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Cell Bio Exam 1

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University at Buffalo
Biological Sciences
BIO 201

Bio 201 Exam 1 • Four main groups of organic macromolecules. -Proteins -Nucleic acids -Carbohydrates (sugars) -Lipids • Polymers are repeating units. - Proteins are polymers of amino acids -DNA and RNA are polymers of nucleotides -Polysaccharides are polymers of sugars - Some filaments are polymers of proteins nm= nanometer (10^-9 meter) μm= micrometer (10^-6 meter) mm= millimeter (10^-3 meter) Prokaryotic: “Before a nucleus”. Bacteria (no prokaryotic plants) Eukaryotic: “True nucleus”. Animals and plants Organelle: A compartment inside of a cell that is surrounded by a membrane (Eukaryotic cells) In vivo: “In life”. As close to real life as possible In vitro: “In glass”. Experimental situation in a test tube, plastic dish, glass beaker, etc. In silico: “In the computer”. Data derived from a computer. Bioinformatics, etc. Cells are complex and organized, usable genetic program, reproduction, acquire and use energy, respond, self-regulate, evolve, mechanical activities. -Bacteria have a plasma membrane but they don’t have a nucleus. Nucleoid is not a nucleus. - not all eukaryotic cells have a nucleus- mature red blood cells do not. Or ER, golgi or mitochondria. -Lysosome: break down food (digestive system) -Golgi: packages protein (package center) -Mitocondia: converting energy for the cell to use -Nucleus: control center -Rough Endoplasmic Reticulum: has ribosomes where amino acids are made into protein Endosymbiont theory -intracellular organelles inside eukaryotic cells used to be free-living prokaryotic cells. they got inside the first eukaryotic cells, liked it and stayed there as endosymbionts. Another theory: protists are plants that lost their chloroplast. • Covalent bonds • Non-covalent bonds -Ionic or electrostatic bonds (full charges) (+, -) -Hydrogen bonds (partial charges) -Van der Waals interactions • Hydrophobic aggregations Not bonds, interactions or forces between molecules. hyrophobic exclusions from water. 1 mole = (6.02x 10^23) Ionic Bonds: two compounds with full and opposite charges (Na+, Cl-) - cations are positive -anions are negative Ionization: process of being disassociated into ions in Na Cl the partial negative of Oxygen in water takes the Na and the partial positive in hydrogen takes the Cl. Molarity: concentration defined by Amount/Volume or #moles/ Liter = Molarity grams/ molecular weight= amount or #moles To multiply exponents you add them To divide exponents you subtract Hydrogen bonding Hydrogen bonds can be seen between partially charged compounds Water is polar but does not carry full charges. (one partial negative and two partial postivies) -Water is in its optimal thermodynamic state each water molecule can bind to as many other water molecules as possible -its thermodynamically unfavorable to get in the way of this but it happens. -water bonds with hydrogen bonding Van der Waals interactions -weak independently -strong together -distant dependant! Separation of centers of the atoms need to be at optimal distance Hydrophobic Aggregations Hydrophillic: usually charged or polar and water soluble Hydrophobic: usually nonpolar, uncharged and not very water soluble Driven by exclusion of hydrophobic molecules from water, not by bonds or interactions just aggregations  Polar: aqueous, hydrophilic, water soluble  cytoplasm, lumen of ER, golgi or lysosomes Non Polar: lipid-like, hydrophobic, water insoluble  membranes Amphipathic: “two natures” one end is polar and the other is non-polar (not 50/50) one end hydrophobic and one hydrophilic.  hydrophobic tail and hydrophilic head. - If its more hydrophobic than hydrophilic it should be a membrane lipid - If its more hydrophilic than hydrophobic it should be a water soluble detergent Poly saccharide: polymer of sugars • Carbohydrates Usually polar. Some can be charged but many are uncharged. o Metabolic sugars. Primarily used for energy. Glucose, glycogen, starch, etc. o Structural. Other polysaccharides, oligosaccharides, complex carbohydrates 1. Cell walls of plants 2. Sugars on glycoproteins and glycolipids in membranes - Glycogen. Metabolic sugar polymer. Storage form of glucose Cellulose. Structural sugar polymer of glucose in cell walls of plants HCL- strong acid NaOH- strong base NaCl- ionic  if strong they always dissociate [H+] means concentration of hydrogen ions, also called protons -7 If pH = 7.0, the [H+] = 1.0 x 10 M H+ pH= -log [H+] low pH= high [H+] Proteins are polymers of amino acids. -The amino acids differ in their side chains. - Free (unbound) amino acids all have an amino group and a carboxyl group. -Amino acids are covalently attached by peptide bonds between neighboring amino and carboxyl groups - The charge on the protein is dependent upon the pH At neutral pH (pH=7.0) amino group is + and the carboxyl group is - on a free amino acid Conformation means its 3-D shape. Function is dependent on shape 4 Types of Proteins: 1- Polar and fully charged at pH=7.0. These are hydrophilic 2- Polar but uncharged at pH=7.0. These are also hydrophilic 3- Nonpolar at pH=7.0. These are hydrophobic (but not lipids) 4- Miscellaneous -the charged amino acids on the outside of soluble proteins determine overall charge (net charge) and solubility Amino acid side chains can have different charges at different pH because of ionization due to deprotonation and protonation. To give up proton and become negative or to add proton. Polypeptide: polymer of amino acids Oxidation: LEO lose electron. Covalent bonds form Reduction: gain election covalent bonds break Water solubility depends on -relative hydrophobicity - The pH of the solution. determines which other side chains are ionized and relative hydrophobicity. - What else is around for the protein to bind to. Might already be bound. A change in pH could affect the charge, conformation and function of a protein. It may not. It depends on: 1. 