BIO 202 Biology Lecture Notes PDF

Lecture 1 Ch. 2 Atoms -​ Composed of subatomic particles -​ Neutrons – no charge (1.7x10^-24g = 1 Dalton = 1 atomic mass unit, amu) -​ Protons – positive charge (1.7x10^-24g = 1 Dalton = 1 atomic mass unit, amu) -​ Electrons – negative charge (1/1000 amu...

Lecture 1 Ch. 2 Atoms -​ Composed of subatomic particles -​ Neutrons – no charge (1.7x10^-24g = 1 Dalton = 1 atomic mass unit, amu) -​ Protons – positive charge (1.7x10^-24g = 1 Dalton = 1 atomic mass unit, amu) -​ Electrons – negative charge (1/1000 amu = negligible mass) -​ Nucleus composed of protons and neutrons -​ Positively charged -​ Keeps electrons close to nucleus, creating atom structure -​ Orbited by electrons Elements -​ Most abundant elements found in living systems are hydrogen, oxygen, nitrogen, and carbon -​ Of the 92 naturally occurring elements, 25 required for humans to live a healthy life -​ Plants only require 17 -​ 96% of living matter is made of oxygen, carbon, hydrogen, and nitrogen -​ Trace Elements – Elements required in very minute amounts -​ Iron required by all forms of life Electrons + Chemical Bonds -​ Atoms w/ incomplete valence electrons can share electrons to another atom, creating a chemical bond Radioactive Isotopes -​ Spontaneously release a subatomic particle from atomic nucleus, then gives off both particle and energy -​ Radioactive decay – leads to changes in atom (isotope/element) and radiation emission -​ Cytotoxic agents – radioactive isotopes that can kill cells (cancer) -​ Biological traces – track molecules in organisms and cells -​ DNA mutations in lab – large changes in DNA like deletions, to study role of genes Chemical Bonds -​ Covalent bond - 2 atoms share a pair of valence electrons -​ Nonpolar covalent bond - electrons at equal distance from nuclei of atoms -​ Polar covalent bond - electrons shifted towards more electronegative atom -​ EX: Hydrogen – N.P. single bond ​ ​ ​ Oxygen – N.P. double bond ​ ​ ​ Water – 2 P. single bonds ​ ​ ​ Methane – 4 N.P. single bonds -​ Ionic bond - differences in electronegativity between atoms is so great that the electrons are stripped from the less electronegative atom -​ Results in 2 oppositely charged atoms/molecules called ions -​ cation = + -​ anion = - -​ cation and anion form a strong attraction -​ Ionic compounds (formed by ionic bonds) = salts -​ Form strong bonds in dry environments, but weak bonds in wet environments Weak Bonds -​ Covalent bonds = strongest -​ Weak bonds -​ Hydrogen bonds -​ A hydrogen atom covalently bonded to 1 electronegative atom (H2) attracts to another electronegative atom (O,N) -​ Van der waals -​ Uncharged (nonpolar) molecules can often adopt transient charges formed by random electron movement -​ Electrons accumulate in ‘hot spots’ on molecule -​ Undistributed electrons in a molecule -​ EX: gecko’s toe hairs and a wall surface Water Molecules -​ Unique properties -​ Cohesive behavior - from hydrogen bonds holding water molecules together in liquid H20, but apart in ice -​ Results in high surface tension -​ EX: Bugs walk on water -​ Adhesion - dissimilar particles or surfaces to cling to one another -​ EX: Water flows upwards a tree -​ Stabilize temperatures -​ High specific heat – absorbs/releases a large amount of heat w/ only a slight change in temperature -​ EX: ice formation -​ Water expands upon freezing -​ Density of liquid water is greater than the density of solid water -​ Decreased density = less mass per volume -​ Ice floats due to its lower density -​ Increased number of hydrogen bonds in ice keeps water molecules further apart, and leads to lower density -​ Water is most dense at 4 degrees celsius -​ Solvent versatility -​ Polar bonds make water an active solvent that can dissolve many substances -​ Solutions = liquids of homogenous mixtures of substances -​ Molecules that dissolve/absorb in water = hydrophilic (polar bonds) -​ Ionic (salts), or polar bonds (sugars) -​ Dissolved substance = solute -​ Molecules that don't dissolve/absorb in water = hydrophobic (nonpolar bonds) -​ Dehydration reactions assemble polymers, hydrolysis reactions break polymers apart Ch. 3 Molarity -​ Number of moles per liter of solution -​ EX: For 1L of 2 Molar NaCl, how many grams is needed?  -​ NaCl molecule weight = 58.439 g/mol -​ 2 mol/L * 58.439 g/mol * 1L = 116.88 g/mol Changing Proton & Hydroxyl Concentrations -​ Acids: Substances that increase [H+] -​ Bases: Substances that increase [OH-] pH scale 0-7: Acids donate H+ in aq. solutions 7: Most biological solutions are between 6-8, except Gastric Juice w/ a pH = 2 8-14: Bases donate OH- in aq. solutions Buffers -​ Substances that minimize changes in [H+] and [OH-] in a solution -​ Mostly weak acids and conjugate bases that work by absorbing protons (pH decreases) or by donating protons or by donating protons (pH increases) -​ In action -​ Carbonic acid (in blood) -​ pH increases, reaction leads to donating protons -​ pH decreases, reaction leads to accepting protons Lecture 2 Ch. 4 Functional Groups Chemical Group​ Compound Name​ EX: Hydroxyl – OH-​ Alcohol​ ​ Ethanol​ ​ ​ Polar Carbonyl – CO​ ​ Ketone Aldehyde​ Acetone, Propanal​ ​ Polar Carboxyl – COOH​ Carboxylic Acid​ Acetic Acid, Ionized form of COOH – Charge Amino – NH2​ ​ Amine​​ ​ Glycine, Ionized form of NH2​ + Charge Sulfhydryl - SH/HS​ Thiol​ ​ ​ Cysteine​ ​ ​ Polar, S-S bonds Phosphate – OPO32-​ Organic Phosphate​ Glycerol Phosphate, ATP​ – Charge & Bulky Methyl – CH3​ ​ Methylated Compound​ 5-Methylcytosine​ ​ Non-polar Ch. 5 Macromolecules -​ A polymer is a long molecule of similar building blocks -​ Large polymers = macromolecules -​ Repeating units that serve as building blocks = monomers -​ Simple sugars = Carbs -​ Nucleotides = Nucleic Acids -​ Amino Acids = Proteins -​ Fatty Acids = Lipids Carbohydrates -​ Sugars -​ Simplest carbs = simple sugars/monosaccharides -​ Usually characterized by multiples of CH2O (1:2:1), carbon/oxygen/hydrogen atoms -​ EX: glucose = C6H12)6 -​ provides energy through cellular respiration -​ Structural component of cell walls  -​ Creates chitin for insect exoskeletons -​ Form complexes w/ lipids and proteins -​ Glycolipids -​ Glycoproteins -​ Polysaccharides -​ Carbohydrate macromolecules = polysaccharides (composed of many simple sugar building blocks) -​ Do not follow same molecular ratios as monosaccharides (CH2O) -​ EX: Sucrose (C10H22O11) -​ Storage structures -​ Starch (plants) and glycogen (animals) = polysaccharide storage structures -​ Store glucose -​ Cellulose is a major component of the tough wall of plant cells Lipids -​ Doesn’t include true polymers -​ Consist of hydrocarbon regions and mix poorly with H2O due to their hydrophobic nature -​ Basic subunit of lipid = fatty acid Fatty Acids -​ Consist of a carboxyl group attached to a long carbon skeleton -​ Sources of energy (greater than glucose) -​ Part of phospholipids (cell membrane) and fats (energy storage) Fats -​ From glycerol and fatty acids -​ In a fat, 3 fatty acids joined to glycerol by ester linkage, creating a triglyceride/triglyceride -​ Fatty acids in a fat can be the same, or 2 or 3 different kinds -​ Chains w/ no double bonds = saturated fats -​ Chains w/ double bonds = unsaturated fats Phospholipids -​ Unsaturated fatty acid chains often have a bend -​ In the cell, this bend prevents too close packing of phospholipids in the membrane -​ Hydrophilic head -​ Hydrophobic tails (group together) Phospholipid Membrane -​ When added to H20, they self-assemble: -​ Micelles – single layer sphere -​ Liposomes – double layered sphere -​ Bilayers – double layered sheets -​ At surface of a cell, phospholipids arranged in a bilayer, w/ hydrophobic tails pointing toward interior -​ Phospholipid bilayer forms a boundary between cell and external environment Sterols -​ Lipid class -​ Lipids characterized by a carbon skeleton w/ 4 fused rings -​ Sterols include cholesterol and its derivatives  -​ Components of plasma membrane – contributing to membrane fluidity/rigidity due to their bulky structure -​ Precursors to steroid hormones Ch. 5 Nucleic Acids -​ Made of monomers called nucleotides and polymers called polynucleotides -​ Each nucleotide consists of a nitrogenous base, pentose sugar, and 1+ phosphate groups DNA & RNA -​ 2 types of nucleic acids -​ Deoxyribonucleic acid (DNA) -​ Ribonucleic acid (RNA) -​ DNA provides directions for its own replication -​ DNA directs synthesis of messenger RNA (mRNA) -​ This process = gene expression Bases -​ 2 families of nitrogenous bases -​ Pyrimidines (cytosine, thymine, uracil) have a 6-membered ring -​ Purines (adenine and guanine) have a 6-membered ring fused to a 5-membered ring Sugars -​ RNA = ribose (oxygen at position 2) -​ DNA = deoxyribose (no oxygen at position 2) -​ Nucleoside = Nitrogenous Base + Sugar -​ Base attaches to sugar at Carbon 1 -​ Carbons 3 & 5 functionally important for creating polymers DNA & RNA Base Differences -​ RNA - base Uracil -​ Lacks a methyl group at position 5 -​ DNA - base Thymine -​ Share purine bases Nucleotides -​ To form a polymer nucleic acid, nucleosides become nucleotides -​ Nucleotides - phosphate ester of nucleoside -​ Esterification occurs at position 5 on sugar -​ nucleoside - 5’ - phosphate = nucleotide Nucleotides Cellular Roles -​ Energy carriers (ATP, GTP) -​ Signals (cyclic AMP) -​ Subunits of DNA and RNA DNA -​ A polymer of nucleotides -​ Phosphates and sugars = backbone of DNA -​ Remain constant -​ Bases change and are variable part of DNA DNA Double Helix  -​ DNA molecules have 2 polynucleotides spiraling around an imaginary