Unit 1 & 2 Chemistry PDF

The Chemistry and Structure of the Cell What to expect: Atoms Electrons Chemical bonds Ionic Covalent Hydrogen Atoms make up everything Atom: The smallest unit of an element that retains its chemical properties Subatomic particles Every atom is made up of:  Electrons: negatively ch...

The Chemistry and Structure of the Cell What to expect: Atoms Electrons Chemical bonds Ionic Covalent Hydrogen Atoms make up everything Atom: The smallest unit of an element that retains its chemical properties Subatomic particles Every atom is made up of:  Electrons: negatively charged  Protons: positively charged  Neutrons: no charge, neutral The charge of subatomic particles controls structure of atom https://www.fastgamsat.com/must-study-maths-gamsat/chemistry-joke-futurama-fry-i-dont- trust-atoms-i-heard-they-make-up-everything/ The Atom Nucleus is composed of protons and neutrons Electrons around nucleus  Elements A substance that can’t be broken down by ordinary chemical means - melting Periodic table organized based on characteristics protons 6 Atomic Number 7 * Atomic number: # of protons Atomic mass: summed mass of protons and neutrons C Element Symbol N 12.011 Atomic Mass 14.007 Number of protons and neutrons in nucleus not always equal… im rons Isotopes Atoms of an element that have different number of neutrons Most elements exist as mixtures of different isotopes is ↑ atom , S Electrons control chemistry Electrons are found in orbitals: area around a nucleus where an electron is likely to be found Orbitals vary in shape:  s orbital  p orbital  d, f, etc.. orbitals No orbital can contain more than two electrons -goiction  Electrons have energy levels Energy: Capacity to cause change by doing work farther from greater  Potential energy: energy something has in relation to its position nucters energy Electrons have varying levels of energy depending on how far they are from the nucleus Orbitals ≠ Shells; Orbital  Orbitals = location, shells = energy - parentnetic potential a energy  insun- > Electrons have energy levels put gain energy (farther) Electrons releasing energy > https://bio1151.nicerweb.com/Locked/media/ch02/excited.html https://www.culturehustleusa.com/products/lit-the-worlds- glowiest-glow-pigment-100-pure-lit-powder-by-stuart-semple Elements Valence electrons: electrons (e-) found in the outermost energy level/shell (energy  Basis for chemical properties of elements  Valence shell can contain no more than 8 e- ↓ Octet rule: atoms will loose or S gain valence electrons to fill valence shell with 8 e-  This explains reactivity of elements Abundance of elements 94 naturally occurring elements 12 found in living systems >0.01% Atomic #s < 21L You are 96.3% CHON Chemical bonds Molecule: Group of atoms held together by energy in a stable association Compound: Molecule that contains atoms of more than one element  Joined together by chemical bonds  Vary in strength and type https://byjus.com/chemistry/nitrous-oxide/ Chemical bonds Chemical bonds  Ions and ionic bonds Atoms may lose or gain electrons to fulfill octet rule and become charged Neutral atom: electrons = O cation i protons d cation uneven Ions: electrons ≠ protons ar gains  Anion: negatively charged atom (gains e-)  Cation: positively charged anion & atom (loses e-) Ions and ionic bonds Atoms may lose or gain electrons to pair off unpaired e- Neutral atom: electrons = protons Ions: electrons ≠ protons  Anion: negatively charged atom (gains e-) https://theconversation.co  Cation: positively charged m/kitchen-science-a-salt- on-the-senses-58633 atom (loses e-) Chemical bonds Covalent bonds Covalent bonds Form when two atoms share one or more pairs of valence e- Each set of e- attracted to both nuclei Valence e- determine # of bonds  # of bonds determines strength of bond Molecule should:  Have no unpaired e-  Satisfy octet rule  No net charge Very stable  Polar and nonpolar covalent bonds dioxide) , Hee Carbon Multiple covalent bonds can exist in - molecules with more than two atoms δ+ δ-  Need to share e- with more than one atom -parcompolar Electronegativity: atom’s affinity for electrons electro-attractivity Nonpolar: equal electronegativity S between atoms  e- shared equally Polar: difference in electronegativity creates partial charges one atom https://chemistrytalk.org/periodic-trends-made-easy/ her "polaposites has ,mighty a Hydrogen bonds Opposites attract Weak bonds that form between polar molecules Common in water, other molecules Too weak to form stable molecules by themselves Power in numbers https://flexbooks.ck12.org/cbook/ck-12-chemistry-flexbook- 2.0/section/9.19/primary/lesson/hydrogen-bonding-chem/ Chemical Reactions What to expect Chemical bonds Energy Thermodynamics Free energy Water and its properties pH chemistry  CH = Nonpolar OH : Polar Nonpolar and polar covalent bonds It’s all about electronegativity Nonpolar: bonds between identical atoms, e- shared equally Polar: atoms that differ in electronegativity, e- not shared equally https://www.geeksforgeeks.org/covalent-bond/ Altering bonds Chemical reaction: formation and breaking of chemical bonds  All about equilibrium  Conservation of mass; # of atoms remains the same Reactants Products