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BIOS 111-Chapter 2

by: Sierra Mongeon

BIOS 111-Chapter 2 BIOS 111

Sierra Mongeon
GPA 3.96

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About this Document

I did make one mistake with the pH information I mixed them up!...a lower pH# is more acidic, and a higher pH# is more basic.
Dr. Kenneth Nickerson
Class Notes
Biology, General Biochemistry
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This 7 page Class Notes was uploaded by Sierra Mongeon on Friday January 15, 2016. The Class Notes belongs to BIOS 111 at University of Nebraska Lincoln taught by Dr. Kenneth Nickerson in Spring 2016. Since its upload, it has received 560 views. For similar materials see Microbiology in Biology at University of Nebraska Lincoln.


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Date Created: 01/15/16
Key chapter 2 concepts to aid in your understanding of microbiology! Chemistry: Atoms: smallest component of a pure substance w/ properties of that substance -can’t be divided w/o losing those properties -combine to form molecules Parts of an atom: nucleus (protons +, neutrons 0), electron field (electrons,e-) If # protons=# electrons, no net charge Atomic number: # protons Atomic Weight: # protons+# neutrons Isotope: # of neutrons differ in atoms of same element Electron configuration: outermost (valence) energy level has to have 8 e- to be stable. **This is why atoms react with other atoms; to achieve 8 valence e- When they react, they form Chemical Bonds: Ionic: One atom takes electrons from another atom, and they become charged particles called ions (ionic bond forms ions) Covalent: electrons are shared between atoms. One atom usually “wants” electrons more than the other one, resulting in polarity. These bonds are stronger and more common. Hydrogen bonds: Hydrogen (H) atom is bonded covalently to a larger Oxygen or Nitrogen atom. However, the sharing is unequal (polar), and a slight positive charge forms on the H atom while a slight negative charge forms on the larger O or N atom. Positive and negative charges attract, but since the charge is only partial, a bond doesn’t form. Rather a “bridge” forms. -Clear diagrams of this concept can be found online (I can’t put them in the notes for copyright reasons!) **Hydrogen bonds and polarity are responsible for giving water its distinct properties!** Distinctive Properties of Water 65-75% all cells are H20! (So we are basically cucumbers with anxiety) But water is the universal solvent for many molecules, and the medium in which almost all biological reactions occur!!* So what makes it special? 1. Polarity- remember those Hydrogen bonds? A water molecule has a slightly negatively charged part (the O atom)and two slightly positively charged parts (the H atoms). Therefore, water can form hydrogen bonds with itself. 2. It takes a great deal of energy to separate water molecules thanks to these H bonds, so water is a great temperature buffer, meaning it resists change in temperature. This is why our body temperature remains so constant. 3. Because of its polarity, it is the universal solvent for any molecule that would dissociate into ions. 4. Density: when it gets colder, it expands (becomes less dense). It is most dense in its liquid form. This is why ice floats! The ice on top of a frozen lake insulates the organisms below. It is because of ice that aquatic life is able to survive the winter. 5. It plays a part in just about every chemical reaction that takes place in an organism, either as a reactant (actively reacting) or as a product (what’s produced). Chemical reactions: Endothermic and Exothermic Endo=in Exo=out Therm=energy -requires energy input to form bonds, and energy is released when bonds break **can also be called exergonic or endergonic, but meaning is the same** Making bonds=absorbs energy=endothermic Breaking bonds=releases energy=exothermic Molarity Atomic #= # of protons. Can be found on periodic table. Atomic weight= # of protons + # neutrons in an atom (measured in amu’s-atomic mass units) Molecular weight=sum of atomic weights of all atoms in a molecule (amu) A mole of a substance is that substance’s molecular weight expressed in grams Ex. Glucose molecule molecular weight is 180 amu 1 mole of glucose is 180 grams 1 M=1 mole of solute/Liter solute=what’s dissolved in the solvent (example: salt dissolved in water) Acids and Bases Acids: substances that dissociate into H+ ions in water Ex. HCl  into H+ and Cl- ions Bases: Substances that dissociate into OH- (hydroxide) ions in water Ex. NaOH into Na+ and OH- ions Salts: still dissociates into ions when dissolved in water, but these ions are not H+ or OH- Ex. NaCl Na+ and Cl- pH: “potential of Hydrogen” pH scale: shown below higher #= more acidic lower #=more alkaline (basic) The pH scale diagram can be found online very easily! (sorry I can’t put it in the notes because of copyright reasons, but I recommend looking it up!) -organisms are EXTREMELY SENSITIVE to even small changes in pH- So…many biological systems use buffers! Buffers: prevent drastic pH changes by replacing strong