Catabolic and Anabolic Pathways

• These are notes on cellular biology

Robert Hooke

• Built the first compound microscope, magnifying objects 30x
• First to observe cell-like blocks in cork
• Coined the term "cells"
• Observed multicellular organisms: nematodes, fungi, mites
• First to publish microscopic observations

Antoni van Leeuwenhoek

• Lens maker
• Built his own microscope, able to see objects 300x closer
• First to observe a single-celled microbe

Cell Theory

• Proposed by Schleiden and Schwann in the mid-19th Century
• Further revised by Robert Virchow
• All organisms are made of cells, which are fundamental building blocks for plants and animals
• The cell is deemed the smallest unit of life
• All living things originate from pre-existing cells via cell division

Prokaryotic versus Eukaryotic Cells

• Prokaryotic cells are simple, small, and lack membrane-bound organelles
• Prokaryotic cells dont have a defined nucleus, but rather a nucleoid
• Cellular processes occur in the cytoplasm and plasma membrane of prokaryotic cells
• DNA is free-floating in the cytoplasm of prokaryotic cells
• Ribosomes are scattered throughout the cytoplasm of prokaryotic cells
• Eukaryotic cells have a defined nucleus enclosed by a nuclear envelope and membrane-bound organelles
• Nucleus houses DNA in eukaryotic cells
• Mitochondria, endoplasmic reticulum, and Golgi apparatus are membrane-bound organelles found in Eukaryotic cells
• Metabolic activities commonly occur within the cytoplasm of Eukaryotic cells
• Eukaryotic cells are larger than prokaryotic cells, allowing them to house membrane bound organelles and facilitate life processes

Plasma Membrane

• It’s a selective barrier which controls what enters and exits the cell
• Allows crucial molecules to enter and waste to exit
• Example: transports oxygen to tissues and removes carbon dioxide
• Typically has a double layer of phospholipids called a phospholipid bilayer
• Described as a fluid mosaic model
• Its structure and flexibility allows membrane to adapt and maintain function

Eukaryotic Cell Composition

• Contains internal membranes that partition the cell into organelles
• Plant and animal cells share most of the same organelles
• Lysosome is in only animal cells
• Chloroplast is in only plant cells
• The nuclear envelope encloses the nucleus, separating it from the cytoplasm
• The nuclear envelope’s double membrane structure has nuclear pores, which regulate entry and exit of molecules
• Nuclear lamina maintains the shape of the nucleus via protein filaments that also regulate important processes such as DNA replication and cell division
• The Nucleus is the control center, directing cellular activity by controlling gene expression
• Chromatin is formed by DNA proteins coming together which condenses to form chromosomes
• Nucleolus: Site of ribosomal RNA (rRNA) synthesis, and combines proteins to form ribosomes

Ribosomes

• Particles made of ribosomal RNA and protein
• Essential for protein synthesis within the cytoplasm
• Site where mRNA translates into protein

Protein Synthesis Locations

• Free ribosomes: found in the cytosol
• Bound ribosomes: on the outside of the endoplasmic reticulum or the nuclear envelope

Endomembrane System

• Regulates protein traffic and performs metabolic functions in the cell
• Is a collection of components, continuous OR connected via transfer by vesicles
• The nuclear envelope acts as “the manager”
• The rough endoplasmic reticulum acts as “the assembly line"
• The smooth endoplasmic reticulum functions as "quality control"
• The Golgi apparatus is "shipping"
• Lysosomes are a "waste disposal and recycling center"
• Vacuoles act as a "storage room"
• The plasma membrane acts as the “security gate"

Endoplasmic Reticulum

• Accounts for more than half of the total membrane in many eukaryotic cells
• Continuous with the nuclear envelope

Smooth ER

• Lacks ribosomes on its surface
• Synthesizes lipids
• Metabolizes carbohydrates
• Detoxifies poison
• Stores calcium

Rough ER

• Has ribosomes studding the surface
• Has bound ribosomes that secrete glycoproteins
• Glycoprotein: proteins are covalently bonded to carbohydrates
• Distributes transport vesicles, which are proteins surrounded by membranes that transports to other areas of the cell such as the Golgi apparatus
• A membrane factory for the cell