Chemical reactions influenced 6H2O + 6CO2 ↔ C6H12O6 + 6O2 by 3 important factors:  Temperature hutter faster  Concentration of reactants and products  Catalysts Energy in chemistry Reactions try to exist in equilibrium; rate in 1 direction = rate in other direction Energy = capacity to do work Kinetic energy = energy of motion Potential energy = stored energy  Potential ↔ Kinetic Many forms of energy  Mechanical, heat, sound, electric, light, radioactivity https://saylordotorg.github.io/text_general-chemistry-principles-patterns-and- applications-v1.0/s09-01-energy-and-work.html Thermodynamics: Transforming Energy ↑ First law of thermodynamics: Energy cannot be created or destroyed, it only changes from one form to another Second law of thermodynamics: Energy cannot be transformed from one form to another with 100% efficiency  Usually lost in the form of thermal energy More ordered, less stable  less & ordered, more stable  Ice in water http://www.quickmeme.com/p/3w26l7  Gibbs Free Energy Free energy: energy available to do work in a system Under constant temperature, pressure, and volume, it’s Gibbs free energy (G) in&  ∆G = ∆H - T∆S need  Bond energy = H, disorder = S - (t) positive AG fel usually E O  endergonic ronspontaneous -. so Activation Energy Most reactions require destabilizing input of energy to get Lexineating up O water ] started & Activation energy: Energy needed to destabilize existing chemical bonds and initiate a reaction Catalysts: substance that lowers the activation energy  Enzymes serve as catalysts in living systems Activation Energy e Most reactions require input of energy to get started Activation energy: Energy needed to destabilize existing chemical bonds and initiate a reaction Catalysts: substance that lowers the activation lowers activation O energy energy  Enzymes serve as catalysts in living systems Reductionto * I reactions transfer of Redox e- Oxidation: molecule or atom that loses electron, is oxidized LEG Reduction: molecule or atom that gains electron, is reduced GER Redox reactions: coupled reduction and oxidation reactions https://byjus.com/jee/redox-reactions/ Water facilitates life Water has many properties that are crucial to life Cohesion Adhesion High specific heat High heat of vaporization Lower density of ice Solvent Water Cohesion and Adhesion Cohesion: Hydrogen bonds among water molecules  Surface tension Adhesion Adhesion: Hydrogen bonds with other polar molecules  Capillary action Cohesion Water Temperature Specific heat: amount of heat 1 g of a substance must absorb or lose to change by 1 °C  Heats slowly and holds temp for longer 1  Allows for maintenance of internal temperature of organisms Heat of vaporization: amount of energy required to change 1 g of substance from liquid to gas  Keeping cool through sweating Solid water is less dense than liquid  Hydrogen bonds in ice are stable and relatively far apart  Water freezes from the top down and prevents lakes http://ponce.sdsu.edu/properties_of_water.html and oceans from completely freezing Water as a Solvent Water gathers closely around any substance with a charge  Substance carries full charge: ion  Substance carries partial charge: polar molecule Water is a solvent: forms hydrogen bonds around molecules  Solute and solubility Formation of hydration shell: surrounds molecule in shell preventing association with other molecules pH Chemistry pH = power of hydrogen concentration pH = + -log[H ] - Acids increase [H+] Bases decrease [H+] neutral pH regulation is crucial to life and small changes can be harmful Buffers Buffers: substances that resist changes in pH; stabilizes pH  Absorb H+ when acid is added  Release H+ when base is added Bicarbonate (HCO3-) is the most important in the human body Macromolecules What to expect: Carbon chemistry basics Macromolecule structures Functional groups Isomers Nucleic acids Lipids Carbohydrates Carbon: Framework of biological molecules Carbon can form 4 covalent bonds Can bind to H, O, N, S, P, C CHONPS Can form chains, branches, rings, balls, tubes, coils Hydrocarbons: molecules consisting of C and H C and H have similar nonpolar electronegativities Release energy when oxidized  Carbon bonding and shapes All nonpolar Double covalent bond Covalent bond Functional Groups Determine reactivity and molecular properties Have definite chemical properties, no matter where they are Functional Groups Determine reactivity and molecular properties Have definite chemical properties, no matter where they are Isomers Isomer: same molecular formula, different forms Structural: differences in the carbon skeleton  Stereoisomers: same skeleton, differences in how functional groups attach to skeleton  Enantiomers = mirror images, chiral molecule most common Chiral molecules come in two varieties:  D (dextrorotatory) and L (levorotatory)  D-sugars and L-amino acids molview.org https://socratic.org/questions/what-are-stereoisomers-give-me-an-example Macromolecules Made up of polymers, which are made up of monomers Monomers become linked by removing dehydration reactions polymer Polymers broken apart by hydrolysis reactions 3 groups + lipids  Carbohydrates adding  Nucleic Acids back ·  Proteins  Lipids poly monomer Carbohydrates