axis, forming a double helix -​ Backbones run in opposite directions, is antiparallel -​ 5’ 3’ -​ 5’ end w/ a free phosphate group -​ 3’ end w/ a free hydroxyl group -​ Some viruses do have single-stranded DNA Base Pairing -​ Complementary base pairing -​ adenine (A) – thymine (T) -​ 2 hydrogen bonds -​ guanine (G) – cystine (C) -​ 3 hydrogen bonds -​ Allows; -​ Information preservation during DNA replication -​ Template for mistake repair -​ Transfer of information (during transcription & translation) -​ A&U pair -​ Complementary pairing can occur between 2 RNA molecules or between parts of same molecule -​ RNA can form many shapes and is integral to protein synthesis Nucleic Acid Functions -​ Storage of genetic information (DNA) -​ Transfer of genetic information (mRNA) -​ Structural (folded into a specific shape) -​ ribosomal RNA, rRNA -​ Enzymatic activity (ribozymes) -​ Regulation of gene expression -​ microRNA, miRNA -​ short interfering RNA, siRNA Macromolecules 1.​ Carbs 2.​ Proteins 3.​ Lipids 4.​ Nucleic Acids Monomers​ ​ ​ ​ ​ ​ Polymers 1.​ Carbs monosaccharides (simple sugars)​ ​ ​ polysaccharides (complex sugars) glucose, fructose​ ​ ​ ​ ​ starch (cellulose storage in plants) ​ ​ ​ ​ ​ ​ ​ ​ cellulose (for structure in plants) ​ ​ ​ ​ ​ ​ ​ ​ glycogen (for energy storage in animals) ​ ​ ​ ​ ​ ​ ​ ​ sucrose 2.​ Proteins​ ​ ​ ​ ​ ​ amino acids​ ​ ​ ​ ​ ​ polypeptides  3.​ Lipids fatty acids + glycerol​ ​ ​ ​ ​ triacylglycerol (fat), phospholipids, sterols ​ ​ ​ ​ ​ ​ ​ ​ cholesterol 4.​ Nucleic Acids nucleotides​ ​ ​ ​ ​ ​ polynucleotides ​ nitrogenous base, pentose sugar, ​ ​ ​ DNA, RNA 1+ phosphate groups Structures Carbs - CHO Proteins - CHON, central carbon, carboxyl + amino groups on ends, side chain (R group) Lipids - CHO, long chains of C Nucleic Acids - CHOMP Functions Carbs - energy Proteins - enzymes w/ catalysts Lipids - hormones, energy, cell structure Nucleic Acids - genetic code Lecture 3 Ch. 5: Pt. 2 DNA to RNA to Protein Central Dogma -​ Transcription = DNA, RNA -​ Translation = mRNA, protein -​ Amplifies gene signal RNA Types -​ messenger RNA (mRNA): encodes protein -​ transfer RNA (tRNA): adaptor between mRNA and amino acids -​ ribosomal RNA: forms ribosome -​ small nuclear RNA (snRNA): functions in various nuclear processes (splicing) -​ small nucleolar RNA (snoRNA): facilitates chemical modification of RNA’S -​ micro RNA (miRNA): regulates gene expression -​ short interfering RNA (siRNA): silences gene expression -​ long non-coding RNA (lncRNA): regulates gene expression Translation -​ tRNA anticodon complementary to mRNA sequence Codons -​ Read in sets of 3 nucleotides called codons which code for 20 amino acids -​ 64 possible 3 nucleotide combinations -​ 3 codes for protein termination called stop codons Ribosome -​ Binds to mRNA and recruits correct tRNA for mRNA sequence -​ Reads genetic code -​ Ribosomes made of almost 100 proteins + RNA  -​ tRNA bring amino acid corresponding to their anticodon to ribosome and there it can join the growing protein chain Reading Frame -​ Correct reading frame = open reading frame (ORF) -​ Start codon = methionine (AUG) -​ Stop codons = UAA, UAG, UGA Amino Acids -​ Organic molecules w/ amino & carboxyl groups -​ Differ in their properties due to differing side chains , R groups -​ Each amino acid has a name, a 3 letter abbreviation, a 1 letter abbreviation Nonpolar & Hydrophobic​ Polar & Hydrophilic ​ Charged & Hydrophilic Glycine (Gly/G)​ ​ Serine (Ser/S)​ ​ Aspartic acid (Asp/D) - ACIDIC Alanine (Ala/A)​​ ​ Threonine (Thr/T)​ Glutamic acid (Glu/E) - ACIDIC Valine (Val/V)​ ​ ​ Cysteine (Cys/S)​ Lysine (Lys/K) - BASIC Leucine (Leu/L)​ ​ Tyrosine (Tyr or S)​ Arginine (Arg/R) - BASIC Isoleucine (Lle/l)​ ​ Asparagine (Asn/N)​ Histidine (His/H) - BASIC Methionine (Met/M)​ ​ Glutamine (Gln/Q) Phenylalanine (Phe or F) Tryptophan (Trp or W)​ Proline (Pro/P) Polypeptide Formation -​ Polymers of amino acids -​ A biologically functional polypeptide is a protein Protein Folding -​ Specific activities of proteins result from their intricate & 3-dimensional structure -​ A functional proteins consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape -​ Sequence of amino acids determines a protein's 3-dimensional structure -​ A protein’s structure determines how it works Levels of Protein Organization -​ Primary: Sequence of amino acids -​ Secondary: Sequence of amino acids folded into a 3-dimensional shape -​ alpha helix (H bond every 4th peptide bond) -​ beta strand/sheet (H bonds between strands) -​ Random coil -​ Tertiary: A mature protein folds upon itself -​ Quaternary: A protein consisting of greater than 2 polypeptide chains form 1 macromolecule Denaturation -​ In addition to primary structure, physical + chemical conditions can affect structure -​ pH