BIOL 1107: Test 1
149 Cards in this Set
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molarity
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mol/liters
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polar covalent
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when an atom is bonded to a more electronegative atom, the electrons of the bond are not equally shared
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non-polar covalent
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a covalent bond between two atoms of the same electronegativity (or very close) so the electrons are equally shared
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ionic bond
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when two atoms have a very large difference in electronegativity so the more electronegative one strips the other of its valence electrons, ex. NaCl
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covalent bond
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two atoms share their valence electrons
ex. H2, O2, H2O, CH4
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electronegativity
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the attraction of a particular atom for the electrons of a covalent bond is called its _______.
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what happens when an atom is more electronegative
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the more electronegative an atom is, the more strongly it pulls shared electrons towards itself.
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salts
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made up of ionic bonds (also called ionic compounds)
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hydrogen bond
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a partial positive hydrogen covalently bonded with an electronegative atom is allowed to noncovalently bond with another electronegative molecule nearby
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van der wals
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ever changing regions of a molecule of positive and negative charges that enable all atoms and molecules to stick together
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why is molecular shape crucial to biology?
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it determines how biological molecules recognize and respond to one another with specificity. biological molecules often bind temporarily to one another by forming weak bonds but can only do this if their shapes are complimentary.
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why does the structure H-C=C-H fail to make sense chemically?`
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each carbon only has three covalent bonds instead of four
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what hold the atoms together in a crystal of magnesium chloride (MgCl2)?
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the attraction between oppositely charged ions, forming ionic bonds
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chemical reactions
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the making a breaking of chemical bonds, leading to changes in the composition of matter
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reactants + reaction --> products
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N/A
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photosynthesis
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takes place within the cells of green plant tissues
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chemical equilibrium
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the point at which the reactions offset one another exactly - reactions are still going on but with no net effect on the concentration
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what is one factor that effects the rate of a reaction?
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concentration of reactions - the greater the concentration of reactant molecules, the more frequently they collide with one another and have an opportunity to react and form products.
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at equilibrium which chemical reaction occurs faster at equilibrium: the formations of products from reactants or reactants from products?
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at equilibrium, the formation of products from reactants is EQUAL to reactants from products - neither is faster than the other
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cellular respiration
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the opposite of photosynthesis - the products of photosynthesis are the reactants and the reactants of photosynthesis + energy are the producsts
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molecule
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two or more covalently bonded atoms
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how do weak bonds help a molecule?
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they reinforce the structure and help the molecules stick together
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what determines a molecules shape?
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the positions of the atoms' valence orbitals
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what is the basis for the recognition of one biological molecule by another?
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shape
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in terms of electron sharing what is the difference between nonpolar covalent, polar covalent and ion forming
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nonpolar covalent - shares electrons equally (same electronegativity)
polar covalent - the shared electrons are pulled towards the more electronegative atom
ion forming - the shared electron is completely removed and adhered to the more electronegative atom
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if more reactant was added to a reaction that is already at equilibrium, what happens to the chemical equilibrium?
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when more reactant is added to a reaction already at equilibrium, it will increase the concentration of products as they are converted to products... soon equilibrium will be reached again and the ratio will be back to where it was
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trace element
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an element absolutely needed for life but required in extremely minute amounts - ex: iron and zinc
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how is 31P different than 32P (the radioactive isotope)?
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32P has one more neutron
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where does the reactivity of an atom arise from?
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the existence of unpaired electrons in the valence shell
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when an atom has more electrons than protons it is a...
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anion
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8 protons, 10 neutrons, 8 electrons represents what atom?
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oxygen
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what is the only substance to exist in all three states of matter in a natural environment?
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water
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what kind of molecule is water? what kind of bonds does it have?
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water is a polar molecule with nonpolar covalent bonds (because O is more electronegative than H)
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describe the hydrogen bonds in water in the liquid stage
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the h-bonds in the liquid stage are very fragile breaking and forming frequently
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what would be the effect on the properties of the water molecule if oxygen and hydrogen had equal electronegativity?