General formula: (CH2O)n Monosaccharides: simplest carb Disaccharides: two linked monosaccharides, transport Polysaccharides: longer chains, storage and transport Monosaccharides Simple sugars 3-7 C atoms 5-6 C sugars can form straight chains or ring forms Structural Isomers Stereoisomers Ribose and ribulose are…? Ribose and ribulose are…? func m groups diff place Structural Isomers Glucose Major cellular fuel Forms transport disaccharides Stereoisomers:  α-glycogen and starch  Β-cellulose Disaccharides Two monosaccharides joined by dehydration (glycosidic linkage) Carbohydrates 100-1000s monosaccharides joined by glycosidic linkage Storage polysaccharides Starch - plants Glycogen - animals Structure polysaccharides Cellulose – plants Chitin – arthropod exoskeleton Starch α-glucose polymer Stored as granules (plastids) in plants Two forms: Amylose (unbranched) Amylopectin (16 linkages, branched) Glycogen Animal equivalent to starch Stored in granules in muscle and liver cells Animal equivalent to starch Stored in granules in muscle and liver cells storage ,n animals Cellulose β-glucose polymer (14) Cellular wall in plants Linear, unbranched macromolecule Hydrogen bonds between cellulose molecules Animals cannot break down cellulose Chitin N-acetyl glucosamine polymer Hydrogen bonds between molecules Resilient structure  Protein cross-linking  Calcium carbonate (CaCO3) precipitation within chitin increases hardness Nucleic acids Polymer of nucleotides joined by phosphodiester linkage 2 classes:  DNA = Deoxyribose nucleic acid  RNA = Ribonucleic acid Contain genetic information, control gene expression, hereditary info Nucleotides Monomer components:  5-C sugar (ribose/deoxyribose)  Phosphate group Nitrogenous bases  Nitrogenous base A G - f C T U DNA : AGCT RNA AGCU : Sugar-Phosphate Backbone.. Phosphodiester bond between phosphate and sugar Sugar-phosphate backbone and protruding nitrogenous bases Polynucleotide (nucleic acid) is polar Phosphate group = 5’ end Hydroxyl group (-OH) = 3’ end DNA & RNA DNA = two polynucleotide strands winding around each other (ATCG)  Double helix (two strands)  Antiparallel – sugar backbones run in opposite directions  Nucleotide pairs Our together  Bases in opposite strands attracted by hydrogen bonds  complementary bases  complementary strands Doorvana RNA = single polynucleotide strand (AUCG)  Complementary base pairing possible (other or self)  Transfer-RNA (tRNA) DNA & RNA (+ ) Nitroge,- Other nucleotides Adenosine TriPhosphate (ATP) = energy currency of the cell Electron carriers Nicotinamide Adenine Dinucleotide (NAD) Flavin Adenine Nucleotide (FAV) Proteins Monomer = amino ↑ acid Polymer = polypeptide  Amino acid linked by peptide bond Protein = one or multiple polypeptides Multiple classes and functions Amino Acids α-symmetric carbon atom  Amino group (-NH2) -  Carboxyl group (COOH)  Side chain – R-group that determines chemistry 20 amino acids defined by their side chain Can become ionized, makes them resistant to small pH changes  -COOH-  -NH3+ Peptide Bond Dehydration (condensation) between amino and carboxyl Dipeptide = 2 amino acids Polypeptide = more than 2 amino acids georder e Forms rigid bond (no free rotation) Amino acids Grouped based on their R group properties  Nonpolar (hydrophobic) doesn't mix well with water  Polar uncharged (hydrophilic) attracted to water  Charged (hydrophilic)  Acidic  Basic Special functions  Methionine – 1st in polypeptide chain  Proline – kinks in chains  Cysteine – links chain (disulfide bond througha Nonpolar Amino Acids C It-similiar electronegativities Polar Uncharged Amino Acids Charged Amino Acids & & & Proteins: Structure Shape defines function Sequences of amino acids determine structure  Internal = non-polar  Surface = polar and charged Four structural levels  Primary: amino acid chain (sequence)  Secondary: hydrogen bonding patterns (backbone)  Tertiary: Interactions between side chains 3D -  Quaternary: interactions between multiple polypeptides generating a single functional https://www.quora.com/What-is-the-denaturation-of-protein unit Primary Structure Amino acid sequence 20 amino acids might appear in any position  Allows for great diversity Sequence encoded in hereditary genetic information Primary structure dictates secondary and tertiary structure Secondary Structure Regions stabilized by hydrogen bonds between atoms of polypeptide backbone (not side chains) (not) α-helix (coil, cylindrical)  Hydrogen bond every 4th amino acid  Dominates in α-keratin (hair) β-pleated sheet (folds, planar)  Two parallel (or antiparallel) segments connected by hydrogen bonds  Core of globular proteins  Silk protein Tertiary Structure Interactions among side chains (r) Final folded 3D shape Different interactions determined by side-chains  Hydrogen bonds  Electrostatic attraction  Hydrophobic interactions and Van der Waals; non-polar groups associate as they are excluded from surrounding water  Disulfide bridge (covalent bond) Quaternary Structure Interaction among polypeptides Aggregation of Change in 1 amino acid polypeptide subunits Protein denaturation Denaturation = loss of protein shape, becomes biologically inactive Small globular proteins re-naturalize if returned