alterations, salt concentration, temperature, etc. can cause a protein to unravel -​ Loss of a protein’s native structure = denaturation Protein Representation -​ Molecular structure of proteins -​ X-ray crystallography, CryoEM, NMR  -​ Ways of representation -​ Atoms, protein backbone, space filling, simplified models Proteins -​ Most abundant macromolecule in cells -​ Proteins that speed up chemical reactions = enzymes -​ Enzymatic Proteins -​ Enzymes = proteins -​ Perform functions repeatedly, catalyzing multiple reactions per protein -​ EX: Lipases – catalyze hydrolysis of bonds in fat Protein Function -​ Defense, storage, transport, cellular communication, movement, structural support -​ Defensive Proteins -​ Disease protection -​ EX: antibody – identifies bacteria/viruses -​ Storage proteins – Amino acids’ storage in a cell -​ EX: casein – a milk protein providing amino acids for baby mammals -​ Transport proteins – Substance movement in cell -​ EX: Sodium channel – moves sodium ions into specific cell compartments -​ Hormonal proteins – organism wide signaling coordination -​ EX: insulin – blood sugar regulation -​ Receptor proteins – Detects chemical stimuli – triggers cell responses -​ EX: G-protein-coupled receptors (GCPRs) detect a range of hormones like lipids and hormones -​ Contractile and Motor Proteins – Movement coordination in cells and organisms -​ EX: myosin – muscle contraction -​ Structural PRoteins -​ Cell support and organismal shape and function -​ EX: Collagen – connective tissues in animals (between cells) Lecture 4 Ch. 6 Cells -​ Basic features -​ Plasma membrane -​ Semifluid substance (cytosol) -​ Chromosomes (carry genes) -​ Ribosomes (make proteins) Prokaryotes vs. Eukaryotes -​ Prokaryotes -​ Lacking a nucleus -​ 1-5 microns in size -​ Bacteria and Archea -​ Eukaryotes -​ Have a nucleus -​ 10-100 microns in size  -​ Compartmentalized -​ Proteins, Fungi, Animals, Plants Plasma Membrane -​ A selective barrier that allows sufficient passage of oxygen nutrients, and waste to service the volume of every cell -​ Surface area to volume ratio is critical -​ As a cell increases in size, its volume grows proportionately more than its surface area Cells are Small -​ Need to interact w/ their environment -​ Absorb nutrients -​ Remove cell waste -​ Transport in cell is greatly affected by surface area to volume ratio -​ Volume increases more quickly than surface area -​ Metabolic requirements set upper limits on cell size -​ If a cell was too big, it couldn’t absorb enough nutrients for its entire volume Multiple Cells -​ Multicellular organisms addresses the volume to surface ratio problem by creating groups of small cells that assemble into something bigger Prokaryote Cell Model -​ Prokaryotic cells -​ No nucleus -​ DNA in unbound region (nucleoid) -​ No membrane-bound organelles -​ Cytoplasm bound by plasma membrane -​ Ribosome present Compartmentalization -​ A eukaryotic cell has internal membranes that divide the cell into compartments – the organelles -​ Cell’s compartments provide different, local environments for incompatible processes to occur in a single cell -​ Organelles create optimal transport conditions, since they are smaller than the cell, and molecules diffuse quicker Animal Cell -​ Basic fabric of biological membranes is a double layer of phospholipids and other lipids -​ Plants and animal cells have most of the same organelles -​ Centrosome, microvilli/cilia Plant Cell -​ Cell wall, chloroplasts, big central vacuole, plasmodesmata Methods to Study Cells Microscopy -​ Parameters -​ Magnification: Ratio of object’s image size to its real size -​ Resolution: Measure of image clarity or minimum distance of 2 distinguishable points -​ Contrast: Visible differences in brightness between sample parts Light Microscopy  -​ Visible light passed through a specimen and then through glass lenses -​ Lenses refract (bend) the light for a magnified image -​ Light microscopes can magnify up to 1000x size of actual specimen -​ Highest resolution is around 200 nm -​ Contrast and enable cell components to be stained/labeled -​ Labeling individual cells w/ fluorescent markers to improve detail seen -​ Confocal microscopy and removes out of focus light and provides sharper images of 3-dimensional tissues and cells Super Resolution Microscopy -​ Exceeds 200 nm resolution -​ Lowest: 20 nm -​ Through computational/mechanical processes Electron Microscopes (EM) -​ EM – used for subcellular structures -​ Scanning electron microscopes (SEM’s) -​ Provide 3-D images -​ Transmission electron microscopes (TEM’S) -​ Focus a beam of electrons through a thin section of a specimen Cryogenic Electron Microscopes -​ Preserves of specimens at very low temperatures -​ Allows visualization of structures in their cellular environment, w/o