acids and bases with weaker ones that don’t break into as many H+ or OH- ions Organic Molecules *-contain carbon, hydrogen, oxygen and nitrogen -the carbon forms a “skeleton”, which the other atoms are covalently bound to. -most C are bonded to H atoms, but other functional groups with specific properties may be attached. A table of these functional groups and what they are found in can be found in the Tortora text, 11 thedition on page 36 Terms to know: Monomer- (mono=one) the “building block” of an organic molecule, the simplest unit that still contains the properties of that type of molecule. If you were building a wall, the monomer would be one of the bricks. Polymer- monomers join to form polymers. using the wall analogy, the polymer would be the entire wall, made out of all the bricks Dehydration synthesis: This is how monomers join to form polymers! One monomer loses an H atom, and the hydroxyl group (OH) of another monomer is lost and the two combine to form a water molecule. Dehydration means water is being lost Hydrolysis: the opposite of dehydration synthesis! A water molecule is added to the polymer, and it separates the two monomers again. Isomer: not related to the building of a molecule! It means: two or more molecules that have the same chemical formula, but are structured differently. An example of this is the carbohydrates glucose, fructose, and galactose. Both have the same chemical formula C6H12O6, but different physical structures and chemical properties. Carbohydrates-“hydrated carbon” -saccharides=sugar -these are the sugars and starches Functions: structural component of cell walls/membranes/DNA, fuel cells with energy -made of C, H, O atoms. **Ratio of H to O atoms is 2:1 Monomer=monosaccharide Example: glucose Disaccharide=2 monosac. bound together Polysaccharide=multiple monosac. (can be 10’s or 100s!) Ex. Glycogen, cellulose Lipids Functions: structure and functional unit of cell membranes, energy storage **non polar and insoluble in water** Simple lipids Triglycerides: glycerol molecule with 3 fatty acid chains attached (Diglycerides/monoglycerides=2 or 1 fatty acid chain) Fatty acid=carbon skeleton with attached hydrogen atoms Saturated=no double bonds, MAXIMUM amount of H atoms possible -solid at room temp., no “kinks”, stick together more easily Unsaturated=double bonds, liquid at room temp, “kinks” in the chain so they can’t be as tightly packed Complex lipids **Phospholipids-phosphate group+glycerol+sat. fatty acid chain+unsat. fatty acid chain -polar hydrophilic (water loving) head-phosphate group faces water -nonpolar, hydrophobic fatty acid “tails” forms a bilayer (double layer) with tails facing in and heads facing out, which is the main structural component of a cell membrane -other complex lipids are waxes and glycolipids, which are also found in cell membranes Steroids (yes, these are lipids!) -interconnected carbon rings -structural component of cell membranes (cholesterol) -keep the phospholipids from sticking together, preserves fluidity of membrane Ex of steroid= Hormones (estrogen, testosterone) *Proteins -have nitrogen and sometimes sulfur as part of their chemical structure! Unlike other org. molecules Function: 1. enzymes-speed up biochem. Reactions 2. transport proteins 3. muscle contraction (actin and myosin) 4. some hormones 5. antibodies- part of immune defense system 6. structural component of cell membranes Monomer=amino acid Stereoisomer= amino acids exist in either of 2 forms/configurations, which are mirror images of each other. D and L- D is right handed, L is left handed **amino acids found in proteins are most often the L form** -D isomers occur in bacteria cell walls and antibiotics Amino acids “link” together via peptide bonds, forming a polypeptide chain ( I will cover this more in my next posting of notes over ribosomes and protein synthesis) Protein structure-4 levels 1. Primary structure=the sequence of amino acids (like beads on a necklace) 2. Secondary= the folding and twisting of the polypep. chain into either a helix or pleated sheet -held together by H bonds 3. Tertiary=the unique three-dimensional shape of the protein Most proteins stop here, but some have 4. Quaternary=how 2 or more polypep. chains join to make one functional protein Shape=function. If a protein loses its shape (denatures) it can no longer perform its function. Denaturation can occur w/ high temperatures, pH values, or salt conc. Nucleic Acids DNA-deoxyribonucleic acid RNA- ribonucleic acid Monomer=nucleotide Nucleotide=simple sugar, phosphate group and nitrogenous base Bases form pairs: -in DNA, bases are A, T, C, G AT CG -in RNA, bases are A,U,C, G AU CG DNA=genetic material of an organism. RNA=3 types-tRNA, mRNA, rRNA (will be covered more in upcoming notes) Adenosine Triphosphate(ATP) -the principal energy carrying molecule of all cells! -3 phosphate groups=ATP When ATP is “used”, the third phosphate group splits off and it becomes ADP (what’s left) and Pi (the phosphate that splits off) -The reaction goes in the reverse direction to replenish the ATP supply


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