to physiological conditions get temp - downback https://web.njit.edu/~mitra/green_chemistry/EXP_3.htm Protein Motifs Motifs = similar structures among otherwise dissimilar proteins  Helix-turn-helix: interaction with DNA  “Rossmand fold”: nucleotide binding site  β-barrel motif  β-α- β motif Domains = functional units within a larger structure Lipids Groups of big molecules characterized by their hydrophobic behavior what makes  Hydrocarbon chains (non-polar)  Varied in form and function Fats, phospholipids, steroids Fats Large molecules assembled from smaller molecules by dehydration Iycerel fattyads 9 & - Structure:  Glycerol  3 fatty acids  Joined by ester linkage (dehydration reaction) Fatty acid: long (16-18) hydrocarbon chain Energy storage (very reduced molecule)  Support and insulation Ester linkage Fats Saturated = animal fats; no - double bonds Unsaturated = vegetable fats; cis double bond O Phospholipids Major constituents of cell membranes Structure:  Glycerol  2 fatty acids (tails) Spolar Spri  1 phosphate (optional attachment: small charged polar molecule Different behavior  Polar head and two non-polar tails  Hydrocarbon tail  Hydrophobic  Phosphate (+ attachment)  hydrophilic Membranes In aqueous environments, phospholipid membranes form spontaneously  Micelle (droplets)  Phospholipid bilayer  Cell membrane Micelle Phospholipid bilayer heads ↑ - fails Cell Structure Cell Theory We’ve known about cells for a while: Cells first observed by Robert Hooke in 1665 Anton van Leeuwenhoek first to observe living cells Matthias Schleiden stated plants made of cells Theodor Schwann reported animal tissues consist of cells https://www.researchgate.net/figure/Left-Hookes-microscope-Robert-Hooke-Micrographia-London- 1665-Scheme-1-opposite_fig1_281514948 Cell Theory There are 3 principles to cell theory: 1. All organisms are composed of one or more cells, and the life processes of metabolism and heredity occur within these cells 2. Cells are the smallest living things, the basic units of organization and all organisms 3. Cells arise only by division of a previously existing cell Cell Theory in plain English There are 3 principles to cell theory: 1. All life is made up of one or more cells. These cell(s) must be able to “eat/breath” and make carbon copies of themselves by themselves 2. There is no living thing smaller than a cell, the Lego brickette of life 3. There are no new cells spontaneously forming at the current moment Rate of diffusion keeps cells small Cells rely on diffusion to bring substances into and out of them Diffusion affected mostly by surface area and distance to diffuse  Also controlled by temperature and concentration gradient Cells need to be small to increase surface area-to-volume ratio  It takes too long to transport things from the membrane to the center if too big  Larger cells have adaptations such as multiple nuclei or are long and skinny  # There are some common features among all cells Genetic material Nucleoid or nucleus Cytoplasm Ribosomes -Tape Synthesize proteins Plasma membrane https://rsscience.com/eukaryote-prokaryote/ Genetic material: Blueprint for life Prokaryotes: No nucleus  Single, circular DNA molecule  Nucleoid: centrally located region https://project8p.org/chromosome-101/ Eukaryotes:  Usually linear, multiples DNA chromosomes  Genetic material is separated by membrane  Nucleus = nuclear Y envelope https://www.coursehero.com/study-guides/ivytech-bio1-1/reading-dna-packaging-in- eukaryotes-and-prokaryotes/ Cytoplasm Semifluid matric filling the inside of the cell Contains sugars, amino acids, proteins, ions, etc. Aqueous medium, but would feel like Jell-O Consists of cytosol and organelles  Cytosol = part that contains organic molecules and ions  Organelles = macromolecular structure specialized for particular function https://www.quora.com/What-is-cytoplasm-and-where-is-it-located-What- function-does-it-serve Plasma membrane Lipid layer that encloses cell and separates it from its surroundings Functions as selective barrier; allows certain things in and others out Phospholipid bilayer has embedded proteins  Can be 5-10 nm thick https://www.novusbio.com/research-areas/cellular-markers/plasma-membrane- markers.html Ribosomes Protein synthesis machinery  Prokaryotes: Free ribosomes  Eukaryotes: Free ribosomes & of cell endomembrane bound -Inside Composed of ribosomal RNA (rRNA) and proteins  Large and small subunits  Only join when synthesizing protein Need messenger RNA (mRNA) and transfer RNA (tRNA)  mRNA carries coding info from DNA  tRNA carries amino acids https://www.khanacademy.org/science/biology/structure-of-a-cell/prokaryotic- and-eukaryotic-cells/a/nucleus-and-ribosomes The Domains of Life Eukaryotes Prokaryotes Prokaryotes Tend to be “smaller and simpler”  ~1 μm  Cytoplasm surrounded by plasma membrane  Encased in rigid cell wall  No distinct interior compartments/membrane- bounded organelles Unicellular: cell = organism Two main domains:  Archaea  Bacteria Prokaryotes: Distinguishing features No nuclear envelop  Nucleoid Lack of internal compartmentalization  No membrane bound organelles  No internal membrane systems membrasa All bits of cytoplasm have access to all parts of the cell Plasma