need for preservatives -​ Studying protein structures -​ Cryogenic electron tomography (cryoET) -​ More common for cell structures Cell Fractionation -​ Takes cells apart and separates major organelles from one another -​ Centrifuges fractionate cells into their component parts (differential centrifugation) -​ Biochemistry and cytology help correlate cell function w/ stricture Nucleus -​ Contains most of cell’s genes and is the most visible organelle -​ Nuclear envelope – encloses nucleus, separating it from cytoplasm -​ A double membrane -​ Each membrane consists of a lipid bilayer Nuclear Pores -​ Pores, lined w/ a structure called a pore complex, regulate the entry and exit from nucleus Nuclear Lamina -​ Nuclear side of envelope is lined by nuclear lamina -​ Composed of proteins and maintains’ nucleus’ shape -​ Evidence for a nuclear matrix – a framework of protein fibers throughout nucleus Information Center for Cell -​ In the nucleus, DNA organized into discrete units, chromosomes -​ Each chromosome contains 1 DNA molecule associated w/ proteins, chromatin -​ Chromatin condenses to form discrete molecules as cell prepares to divide -​ Nucleolus – located within nucleus, is the site of ribosomal RNA (rRNA) synthesis Ribosomes -​ Complexes made of rRNA & protein -​ Build proteins in cytosol (free ribosomes) and on outside of ER or nuclear envelope (bound ribosomes) Endomembrane System -​ Consists of: -​ Nuclear envelope, ER, Golgi apparatus, Lysosomes, Vacuoles, Plasma membrane -​ These components are either continuous or connected via vesicle transfer -​ Vesicles are small membrane-bound sacs that store and transport substances within a cell Smooth vs. Rough ER -​ Smooth – lacks ribosomes -​ Functions: -​ Synthesizes lipids, detoxifies drugs and poisons, and stores calcium ions -​ Rough – has ribosomes -​ Functions: -​ Protein production (glycoprotein – covalently bonded to carbs), secreted proteins, membrane proteins) -​ DIstributes transport vesicles, secretary proteins surrounded by membranes -​ Memory factory for cell Lecture 5 Ch. 6 Golgi Apparatus -​ Consists of flattened membrane sacs -​ Functions: -​ Modifies ER products -​ Manufactures certain macromolecules -​ Sorts & packages materials into transport vesicles -​ Transport -​ Cis face receives vesicles from ER -​ Trans face ships out vesicles to cytosol -​ Vesicles transport proteins through Golgi cisternae Lysosome -​ A membranous sac of hydrolytic enzyme that can digest molecules -​ Lysosomal enzymes work best in the acidic environment inside lysosome -​ Made by rough ER then transferred to Golgi apparatus by vesicles for further processing -​ Some arise from budding from trans face of Golgi apparatus Endocytosis -​ Taking matter into a living cell by forming a food vacuole -​ Engulfing a large particle (like another cell) is called phagocytosis -​ A lysosome fuses w/ food vacuole (endocytic vesicles) and digests the contents Autophagy -​ Lysosomes use enzymes to recycle the cell’s own organelles and macromolecules -​ Breaks down damaged/old parts to build new ones Vacuoles  -​ Large vesicles from ER & Golgi apparatus/endocytosis Central Vacuoles -​ In plant cells -​ Has sap -​ Storage for inorganic ions, K and Cl -​ Growth Other Vacuoles -​ Food – formed by endocytosis/phagocytosis after cells bring matter into cell -​ Contractile – found in freshwater particles, pumps excess water Mitochondria & Chloroplasts -​ Mitochondria – sites of cellular respiration, generate ATP -​ In eukaryotic cells -​ Smooth outer membrane, inner membrane folded into cristae -​ Inner membrane has 2 compartments – intermembrane space and mitochondrial matrix -​ Dynamic Mitochondria Networks -​ Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix -​ Cistae present a large surface for enzymes that synthesize ATP -​ Mitochondria separate and fuse, forming dynamic networks in the cell -​ Chloroplasts – in plants/algae, sites of photosynthesis -​ Green pigment – chlorophyll, as well as enzymes and other molecules in photosynthesis -​ Internal organization: Thylakoids – membranous sacs, stacked to form a granum ​ ​ ​ ​ Stroma – internal fluid​ 1 group of plant organelles – plastids -​ Both have similarities with bacteria -​ Enveloped by a double membrane -​ Has free ribosomes and circular DNA molecules -​ Grows and reproduces somewhat independently in cells -​ Endosymbiont Theory - Early ancestor of eukaryotes engulfed prokaryotic cells, forming a beneficial relationship w. host cell becoming an endosymbiont -​ Endosymbiont – evolved to become mitochondrion and chloroplasts -​ Suggests an oxygen using photosynthetic prokaryote cell was engulfed first -​ Some cells took up a photosynthetic prokaryote, evolved into a chloroplast Peroxisomes -​ Oxidative organelles -​ Unknown relation