Golgi Apparatus

• Consists of flattened membranous sacs called cisternae
• Cis face: "receiving" side of the golgi apparatus Processes
• Modifies products of the ER
• Manufactures certain macromolecules
• Sorts and packages materials into transport vesicles
• Dysfunction in hormone secretion points to an issue with the Golgi apparatus
• Congenital disorders, developmental delays, and immune dysfunctions are examples of things that can go wrong with processes

Lysosomes

• Membranous sac of hydrolytic enzymes that can digest macromolecules
• Contain lysosomal enzymes that can hydrolyze proteins, fats, polysaccharides, and nucleic acids

Vacuoles

• Food vacuoles: formed by phagocytosis
• Contractile vacuoles: pump excess water out of cells and can be found in many freshwater protists
• Central vacuoles: hold organic compounds and water and can be found in many mature plant cells

Mitochondria and Chloroplasts

• Change energy from one form to another
• Not part of the endomembrane systems
• Have a double membrane system
• Have proteins made by free ribosomes
• Contain their own DNA
• Mitochondria: sites of cellular respiration, a metabolic process that generates ATP
• Chloroplasts: sites of photosynthesis, and can be found in plants and algae
• Peroxisomes: oxidative organelles

Mitochondria

• Found in nearly all eukaryotic cells
• Has a smooth outer membrane
• Inner membrane is folded into cristae, which helps increasing surface area
• Creates two compartments: intermembrane space and mitochondrial matrix
• Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix
• Cristae provides a large surface area for enzymes that synthesize ATP

Chloroplasts

• Plastids: family of organelles and chloroplasts are a part of this
• Contain green pigment called chlorophyll
• Found in leaves and other green organs of plants and algae
• Structure
  • Thylakoid: membranous sacs
  • Granum: stacked thylakoids
  • Stroma: internal fluid surrounding granum
  • They consist of enzymes crucial for the Calvin Cycle stage of photosynthesis

Peroxisomes

• Specialized metabolic compartments bounded by a single membrane
• Produce hydrogen peroxide and converts it to water
• Oxygen is used to break down different types of molecules

Cytoskeleton

• Network of fibers extending throughout the cytoplasm
• Helps to support the cell and maintain its shape
• Interacts with motor proteins to produce motility
• Vesicles can travel along “monorails" provided by the cytoskeleton
• Possibly helps regulate biochemical activities
• Organizes the cell's structures and activities
• Three types of molecular structures: microtubules, microfilaments, and intermediate filaments

Microtubules

• Hollow rods about 25 nm in diameter and about 200 nm to 25 microns long
• Include shaping the cell and guiding movement of organelles as functions
• Act as a "track" from the Golgi apparatus to the plasma membrane
• Separate chromosomes during cell division
• Play a key role in maintaining health and organization of the cell

Centrosome

• Where microtubules grow out of near the nucleus
• MTOC: “microtubule-organizing-center"
• Centrioles: nine triplets of microtubules arranged in a ring
• Each Centrosome has a pair in animal cells
• Key function in meiosis is the meiotic spindle

Cilia and Flagella

• Microtubules make and control the beating pattern of cilia and flagella
• Cilia and flagella differ in beating patterns
• Function: locomotion/movement of fluids over surface of cells
• Cilia: back and forth motion, used for movement of other things, and moves trapped mucus and particles
• Flagella: swimming, wave-like or spinning motion Movement of itself that propels the sperm during the egg for fertilization Cellular dyskinesia: affects the cilia which does not allow the mucus to move along Flagellular dysfunction: causes infertility in sperm cells
• Microtubules arranged in with 9 outer microtubules and 2 central microtubules
• Share a common ultrastructure: a core of microtubules sheathed by the plasma membrane

Basal Body and Dynein

• Basal body: anchors the cilium or flagellum to the cell
• There is also dynein, a motor protein which drives the bending movements of a cilium or flagellum via coordinated arm movement and protein cross-links for sliding
• Forces exerted by dynein arms cause doublet to curve, bending the cilium/flagellum