membrane carries out some functions of organelles by -  Infoldings of plasma membrane Cell shapes 3 common cell shapes: Coccus (Cocci, plural) = spherical Bacillus (Bacilli, plural) = rod Spiral Cell wall outside Extracellular structures that enclose the entire cell, including plasma membrane Rigid in structure  Allows protection, maintenance of shape, prevents excessive water uptake or loss Made of peptidoglycan = carbohydrate matrix cross-linked by short-polypeptides  Gram-positive: thick peptidoglycan  Gram-negative: thin peptidoglycan & outer membrane Archaeal cell walls and lipids Archaeal cell walls are different Chemical structure of archaeal lipids distinct from bacteria Have S layers = membrane lipid layer that includes saturated hydrocarbons and a monolayer  Also found on outer layers of Gram + & - bacteria  Many functions such as attachment, protection, trapping, selective permeability https://www.researchgate.net/figure/S-layers-in-Archaea-Electron- micrographs-of-a-euryarchaeote-Methanocaldococcus_fig1_282030460 Capsules Some bacteria have additional gelatinous layer Jelly-like protective coat  Capsule = compact matric  Slime layer = relaxed matrixkeepee Made of polysaccharides (glycocalyx) Flagella: How cells move Locomotion organelle: works through rotation Long, threadlike structure protruding from the surface Single filament = filamin https://youtu.be/JOYy V19fGiQ Endospores where get you food poisoning In times of environmental stress, bacteria can from endospores  Dormant, tough, and non- reproductive structure that forms around genome When environmental conditions become favorable, germination (reproduction) occurs  Fimbriae Thin, hair-like filaments/structures Allows for attachment to surfaces - Surround bacteria - reduce metal Eukaryotes Structures unique to eukaryotes Typically larger (~10 μm) Nucleus: contains DNA separated by nuclear envelope Endomembrane system  Nuclear envelope  Endoplasmic reticulum (smooth & rough)  Golgi apparatus  Vesicles Membrane bound organelles Cytoskeleton Cell wall found in some eukaryotic cell: plants https://www.sciencetopia.net/biology/euka ryotic-cell-structure-and-reproduction (cellulose), fungi and some animals (chitin) Animal cell Plant cell  # Cellular diversity Eukaryotes can live as: Unicellular organisms Colonial: Usually same type of cell (can be different types) that work - together but maintain individuality Multicellular: Different types of cells that share - genetic code Nucleus Nucleus Contains DNA, genetic and inheritance info Divided into multiple linear chromosomes, organized with proteins into chromatin  Chromatin in nondividing cells: loosely organized, diffused  In dividing cells: condenses to form chromosomes Typically located centrally in animal cells Most cells have one nucleus, can have multiple nuclei https://socratic.org/questions/is-chromatin-the-same-as-a-chromosome Nuclear envelope Membrane enclosing nucleus Two membranes separated by narrow space Nuclear pores: regulate entry and exit of proteins, RNA, and ribosomes Nuclear lamina: protein filaments that line the inner surface of the nucleus envelope and gives it shape Continuous with the endoplasmic reticulum ↳ nextoe Endoplasmic Reticulum Endoplasmic Reticulum (ER) Composed of phospholipid bilayer embedded with proteins Can be folded sheets, flattened sacs (cisternae), and complex tubular shapes  Space inside ER is cisternal space or lumen - Largest internal membrane system Two types of ER:  Rough ER (ribosomes on surface)  Smooth ER Transport vesicles used to transport materials from ER to other endomembrane systems organelles Rough ER (RER) Synthesizes proteins on surface Secrete proteins to other organelles Y  Lysosomes  Vacuoles Amino acid sequence determines whether protein stays in RER or not Proteins can be modified with short-chain carbohydrates  glycoproteins https://www.amoebasisters.com/gifs.html Smooth ER (SER) Structure can be tubules, flattened sacs, or higher- order tubular arrays cons Membranes contain enzymes  Synthesize carbs and membrane lipids calcium-cation Store intracellular Ca2+ Detoxes  Breaks down molecules to make https://thebiologynotes.com/smooth-endoplasmic-reticulum/ them soluble SER and RER take of to art proteinsnet Peel a Golgi Apparatus Golgi Apparatus/Body Stack of flattened sacs = cisternae Varies in number transport  1 or few in protistsCellulares  20 or more in animals  100s in plant cells respe Collects, packs, and distributes molecules through 2 faces Shipping  cis face: located near ER; receiving site via side transport vesicles &  trans face: shipping site; uses secretory vesicles O secretory vercick ↓ exocytosis Modifies proteins and lipids https://gfycat.com/discover/golgi-apparatus-gifs  Forms glycoproteins and glocolipids  Golgi Apparatus https://gfycat.com/cooperativehardtofinddanishsw edishfarmdog-science-technology-visualisation Lysosomes Formed from Golgi body Digestive vesicles  Degrade proteins, nucleic acids, lipids, carbs Intracellular digest, needs lower pH to digest Activated when fused with: to by  Food vesicle  Phagocytosis -helps  Old/worn out organelle  Autophagy Lysosomes Formed from Golgi body Digestive vesicles  Degrade proteins, nucleic