to other organelles -​ Specialized metabolic compartments by a single membrane -​ Contain enzymes that remove H atoms from various substances and transfer them to oxygen atoms, forming Hydrogen Peroxide. -​ Functions: -​ Use oxygen to break fatty acids into smaller molecules used for fuel in respiration -​ In the liver, it detoxifies alcohol, etc. -​ Glyoxysomes (specialized peroxomies_ in the fat-storing tissues of plant seeds, convert fatty acids to sugar to feed emerging seedling Organelles  Cell Component Structure Function ER Network of membrane-bounded Smooth ER: lipid synthesis, tubules and sacs; separates carbohydrate metabolism, lumen from cytosol, and is detoxification of drugs & continuous w/ nuclear envelope poisons Rough ER: Synthesis of secretory, membrane, and glycogen proteins Golgi Apparatus Stacks of flattened membranous Modification of proteins, carbs sacs; has polarity (cis and trans on proteins, and phospholipids; faces) synthesis of many polysaccharides; sorting of Golgi products – released in vesicles Lysosome Membranous sac of hydrolytic Breakdown of ingested enzymes (in animal cells) substances, cell macromolecules, and old organelles for recycling Vacuole Large membrane-bounded Digestion, storage, waste vesicle disposal, water balance, cell growth, protection Mitochondria Bounded by double membrane; Cellular respiration inner membrane has foldings Chloroplast 2 membranes around fluid Photosynthesis stroma, has thylakoids stacked into grana Peroxisome Specialized metabolic Has enzymes that transfer compartment bounded by a hydrogen atoms from substrates single membrane to oxygen, H2O2 converted to H2O Cytoskeleton -​ A network of fibers extending throughout cytoplasm -​ Organizes cell’s structures and activities, anchors many organelles and maintains cell shape -​ 3 molecular structures -​ Microtubules -​ Microfilaments -​ Intermediate filaments Microtubules Microfilaments Intermediate Filaments  -​ Thickest (25 nm w/ 15 -​ Intertwined strands of -​ Fibers w/ diameters in nm lumen) actin mid range (8-12 nm) -​ Hollow tubes -​ Thinnest (7 nm) -​ Includes keratin -​ Tubulin -​ Functions: -​ Functions: -​ alpha -​ Maintains cell -​ Maintains cell -​ beta shape, cell shape, -​ Functions: shape changes, anchorage of -​ Maintains cell muscle nucleus + other shape, cell contraction, organelles; motility, cytoplasmic nuclear lamina chromosome streaming (plant formed movement cells), cell -​ Grow out from a motility, cell centrosome (in animal division (animal cells) near nucleus cells) -​ A pair of -​ Form a cortex inside centrioles (each plasma membrane to w/ 9 triplets of support cell shape microtubules -​ Bundles of it make up arranged in a core of microvilli of ring) intestinal cells -​ Other -​ Those that function in eukaryotic cells cellular motility contain organize motor protein microtubules in -​ Cells crawl along a absence of surface by extending centrosomes w/ pseudopodia (cellular centrioles extensions) and move -​ Motor proteins – toward them interact w/ cytoskeleton -​ Cytoplasmic streaming, to produce cell motility in plant cells, is a circular flow of cytoplasm within cells Cilia and Flagellum -​ Control beating of flagella and cilia but differing in their beating patterns -​ Many unicellular protists are propelled through water by flagella or cilia -​ Motile cilia found in large quantities on a cell surface, whereas flagella are limited to 1 or a few per cell -​ Motion: -​ Flagella – direction of swimming -​ Cilia - direction of organisms’s movement -​ Share a common structure -​ Group of microtubules sheathed in an extension of plasma membrane -​ 9 doublets of microtubules arranged in a ring w/ 2 single centered microtubules -​ Basal body – anchors cilium/flagellum -​ Motor protein, dynein, drives bending movements of a cilia/flagellum rather than sliding because microtubules are held in place -​ Protein domains act as feet, one maintains contact, other releases + reattaches 1 step further Lecture 6 Ch. 6 Pt. 2 Cell Wall -​ In plant cells, prokaryotes, fungi, and some protists -​ Protects shape, maintenance, prevents excessive uptake of water -​ Made of cellulose fibers embedded in other polysaccharides and protein -​ Layers: -​ Primary cell wall: Thin and flexible, secreted first -​ Middle lamelia: Thin layer between primary walls, has polysaccharides, petins -​ Secondary cell wall: In some cells, added between plasma membrane and primary cell wall Plasmodesmata -​ Channels that connect plant cells -​ Water and small solutes (sometimes proteins & RNA) can pass from cell to cell Extracellular Matrix (ECM) -​ Instead of cell walls, animals have an elaborate ECM -​ Made up of glycoproteins like collagen, proteoglycans, and fibronectin -​ Fibronectin and other ECM proteins bind to receptor