Microfilaments

• Also known as Actin Filaments
• Solid rods about 7 nm in diameter built as a twisted double chain of actin subunits
• Provide a structural role - to bear tension, resisting pulling forces
• Cortex forms a 3D network inside the plasma membrane to provide support inside the cell
• Prevent deformation under external pressures
• Bundles of microfilaments make up the core of microvilli of intestinal cells, which are essential for nutrient absorption in the intestine
• Myosin: protein present in microfilaments that function in cellular motility and can allow cells to move or contract
• Muscle cells: many actin filaments are arranged parallel to one another with some myosin filaments integrated between them to allow the sliding of actin and myosin filaments for muscle contractions
• Amoeboid movement: driven by localized contraction brought about by actin and myosin
• Pseudopodia: extend and contract through reversible assembly and contraction of actin subunits into microfilaments
• Cytoplasmic streaming: speeds the distribution of materials within the cell with Actin-myosin interactions and sol-gel transformation

Intermediate Filaments

• Range in diameter from 8-12 nm and are larger than microfilaments but smaller than microtubules
• Important in supporting cell shape and keeping organelles in place
• More permanent cytoskeleton fixtures, they support supports cell membrane and internal structures of the cell
• Examples are keratin filaments in animal cells found in the nuclear lamina

Extracellular Components and Connections

• Most cells synthesize and secrete materials that are external to the plasma membrane which forms extracellular structures like:
• Cell walls of plants; made of cellulose to provide structural support to help plant maintain shape, and they don't exist in animal cells
• Extracellular matrix (ECM) in animal cells in connective tissues
• Intercellular junctions in tight, desmosomes, and gap junctions

Cell Walls

• Extracellular structure that distinguishes plant and animal cells which prokaryotes, fungi and some protists also have
• Protects plant cells, maintains shape and prevents excess water uptake
• Made up of cellulose fibers embedded in other polysaccharides and proteins Two layers
• Relatively thin and flexible primary cell wall
• Thin layer that glues adjacent plant cell wall together, middle lamella

Secondary Cell Wall

• Formed after the primary cell wall (in some cells,) it's typically thicker and more rigid for additional strength and protection
• Plasmodesmata: channels between adjacent plant cells

Extracellular Matrix

• Animal cells lack cell walls, but covered by an elaborate extracellular matrix (ECM) and made up of glycoproteins such as collagen, proteoglycans and fibronectin
• Integrins: receptor proteins in the plasma membrane ECM proteins bind to Functions
• Support, adhesion, movement, and regulation

Intercellular Junctions

• Neighboring cells/tissues/organs often adhere, interact and communicate through direct physical contact; facilitated by intercellular junctions
• Plasmodesmata: channels that perforate plant cell walls, water and small solutes can pass from cell to cell to conserve water during droughts
• Tight junctions: membranes of neighboring cells are pressed together to prevent leakage of extracellular fluid and maintain the integrity of epithelial tissue in the lining of the intestines
• Desmosomes: fasten cells together into strong sheets also known as anchoring junctions, found often in skin cells
• Gap junctions: provide cytoplasmic channels between adjacent cells, also known as communicating junctions, such as in heart muscle cells where need rapid communication for contractions

The Cell

• A living unit greater than the sum of its part (emergent property) needing integration of structures and organelles for its function
• A macrophage's ability to destroy bacteria involves whole cell coordinating components (cytoskeleton, lysosomes, plasma membrane)
• This information is contained within Chapter 7: Membrane Structure and Function

Plasma Membrane Attributes

• Every cell is surrounded by it: a bi-lipid layer, or contains phospholipids (phosphate, glycerol, two fatty acids)
• Amphipathic nature: hydrophilic and hydrophobic regions
• Semi-permeable: allows certain molecules to pass such as Small, uncharged molecules, though charged ones require the help of proteins
• Fluid mosaic model: fluid and freely moving with various embedded proteins Contains glycolipids and sterols

Protein Passage and Attributes

• Proteins are amphipathic themselves
• Hydrophilic versus hydrophobic amino acids are in different locations
• Hydrophilic proteins are polar and hydrophobic are nonpolar
• Fluidity is not static (constantly moving) held together via hydrophobic interactions (allows movement within bilayer)
• Lipids and some proteins can move: lateral (switching next to each other) across membrane is "flip-flop"
• Temperature affects membrane fluidity and higher the temperature, the more fluid it is; too high it loses function but low temperatures slow down lipid movement which can lead to cracking or reduced function
• Movement of molecules is allowed allowing for shape changing and cell signaling while preventing rigidity
• Fatty acids rigidity is increased with saturated ones (common in heat adapted organisms)
• Fluidity is increased by unsaturated fatty acids (common in cold adapted organisms)
• Cholesterol: acts as a fluidity buffer to the plasma membrane as at 37°C it makes membranes less fluid but at lower temperatures it will prevent tight packing of phospholipids (cold environments)