acids, lipids, carbs Intracellular digest, needs lower pH to digest Activated when fused with:  Food vesicle  Phagocytosis  Old/worn out organelle  Autophagy https://www.amoebasisters.com/gifs.html Microbodies Vesicles that contain enzymes Way for eukaryotes to organize metabolism https://www.geeksforgeeks.org/microbodies/ Peroxisomes Spherical membrane Contain enzymes to oxidize fatty acids Produce hydrogen peroxide as byproduct  Hydrogen peroxide is reactive  Peroxisomes have catalase enzyme Breakdown  Decomposes hydrogen peroxide Vacuoles Centrally located, membrane- bound structure Tonoplast = membrane that contains water channels for osmotic balance In plants: vacuoles  Water balance - used o  Nutrient storage  Waste storage In protists, fungi, and some animals:  Food vacuoles  phagocytosis  Contractile vacuole  water balance absorb or ro exper Balance https://slideplayer.com/slide/14989136/ Vesicles Spherical membrane-enclosed organelle Transport material within organelles or to/from exterior througa mov madeMenta Mitochondria Found in ALL eukaryotes Multiple mitochondria per cell or one large single mitochondrion  # correlates to cell’s level of metabolic activity capsulated Two phospholipid bilayers defining two internal compartments  Outer membrane (smooth): porous  Inner membrane: contiguous layers form cristae Two internal compartments:  Intermembrane space: region between inner and outer membranes  Matrix: enclosed by inner membrane and contains enzymes, proteins, ribosomes, and mtDNA a mitochondral  Mitochondria batenario * Contain their own circular DNA  mtDNA = mitochondrial DNA Some proteins produced from mtDNA but many are imported The memes are right, they are the powerhouse of the cell  Chemical energy converters; aerobic respiration to synthesize ATP Dynamic: change shape constantly through fission and fusion In animals: maternal origin Chloroplasts Only present in photosynthetic organisms Contain chlorophyll (green photopigment) and enzymes involved in production of photosynthetic sugars Two membranes:  Outer: two phospholipid bilayers with very narrow intermembrane space  Inner: flattened sacs = intra-chloroplast membranous system  Granum = stack of thylakoids = light capturing pigments Chloroplasts 3 inner compartments:  Intermembrane space: very narrow  Stroma: fluid containing ribosomes, chloroplast DNA and enzymes ---  Thylakoid space or thylakoid lumen Contain their own circular DNA Some proteins produced in chloroplast, but many imported Capture light energy and convert it into chemical energy  Photosynthesis Dynamic: change shape constantly through fission and fusion Origin of mitochondria and chloroplast Display similarities with bacteria Endosymbiotic theory: evolved from free-living bacteria Host cell engulfed bacteria, provided certain advantages associated with special metabolic abilities  Occurred multiple times Evidence for endosymbiosis theory:  Double membrane  Own circular DNA and ribosomes  Cytoskeleton Network of protein fibers 3 types of fibers:  Actin filaments (microfilaments)  Microtubules  Centrosomes and centrioles  Intermediate filaments - > - Anchors organelles to fixed locations Supports shape of cell Cell motility  Molecular motors Actin filaments Long fibers, 7 nm in diameter Actin is globular protein Two protein chains loosely twined together like two strands of pearls Exhibit polarity: positive (+) and negative (-) end positive > - negative Constantly polymerizing and depolymerizing Maintain cell shape Change cell shape Muscle contraction Microtubules Largest filament: hollow, 25 nm in diameter Ring of 13 protein protofilaments  Subunit: dimers of α and β tubulin  Exhibit polarity: positive (+) and negative (-) end towards nucleation center Constantly polymerizing and depolymerizing Maintain cell shape Cell motility Chromosome movement in cell division Organelle movements Intermediate filaments 8-12 nm in diameter Present in cells of some animal cells Fibrous proteins coiled into cables  Protein subunits called vimentin  Keratin and neurofilaments Very stable Maintain cell shape Anchor nucleus and certain other organelles Cytoskeleton Centrosomes and centrioles Centrosome = microtubule organization center (MTOC) in animals and some protists Usually located near nucleus and contains two centrioles  Centrioles = barrel shaped organelles each composed of nine sets of triplet microtubules arranged in ring  Positioned at right angles to each other Centriole Centrioles duplicated before cell division Participate in formation of mitotic spindle Molecular motors Proteins that use microtubules as tracks to transport cargo (vesicle) Kinesin = moves towards the (+) end of microtubule track (MT) Dynein = moves towards (-) end of MT Myosin = actin based molecular motor https://youtu.be/wJyUtbn0O5Y Flagella and cilia Motile appendages containing microtubules that undulate 9 + 2 arrangement of microtubules surrounded by plasma membrane Dynein proteins move microtubules by forming and breaking cross bridges on adjacent pairs of microtubules Microtubules of flagellum derived from basal body, situated just below point where flagellum protrudes from surface of cell Viruses Nucleic acid surrounded by protein coat Viral