proteins in plasma membrane that trigger chemical signals Membrane Carbs -​ Cell recognition by binding to molecules on membrane surface -​ Surface molecules are bonded to short, branched chains of carbs -​ Glycolipids -​ Glycoproteins -​ Function – cell markers for identification Cell Junctions -​ Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact -​ 3 Types in Epithelial Tissues -​ Animals​ ​ ​ ​ ​ ​ Plants -​ Desmosomes - anchors cells​ ​ ​ Cell Junction - plasmodesmata -​ Tight Junctions - prevent leakage -​ Gap Junctions - cell communication Ch. 7 Cell Membranes -​ Composed of phospholipids, other lipids, proteins and carbohydrates -​ Phospholipids are amphipathic molecules because they contain both hydrophilic and hydrophobic regions -​ Form a bilayer w/ hydrophobic tails grouped inside membrane, and hydrophilic heads exposed to water on either side Amphipathic Proteins -​ Most membrane proteins -​ Hydrophilic regions of the protein are oriented toward cytosol and extracellular fluid inside+outside the membrane  -​ Hydrophobic regions are embedded in the bilayer Fluid Mosaic Model -​ Depicts membrane as a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids -​ Proteins not randomly distributed in the membrane; form groups that carry out common functions Membrane Fluidity -​ Held together mainly by weak hydrophobic interactions -​ Most lipids and some proteins can move sideways within membrane -​ Rarely does a lipid flip-flop across membrane -​ As temperature decreases, membranes switch from a fluid to a solid -​ Depends on types of lipids -​ Membranes rich in unsaturated (double bonds) fatty acids are more fluid that those rich in saturated (no double bonds) fatty acids -​ Membranes must be fluid to work properly Cholesterol (steroid lipid) -​ A membrane component in animal cells w/ variable effects on membrane fluidity at different temperatures -​ At normal body temp (37 degrees celsius), cholesterol restrains movement of phospholipids (less fluidity, more flexibility) -​ At lower body temp, cholesterol maintains movement of phospholipids (more fluidity/less flexibility) -​ Plants use different but related steroid lipids to buffer membrane fluidity Adaptation of Membrane Composition -​ Fluidity affects permeability and movement of transport proteins -​ EX: -​ Fish in very cold temperatures have a high proportion of unsaturated hydrocarbon tails in their plasma membranes -​ Wheat have a high proportion of unsaturated phos Ch. 7 Membrane Proteins -​ A membrane is a collage of different proteins, often clustered in groups, embedded in a fluid matrix of lipid bilyaer -​ Proteins determine most of the membrane’s functions -​ Protein composition of membranes varies among cells and among intracellular membranes -​ Types: -​ Peripheral proteins – bound to surface of membrane -​ Integral proteins - penetrate the hydrophobic core Integral Proteins -​ Types: -​ Transmembrane – span the membrane Path of a Transmembrane Protein from ER to Plasma Membrane – Synthesized in Rough ​ ER → Golgi Apparatus → Packaged into vesicles that fuse with plasma membrane -​ Non-transmembrane - contain a peptide region in lipid bilayer -​ Hydrophobic regions have nonpolar amino acids, coiled into alpha helices Peripheral Proteins  -​ Not embedded in bilayer and can dissociate from membrane -​ Held in place by: -​ Attachment to cytoskeleton inside cell near membrane -​ Attraction to membrane (electrostatic interaction) -​ Interaction w/ hydrophobic amino acid residues -​ Attachment of protein to lipid Membrane Protein Functions -​ Transport -​ Enzymatic activity -​ Hydrolysis, Dehydration -​ Signal Transduction -​ Cell-cell recognition -​ White blood cell recognizing bacteria -​ Important in medicine – Drugs mask HIV (CCR5) and block HIV in non-immune individuals -​ Intercellular joining -​ Attachment to cytoskeleton & ECM Membrane Asymmetry -​ Has distinct inside and outside faces -​ Composition of proteins, lipids, and carbohydrates is asymmetrical Selective Permeability -​ Plasma membrane controls exchange of materials between cells and surroundings -​ Nonpolar hydrophobic molecules dissolve in lipid bilayer and pass membrane -​ Hydrocarbons (CO2, O2) -​ Polar hydrophilic molecules impeded and pass slowly, if at all (sugars, ions) -​ Depends on lipid bilayer and specific transport proteins Transport Proteins -​ Channel – hydrophilic channel used as a tunnel -​ Aquaporins – channel proteins increases water passage -​ Carrier – bind to molecules and change shape to shuttle across -​ Often specific -​ Glucose carrier proteins only transport glucose Lecture 7 Ch. 7 Pt. 2 Diffusion -​ Movement of particles of any substance so that they spread out evenly in available space -​ Goes down concentration gradient, the region along which the density