Fluidity Considerations

• Needs to be balanced to maintain proper function
• Being too fluid prevents proper protein function where the membrane could rupture, but too solid changes permeability which doesn't allow proteins to move around
• Organisms will change their membrane structure to suit observed environment most often for optimized function.

Selective Permeable Membrane

• Helps cell maintain inside composition, stability but still require ways to access external environment
• Solute: substance dissolved in a solution
• Solvent: dissolving agent of a solution (ex: water)
• Solution= solute + solvent
• Small, uncharged and nonpolar molecules: get through But some small polar molecules go through slowly and large, charged and polar molecules have problems getting through i.e. water, glucose/Na+/K+/proteins/nucleic acids

Membrane Permeability: A Semipermeable Membrane Allows

• Certain molecules enter the membrane but not cross to other side and others cross membrane until reach equal concentrations on both sides with ones crossing being dependent upon their chemical characteristics
• Transport proteins: transmembrane ones integrated within membrane: hydrophilic channel acts as automatic sliding doors for aquaporins and carrier ones change shape, hauling molecules into the cell like glucose transporters

Integral Proteins

• Contain nonpolar amino acids in the center (hydrophobic), allowing to interact with core membrane via channels for passage or certain ions/solutes

Peripheral activity

• Located on the surface of cells inside the cytoskeleton or outside into the extracellular matrix

Protein activity

• Transport moves substances across membranes such as the Sodium-Potassium pump
• Enzymatic activity catalyzes reactions like ATP synthesis

Signal Transduction

• Cellular response, receive/relay signals from environment like hormone receptors
• Cell-cell recognition where two different cells identify each other like glycoproteins
• Intercellular where joining brings together organ transplants and attachment anchors cytoskeleton and ECM and maintains shape

Passive Transport

• Occurs naturally without the need for Adenosine Triphosphate (ATP) from a high to low concentration areas
• Osmosis involves the movement of water molecules across semipermeable membrane due to differences in solute concentrations, though type of passive transport where while solutes cannot move, water can
• Facilitated transport requires transport protein and is a type of passive transport using a protein channel to create a hydrophilic pathway Diffusion allows passive transports but not requiring energy, they passively diffuse due to concentration gradient

Water Balance: Tonicity

• The ability of a surrounding solution to cause cell water gain or loss (solutes which cannot cross the membrane) can leads into 3 conditions known as isotonic, hypertonic and hypotonic

Isotonic Conditions

• Iso = same, meaning environment same inside and outside cell resulting in no movement of of water.
• Intravenous fluids are used to maintain homeostasis in this way

Hypertonic

• Hyper = more, meaning more solute on the outside of the cell than inside
• Net movement of water out of the cell result in dehydration

Hypotonic Conditions

• Hypo = less
• Meaning less solute on the outside of the cell than the inside
• Resulting in net movement of water into the cell

Solute Concentration

• Help organism intake/lose water properly through Osmoregulation and specialized vacuoles which help collect/expel in protisis ex. Paramecium caudatum

Cell Walls and Diffusion

• Acts as a barrier to help the cell keep from bursting when taking in water - ex. In plant cells
• Facilitated diffusion: transport across the membrane not using energy via channels (aquaporins) and carrier proteins that assist in the diffusion of substances that normally diffuse slowly or don't at all; and does not use additionaly energy because it's a form of passive transport

Ion Channels and Active Transport

• Work through facilitated diffusion not requiring energy to maintain ion balance inside and outside of the cell through stimulation
• Cannot have charged ions crossed through a membrane, which can require active transport.