genome:  Double or single stranded RNA  Double or single stranded DNA Capsids and envelopes:  Capsid = protein shell enclosing viral genome; diverse morphology  Envelope = membrane derived from a b allhaveenvelop host cell not e Viruses Biological Membranes STRUCTURE AND FUNCTION Plasma membrane Structure: Phospholipid bilayer & other lipids (i.e. cholesterol) Membrane proteins Interior protein network Cell-surface markers: glycoproteins and glycolipids Plasma membrane Function: selectively permeable barrier that separates interior of cell from extracellular environment Receives info about changes in environment Regulates passage of molecules and materials in and out of cell Communicates with other cells Participate in and serve as surface for biochemical reactions Membrane structure Fluid mosaic model: cell membrane consists of fluid bilayer of phospholipid molecules in which proteins are embedded or otherwise associated This mosaic patter is not static! Positions of proteins constantly change https://gifs.com/gif/the-fluid-mosaic-model- phospholipid-bilayer-rNAGZQ  Move like icebergs in fluid sea of phospholipids # Phospholipids Building unit of biological membranes Amphipathic macromolecules  Contain both hydrophilic and hydrophobic regions  Hydrophilic heads present on both surfaces and in contact with cytosol and extracellular environment  Hydrophobic tails located in interior of bilayer Membrane fluidity Membrane fluidity can be affected by:  Phospholipid composition; unsaturation  Lipid composition; cholesterol (in animal cells) Two dimensional fluids  Phospholipids move very fast laterally  Proteins move laterally slowly  Some proteins anchored to specific https://gfycat.com/linearinferiorkingsnake region of membrane by cytoskeleton Membrane proteins Embedded in biological membranes Peripheral proteins  Adhere temporarily to membrane and tend to be extracellular Integral proteins  Permanently attached to membrane https://www.creati ve- biolabs.com/blog/in  Penetrate hydrophobic region of bilayer dex.php/membrane -protein-overview/  Transmembrane proteins completely span membrane Not randomly distributed  Groups of proteins often associated in https://gfycat.com/ uk/disguisedpalebla specialized patches = protein rafts ckbuck Membrane protein functions Transport – allows certain solutes to enter or leave Enzyme – carry out chemical reactions Cell-surface receptors – detect chemical messages Cell-surface identity markers – cellular ID tag Cell-to-cell adhesion – self explanatory Attachment to cytoskeleton – linking of surface proteins to cytoskeleton Affecting membrane structure – cause membranes to bend https://www.pinterest.com/pin/305470787201097659/ Concentration gradients Difference in concentration across membrane causes movement  diffusion * Factors that affect ion transport across membranes:  Relative concentration on either side of membrane  Voltage difference across membrane = membrane potential  Gate status and voltage https://www.labxchange.org/library/pathway/lx-pathway:7efd224b-97a8-442a-b6a5- potential of ion channels a3a44745f6ac/items/lx-pb:7efd224b-97a8-442a-b6a5-a3a44745f6ac:html:c6001d3d Passive transport Transport of molecules and ions across concentration gradient No energy requirement Simple diffusion = movement of substances from regions of high concentration  low concentrations O2 and small nonpolar molecules Selective permeability Occurs through proteins that control specific molecules/atoms s Channel and carrier proteins Facilitated diffusion = diffusion controlled (facilitated) by proteins/channels  Channel proteins: form passage/channel through which water and certain ions pass through membrane  Aquaporins: water transport across membranes (osmosis)  Ion channels: regulated in response to as key stimulus (gated channels) serves a  Carrier proteins: bind to specific protein to transport them; shape will change to allow - - - molecules to pass Osmosis Occurs in aqueous solutions = solvent (water) + solutes (amino acids, ions, sugars) Osmosis = diffusion of water towards higher solute concentration Osmotic concentration: / determined by concentration of all solutes in solution  Hypotonic = solution with lower osmotic concentration  Isotonic = equal osmotic concentration  Hypertonic = solution with higher e osmotic concentration - Osmosis Osmotic pressure = force needed to stop osmosis Many cells are in hypertonic environment, have strategies to adapt  Extrusion = expel water via contractile vacuole  Isosmotic regulation = match solute concentration to environment  Turgor = hydrostatic pressure against cell wall Passive transport Active transport Uses energy (ATP) to transport ions/molecules across membrane against concentration gradient  Na+/K+ pump Na+ / K+ pump Na+ / K+ pump https://www.amoebasisters.com/gifs.html Coupled transport Concentration gradient generated by active transport  Involves two or more transporters Bulk transport Large molecules can’t cross membrane by diffusion or transport protein  Proteins and polysaccharides Bult#transport = packaged in vesicles and requires energy Endocytosis Endocytosis = molecules enter cells within vesicles that pinch inward from the plasma membrane  Phagocytosis = large