of a chemical substance increases or decreases Equilibrium -​ Net diffusion across regions to reach a state of equilibrium Passive Transport -​ Diffusion of a substance across a biological membrane because no energy is expended by cell -​ Concentration gradient = Potential Energy that drives diffusion -​ Diffusion rate depends on the membrane permeability to specific substance Osmosis -​ Diffusion of free water molecules (water molecules not clustered around another substance) across a selectively permeable membrane, from decreased solute concentration to increased solute concentration -​ So as to reach equilibrium Tonicity -​ Ability of a surrounding solute to cause a cell to gain/lose water -​ Depends on concentration of solutes in solution that cannot cross membrane, relative to that inside cell -​ If the solution has an increased concentration of solutes than inside cell, water will leave, and vice versa -​ Types (w/o cell walls): -​ Hypotonic – Water enters cell, Lysed -​ Isotonic – Water both enters and exits cell, Normal -​ Hypertonic – Water exits cell, Shriveled Cells w Cell Walls must Balance H20 -​ Organisms in hypotonic/hypertonic environments w/o cell walls require osmoregulation (control of solute concentration and water balance) -​ EX: Paramecium live in a hypotonic environment (in freshwater), so, they have a contractile vacuole to pump excess water Cells w Cell Walls must Balance H20 Different -​ Types (w/ cell walls): -​ Hypotonic – Water enters cell, Turgid (Normal) -​ Isotonic – Water both enters and exits cell (Flaccid) -​ Hypertonic – Water exits cell, Shriveled​(Plasmolyzed) Facilitated Diffusion -​ Transport proteins speed passive movement of molecules across membrane -​ Transport proteins include channel and carrier -​ Channel proteins provide corridors that allow a specific molecule/ion to cross membrane -​ Aquaporins facilitated water diffusion -​ Ion channels facilitate ion transport -​ Passive Ion Channels -​ Ion channels/gated channels open/close in response to stimulus -​ EX: In nerve cells, K+ channels open in response to electrical stimulus Carrier Proteins -​ Undergo subtle shape changes that moves solute-binding across membrane -​ Triggered by binding+release of transported molecules -​ Those involved in facilitated diffusion moves substances down concentration gradient; no energy input required Active Transport -​ Requires energy, usually in form of ATP hydrolysis to move substances against concentration gradient -​ Enable cells to maintain solute concentration that differ from their environments  -​ All proteins involved are carrier -​ EX: Na-K pump – energizes trans[prt of K+ into and Na+ out of cell -​ Potassium concentration is higher in cell -​ Sodium concentration is lower inside cell -​ Both move potassium and sodium against concentration gradient; energy required Membrane Proteins -​ Voltage across a membrane -​ Created by diffusion in distribution of positive and negative ions -​ Inside of cell is negative, relative to outside -​ Favors passive transport of cations into and anions out of cell Electrochemical Gradient -​ Drives diffusion of ions across a membrane -​ Chemical force – ion’s concentration gradient -​ Electrical force – effect of membrane potential on ions’ growth -​ Ion diffuses down electrochemical gradient Proton Pumps -​ An electrogenic pump is a transport protein that generates voltage across a membrane, storing energy for cellular work -​ Animal’s electrogenic pump is Na–K -​ Plant’s electrogenic pump is the proton pump – actively transports H+ out cell Cotransport -​ Active transport of a solute indirectly drives transport of other substances -​ “Downhill” diffusion of solute is coupled to the “uphill” transport of another substance against concentration gradient -​ EX: Na-K pump – diarrhea, waste expelled too fast for Na+ reabsorption, Na decreases -​ Gatorade (has salt and glucose) enables uptake in intestinal cells Bulk Transport -​ Phagocytosis - engulfing large particles -​ Goes either direction (in or out cell) Exocytosis -​ Transport vesicles migrate to membrane, fuse w/ it, and release contents out cell -​ Secretary cells use exocytosis to export products -​ EX: Pancreas cells secrete insulin -​ Used to remove waste Endocytosis -​ Macromolecules taken into cell in vesicles -​ Membranes forms a pocket for transport -​ Types: -​ Phagocytosis (large particles) -​ Pinocytosis (small particles) -​ Receptor-mediated (specific particles) -​ EX: Cholesterol, carried in particles, low-density lipoproteins, (LDL’s)  -​ Individuals w/ familial hypercholesterolemia have missing/defective LDL receptor proteins Coat Proteins -​ Parts of plasma membrane that form vesicles lined on inner side w/ coat proteins, forming coated vesicles/pits -​ Pinch off into vesicles