1. How many amino acids in the Charged Polar group are present 2. Their location on the protein 3. The direction and extent of the pH change Water-soluble protein can have many nonpolar amino acids on the outside of it- as long as its relatively hydrophilic Disulfide bonds are covalent bonds Unfolding: broken bonds Reduction Refolding: forming bonds Oxidation Reducing agents and Oxidizing agents Oxidized compound (wants electrons) -> gets reduced by a reducing agent Reducing agent donates electrons and oxidized compound accepts Reduced Compound gets the electrons -> can be oxidized by an oxidizing agent Amino Acid Side Chain Summary 1. Amino acids in the polar charged group have the capability to form ionic bonds (if the pH is right) and make proteins more hydrophilic 2. Amino acids in the polar uncharged group can form hydrogen bonds and make a protein more hydrophilic 3. Amino acids in the nonpolar group don’t form ionic or hydrogen bonds and can make a protein more hydrophobic 4. Cysteine can form covalent bonds (disulfides) with other cysteines when oxidized Peptide bonds are covalent bonds that hold protein together 5 Ways to hold protein together in their conformation 1- Van der Waals 2-Hydrogen bonds 3-Ionic bonds 4-Hydrophobic nonpolar aggregations 5-covalent bonds (peptide & disulfide) All proteins are enzymes. NOT ALL enzymes are proteins *QUIZ QUESTION LIPIDS! Metabolic lipids. Usually in fat droplets - Triglycerides (fats). Hydrophobic and not found in membranes Structural lipids. Usually in membranes. Most membrane lipids are amphipathic. - Phospholipids and Sterols -Free fatty acid. A fatty acid that is not covalently attached to anything -Fatty acyl side chain A fatty acid thats covalently attached .(to a triglyceride, phospholipid or protein) Saturated fatty acid or saturated fatty acyl side chain. No double bonds Unsaturated. At least one double bond Polyunsaturated. Many double bonds. More disordered and fluid at room temp. Cholesterol is a membrane sterol but testosterone is not because Cholesterol is amphipathic and testosterone is more water soluble (more polar) than cholesterol. There are no sterols in bacteria Macromolecules break down -Stage I - Macromolecules disassembled into building blocks (mostly by hydrolysis) -Stage II - Degredation to acetyl-CoA by glycolysis -Stage III - . Conversion of acetyl-CoA into TCA cycle components and high energy products for mitochondria DNA and RNA **Replication: only synthesis of DNA  DNA Transcription: DNA  RNA (RNA synthesis) Translation: RNA  protien (protien synthesis) Reverse Transciptase: RNA  DNA (enzyme) 3 main parts of a nucleotide: Phosphate, Sugar, Base Pentose sugar called ribose   if the (2’) OH is replaced with H it is Deoxyribose the sugar in DNA A = T DNA so DNA = ATCG  Hydrogen bonding between base pairs A = U RNA so RNA = AUCG C =G BOTH Word Prokaryote is WRONG- now use bacteria.  There is a U There is a OH and not an H Therefore this is RNA and not DNA The nucleotides are held together by phosphodiester bonds. Polynucleotide: polymer of nucleotides : DNA or RNA 3 Major Types of RNA - Ribosomal RNA (rRNA) --80 to 90% of the total RNA is rRNA - Transfer RNA (tRNA) --tRNA is required for translation - Messenger RNA (mRNA)-- mRNA is also required for translation DNA- (transcription)  mRNA (Translation needed rRNA and tRNA)  Protein Double stranded tRNA double stranded rRNA ^^NOT ALL RNA is single stranded. ^^ Two ways to cut RNA 1) riboneclease (RNAase) 2) add a ribozyme (a catalytic RNA) DNA can be made from an RNA template but RNA cannot be made from a protein MEMBRANES 1890- Overton used hypertonic shrinkage of plant cells to estimate the composition of plasma membranes -Like dissolved like. hydrophobic membranes permeable to hydrophobic compounds. Prevent hypertonic shrinking Hypertonic Shrinkage is when the outside solute concentration is high and the water concentration outside is low. In a hypertonic solution, water moves down its concentration gradient, from high water concentration to low Since the water concentration is lower outside, water moves out and the cell shrinks  Stop shrinking by adding (permeable) solutes to the inside to balance solute concentration  Adding any solute to water lowers the water concentration Isotonic solution:no swelling or shrinking. No net loss or gain Hyportonic solution: NET WATER GAIN  HYPOTONIC SWELLING solute concentration higher in cell, water concentration lower inside cell. Water moves down its concentration gradient into the cell. Lime green is NOT the plasma membrane The membrane is around the green dots. Cells shrink because water moves out.  HYPERTONIC! compounds that prevented hypertonic shrinking of plant cells were much like fatty oils in their solubilities The plasma membrane of plants must be a fatty oil (hydrophobic lipid). It is a lipid membrane  HYPTONIC -water moves into cell but can’t expand - cell wall prevents expansion. Gorter and Grendel experiment 1925 – membranes are lipid bilayers. And they extracted lipids Tested Using RBC only have one membrane (no mitochondria, nucleus ect.) Extract lipids by added RBC to hexane to dissolve lipids. Then add water to hexane and remove hexane layer. Hexane layer = hydrophobic (contains lipids only) water layer = hydrophilic (contains water soluble compounds) - The measured surface area of the lipids was twice as big as the RBC circumference= phospholipid bilayer. - Phospholipid bilayers self-assemble in water because of hydrophobic aggregations - Gorter and Grendel forgot about proteins in the plasma membrane 50% of the membrane - plasma membr
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