signaling pathways controlled through outside stimulus including integrin clustering
• Inside-out signaling occurs because intracellular signals can lead to the integrin grwoth

Signal Transduction

• Cell to cell signaling is done by hormones (endocrine) and local mediators.
• Distance is important.
  • Autocrine: A cell targets itself.
  • Juxtacrine: A cell targets a cell connected by gap junctions.
  • Paracrine: A cell targets a nearby cell.
  • Endocrine: A cell targets a distant cell through the bloodstream.
• Signal transduction can amplify the cellular response to an external signal from 1 to 108 molecules.
• Response can involve altered protein function (fast) or altered protein synthesis (slow).

Basic Types of Signaling Pathways

• Ligand-gated ion channel
• G-protein coupled receptor (GPCR)
• Enzyme-coupled receptor
• Nuclear receptor

G-Proteins

• Short for GTP-binding proteins.
• Activated when bound to GTP and inactivated when bound to GDP.
• GTP is hydrolyzed into GDP over time by G-protein.
• Associate with receptors on the cytosolic side (peripheral membrane proteins).
• Large, heterotrimeric (Gα, Gβ, G𝛾).
• The largest subunit is α, which binds to GTP and GDP.
• Heterotrimeric means made up of 3 parts, with at least 2 being different.
• The α subunit can detach from β and 𝛾, but they always stay together.

G-Protein Coupled Receptors

• Associate with trimeric G-proteins.
• Similar receptor structures in all cells.
• Contain 7 transmembrane α helices and alternating cytosolic and extracellular loops.
• Many different kinds of trimeric G-proteins.
• Can be stimulatory (Gs) or inhibitory (Gi).
• One receptor can influence multiple pathways, or vice versa, or conflict with others.

G-Protein Activation/Inactivation Cycle

• Resting state: No ligand, G-protein bound to GDP.
• Ligand binds receptor, receptor binds G-protein, Gα switches GDP for GTP.
• Gα and Gβ𝛾 subunits separate.
• G-protein subunits activate or inhibit target proteins, starting signal transduction events.
• Gα subunit hydrolyzes its bound GTP, turning it to GDP and inactivating itself.
• Subunits recombine to form an inactive G-protein.
• The Gβγ duplex can cause ion channels to open.
• Binding of acetylcholine results in the Gβ𝛾 binding with a K+ ion channel, causing it to open.

Definitions

• Receptor: Protein that receives a signal from another cell.
  • Mostly transmembrane and facing exteriorly.
• Ligand: Molecule that binds the receptor.
  • Amino acids, peptide, protein, fatty acids, lipid, nucleotide.
• Signal transduction: Cell’s translation of receptor-ligand interaction.
• Drug Use Receptors

Structure & Metabolism of Cyclic AMP

Protein Kinase-Associated Receptors

Receptor Tyrosine Kinase

Hormones