particle or cell  Pinocytosis = liquids and small solutes  Receptor mediated endocytosis = receptor binds to ligand Cellular Respiration Respiration follows thermodynamics Energy cannot be created or destroyed, only transferred Energy usually released as heat Negative (-) ΔG = exergonic reaction Spontaneously Positive (+) ΔG = endergonic reaction Enzymes lower activation energy Control nearly all biological reactions Enzymes Made of proteins and https://www.nature.com/ apoproteins articles/nrd2353  Apoprotein = polypeptide part of a protein Can have a cofactor = additional chemical component required for function  Inorganic (ion): Mg2+  Coenzyme (organic molecules): NADH/NAD+, vitamins https://www.biovision.com/products/met abolism-assays/coenzymes-cofactors.html Enzyme properties Highly specific  Think lock and key Increase rate of reaction significantly by lowering activation energy makesthina  Biological catalysts Require optimum environment  Work best at specific temperature and pH conditions  Cease to function if conditions get too extreme Enzyme function Serve as biological catalyst  Increases the rate (speed) of a chemical reaction without being consumed Decreases activation energy (EA)  Energy required to get a reaction going https://youtu.be/qgVFkRn8f 10 Enzyme function Active site (center) = 3D region where substrates interact with enzyme (pocket) Forms enzyme-substrate complex  changes shape of enzyme slightly This slight change is induced fit  facilitates the breaking of bonds and formation of new ones Enzyme function Regulation to enzymatic activity: Amount of enzyme produced winmnc Regulating metabolic conditions that influence shape of enzyme (remember, shape = function Inhibitors Inhibitors Competitive inhibitor = substance competes with substrate for active sight Allosteric inhibitor = noncatalytic sites to which an allosteric regulator binds and Changee of modifies enzyme activity enzyme > - changes funchon https://youtu.be/6EDBlowVST0 Inhibitors Inhibition can be reversible or permanent A Reversible inhibitor = inhibitor binds 2 to enzyme by weak interactions B Irreversible inhibitor = combines with an enzyme and permanently inactivates it with covalent bonds Feedback inhibition = formation of an end product inhibits an earlier reaction Z in the metabolic pathway  * Feedback inhibition Sequence of reaction catalyzed by enzymes Product of Reaction 1 is the substrate for Reaction 2 Product 2 is in turn the substrate for Enzyme 3 Product 3 inhibits an earlier reaction in the metabolic pathway  * ATP Adenosine triphosphate (ATP) is immediate energy currency of the cell Donates energy by means of terminal phosphate group  Easily transferred to acceptor molecule  Exergonic = releases energy ATP formed by phosphorylation of adenosine diphosphate (ADP)  Endergonic = requires input of energy ATP and ADP ATP and ADP ATP is the common link between exergonic and endergonic reactions Also link between catabolism and anabolism Catabolism = degradation of large complex molecules into smaller, simpler molecules ATP-ADD Anabolism = synthesis of complex molecules from simpler molecules Making ATP 3 mechanisms for ATP production: Substrate level phosphorylation (i.e. glycolysis) Oxidative phosphorylation (i.e. chemiosmosis) Photophosphorylation (i.e. photosynthesis, chemiosmosis) Energy flow Redox reactions & energy flow Energy is transferred in redox reactions  Oxidation = substance gives up one or more e- to another substance SwHer  Reduction = substance that gains one or more e- from another substance Electrons commonly transferred as part of hydrogen atoms  NAD+ and NADP+ accept e- as part of hydrogen atoms and become reduced to form NADH and NADPH, respectively  These e- (along with some of their energy) can be transferred to other acceptors creates electron transport chain Electron transport and energy Electron carriers Nicotinamide adenine dinucleotide reduced (NAD + ↔ NADH) oxidized Flavin adenine dinucleotide (FAD+ ↔ FADH2) Aerobic respiration: an overview Catabolic process where fuel molecule (such as glucose) is broken down to form CO2 and water Cellular oxidation are usually dehydrogenations Water is lost = catabolism Aerobic respiration: an overview Electron carriers play critical role Redox reactions result in transfer of e- from glucose to oxygen = electron transport chain Glucose becomes completely oxidized and oxygen becomes reduced to H2O Reduced e- carriers (NADH and FADH2) supply their electrons to https://www.pinterest.com/pin/232146555779821698/ electron transport chain Aerobic respiration: an overview Electron transport chain: Mitochondria of eukaryotic cells move e- in steps via electron transport chain to capture energy efficiently Receives e- from electron carriers https://www.thoughtco.com/electron-transport-chain-and-energy-production-4136143 Aerobic respiration: an overview Electron acceptor determines respiration: Aerobic respiration = oxygen as the final electron acceptor for redox reactions Anaerobic respiration = inorganic molecules as acceptors Ciron sulfur) , Fermentation = organic molecules (Milk wheat) as final acceptor , https://www.sciencefacts.net/anaerobic-respiration.html Aerobic respiration: an overview