Active Transport

• Involves movement of molecules against their concentration gradient with help of ATP with From low concentration to high, the movement is "active" aiding cells to maintain more solutes inside/outside them in different environments
• Commonly employs the sodium potassium pump that pump three sodium ions out and two potassium ions in every cell cycle with ATP and is important in maintaining cells internal balance
• Requires constant influx of ATP

Ion and Bulk Pumps

• Use ATP to maintain membrane potential by using electric charge across a cells membrane from differential distribution of ions
• Will diffuse down electrochemical gradients (or be moved up) requiring two forces: difference in number and charge to create ATP and transduction
• Electrogenic pumps: most abundant in plants creating membrane potential by moving charged ions, are mostly in plants and similar to proton pumps and required adenosine triphosphate (ATP) synthesis
• Some large molecules cannot fit through pumps for protein, large carbohydrates, and cells that move material like exocytosis sending waste outside cell(vesicles) and taking them in during endocytosis (vacuole)
• Exocytosis sends bulk material out if it, and endocytosis takes in material to form vacuoles

Endocytosis

• Phagocytosis : cell eating done by cell itself via the cell membrane which extends its pseudopodia to capture and engulf larger particles
• Pinocytosis: cell drinking that folds membrane inwards to take in solutes
• Receptor mediated endocytosis is when specific substances bind to receptors causing the cell to ingest certain molecules
• This information is contained within the following chapter: Chapter 8: Introduction to Metabolism where the cell depends on constant influx of energy to function

Flow of Energy

• All energy on earth derives from the sun: sunlight is gained, then lost back typically as heat in a one-way flow and is not recycled
• Eating a salad involves gaining something’s stored from a plant (derived from the sun)
• As energy flows through different levels of food chians, only 10% will be maintained and kept
• The sun compensates the steady flow of energy lost from trophic levels

Thermodynamics

• The first law of thermodynamics shows that the energy of the universe is constant and can change form, transfer, transform; but is neither created nor destroyed
• The second law of thermodynamics shows every transfer/transformation increases entropy in the universe - or disorder

Fomrs or Energy

• Potential energy: ability to do work and is a form of stored energy, chemical energy, or the potential energy of molecules
• Kinetic energy describes thermal energy and the movement of molecules.
• Energy is transferred between the two forms, and the point where one goes from a high point to low point is referred to as the potential point, which in turn transfers to kinetic energy

Chemical Energy

• Chemical work stores, builds, rearranges and breaks apart substances to break cells, and perform biological functions
• Energy is used to break down nutrients or synthesize proteins
• Electrochemical work: move charged substances into or out of the cytoplasm or organelles (Ex: sodium-potassium pump)

Potential Energy

• Stored chemical energy must be released through exergonic processes using Adenosine Triphosphate (ATP) but required when processes undergo endergonic reaction requiring ATP, all of this requires a central role
• Reactants are substances that are combined/broken apart during chemical reactions while products are the result of actions
• Free energy derives from a chemical reaction that drives cell activities in coupled reactions, when energy is released it can be used to drive another
• Processes such as those that store energy high-end energy bonds require an influx of that said energy

Spontaneity in Reactions

• Endergonic reactions require an input of energy, and do not happen without the initial trigger
• Exergonic reaction: release energy, happen spontaneously

Metabolism Defined

• Totality of an organism's chemical reactions, often follows a path that begins with a specific molecule and is sped up via enzymes that catalyze those high specific reactions
• Catabolic pathways: release energy by breaking down complex molecules into simpler compounds like during cellular respiration which breaks dawn oxygen in glucose
• Anabolic pathways: consume energy to build complex molecules, such as synthisizing protein from amino acids

Catabolic vs Anabolic Pathways

• Catabolic pathways breakdown macromolecules and release energy that catabolic reactions use
• Catabolic reactions can then drive anabolic reactions through energy Coupling
• If ATP isn't used, then not needed to assemble amino acids into proteins during translation

Muscle and Nerve Cells

• Perform work involving synthetic work (building macromolecules or making protein), or mechanical work (moving molecules or shortening muscles)
• They create work for concentration (storing glucose) or electrical activity by in balancing the sodium-potassium
• Energy is recycled in the environment such that producers capture light energy and convert it into organic, then plants, animals, and bacteria break down these organic molecules
• Major source of cell energy in the forms of light and chemical fuel

Organic Compounds

• Enters the ecosystem and gets captured by plants through photosynthesis
• These organic molecules and oxygen can then create ATP

Oxidative vs Anerobic Conditions

• Respiration is always used to convert organic molecules - catabollicaly and is an essential part of creating ATP
• In the presence of no oxygen (anaerobic) ex. In fermentation, it must be done without
• When oxygen is present (aerobic) ex. in cellular respiration, the cell can maintain ATP

Substrate Phosphorilation

• Phosphate group transferred to the phosphorolated group of the molecule ADP to form ATP, which is catalyzed by enzyme that does ATP production directly

This and Oxidative Phosphorilation?

• Occurs directly rather than on the reaction which relies on the electron transport chain; doesn't require a proton gradient (or oxygen) making it essential for conditions without one or in non-mitochodria organisms

Redix and NADH Reactions

• NAD⁺ is reduced to NADH as organic molecules are broken down in what is called the electron cycle

ATP Via Substrates

• Transfers electrons to starting material from NAD⁺ + and gives them later to transport chain
• ADP is used to make ATP in steps within a chain
• Occurs by the synthesis Krebs but requires the enzyme to catalyze without oxygen

Intermidate Processes

• Molecules modified pre-oxidative phosphorolation before entering transport chain
• Pyruvat form glycosis converted to acetyl-CoA before being converted to other products

Energetic Effects of Phosphorylation

• Oxygen is a receptor when water and energy are released, and through the ETC is travel from NADH which powers ATP

Equations and Reactions

• Equation: C6H12O6 + O2 → CO2 + H2O + 36 ATP + heat via catabolic process to bread glucose that fuels cellular activity, it and results in waste product and is an EXERgonic process

Cellular Production Requirements

• Glucose and then powers creation, removed or sustained

Redox Reactions

• Is the transfer of electrons from one molecule to another: transfer of electrons - one molecule transfers one or more electrons to another molecule
• Reduction: gain of an electron and called RIG: Reduction is Gain
• Oxidation: loss of an electron and called OIL: Oxidation is Loss
• Reactions are called electron bond

Cellular Respiration

• Oxidizes the released electrons to form ATP as oxygen become reduced, it all has the following components + process

1. The body undergoes glycolysis
2. Undergoes oxidation
3. It goes through a citric acid cycle

Glycolysis

• Occurs in the cytoplasm, starting and ending with pyruvate
• The investment phase requires 2 ATP to initiate glucose breakdown
  • Breakdown requires 4 and 2
  • Can only take at set number of electrons

If Oxygen is Involved

• Pyruvate is converted to acetyle and transferred into the Mitocondrial Proteins, but can also can be converted to the Cytoplasma
• This process results to NADH+ + for oxidation process
• Krebs acid then will get converted to Pyruvate, so it makes the glucose have a 2 atp result

Citric Acid Cycle

• Continuous product 1ATP 3NADH
• Glycossis results in the cycle turning twice
  • With 2ATP and multiple others
  • Total yield = 2 ATP

Phosporylation

• Transfers from kebs and results in different energy and chemoiosis to result in different processes
• Is linked to the cycle

Electron Chain

• Complex embeded within the inner and outer
• FADH 2 , ATP, and the chains
• If they cant transfer right, they can donate

Process Through Chemiosmosis

• Tranmestere called ATP, energy is stored
• Is powered used to cellular work, is created throughout cycle
• Involves roation, which is catalyzed and turns the ATP and can be caused by high and low processes
• Can use all material effectively

How Much Oxygen

• The oxygen is in the ATP and is used, which causes cell volume
• Fermentation continues with the following functions
• Glyclosis occurs with additional energy but the Keirbs cylce in process is the same
• Alcohol fermentation, and NADH+ +
• Is often an unmonitored process

Production Control

• Occurs with production inhibition to regulate, or alloters enzymes
• Is key a cycle that is affected by many factors
• Is the first step that effects Glyclosis
• Citate is also first and can lead to cell respiration
• Has carbs broken and turned into chains
• The bodies need energy that they have to burn

Explore catabolic and anabolic pathways, enzyme roles, and ATP's significance in cellular processes. Understand exergonic reactions and energy coupling. Learn about cellular respiration, muscle repair, and ecosystem energy flow.