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if O and H had equal electronegativity the water molecules would not be polar and would not be able to form hydrogen bonds with eachother
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cohesion
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when a substance is held together by linkages (like hydrogen bonds in water)
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aqueous solution
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a solution where water is the solvant
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hydrogen ion (H+)
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the hydrogen that detaches from a water molecule
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when a water molecule loses a hydrogen ion, it becomes a...
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hydroxide ion (OH-)
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when a hydrogen ion attaches to a water molecule, it becomes a ...
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hydronium ion (H3O+)
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is the dissociation of water molecules frequent?
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the dissociation of water molecules (the concentration of H+ and OH- ions) is much less than that of the whole water molecules in pure water at room temp.
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in pure water what is the ratio of H+ to OH- ions?
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they are equal
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how does pH affect a cell?
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it can affect its proteins and other complex molecules
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acid
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a substance that increases the hydrogen ion concentration of a solution... ex: HCl is added to water, the H ions dissociate from the Cl ions
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base
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a substance that reduces the hydrogen ion concentration... some bases reduce acidity by accepting H+ ions directly (NH3 + H+ = NH4) and some reduce acidity add OH- to the substance to become H2O.
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in any aqueous solution at 25 degrees C, the product of the H+ and OH- ions concentrations is...
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[H+][OH-] = 10^-14
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what is the pH concentration of a neutral solution at room temperature?
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[H+] = 10^-7
[OH-] = 10^-7
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as pH declines, concentration....
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increases
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buffers
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in biological fluids can resist change in pH - a buffer consists of an acid base pair that combines reversibly with hydrogen ions
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compared with a basic solution at pH = 9, the same volume of an acidic solution at pH = 4 has ___ times as many hydrogen ions.
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10^5 or 100,000
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what is the pH of 0.01 M HCl?
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[H+] = 0.01 M
= 10^-2 M
= pH 2
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given a liter of pure water and a liter solution of acetic acid, what would happen to the pH if you added 0.01 mol of a strong acid to each?
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the pH of the water should decrease from 7 to about 2 and the pH of the acetic acid solution will decrease only a small amount because the CH3COO- molecules will accept the added H+ molecules become CH3COOH
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the bonds broken when water vaporizes are.....
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hydrogen bonds between water molecules (in the gas state, the water molecules move around to quickly to bond together)
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which of the following is a hydrophobic matter:
paper, table salt, wax, sugar, pasta
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wax
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we can be sure that a mole of table sugar and mole of vitamin C are equal in their....
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number of molecules (avagadro's number = x10^23)
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measurements show that the pH of a particular lake is 4.0 - what is the hydrogen ion concentration of the lake?
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[H+] = 10^-4 M
this a fairly acidic lake, pure water is pH 7
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what is the hydroxide ion concentration of the lake with a pH of 4.0?
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[OH-] = 10^-10
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1 kilocalorie = __ joules
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4184 joules
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1 liter = __ kg
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1 kg`
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a slice of pizza has 500 kcal. if we could burn the pizza and use all the heat to warm a 50 L container of cold water, what would be the approx. increase in the temperature of the water? (1L = 1kg)
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10 degrees Celcius
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how many grams of acetic acid (C2H4O2) would you use to make 10 L of a 0.1 aqueous solution of acetic acid? (note: the atomic masses, in daultons are approx. 12 for carbon, 1 for hydrogen, and 16 for oxygen).
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60 g
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why to farmers spray water on their crops before and overnight freeze? how does this protect the plants?
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water has an incredibly high heat of fusion - that is water will hang out at 0C and it takes a long time for the water to freeze. A high heat of fusion means that, even if the temperature of the air changes a lot, water will shelter you from those changes and provide a pretty stable envir…
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what do proteins, DNA, carbohydrates and other molecules that distinguish living matter have in common?
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made up of carbon atoms bonded to one another - organic chemistry
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in organic molecules is there a cuttoff to how many carbons a molecule can have?
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no they range from simple methane (CH4) to complex molecules with an unknown number of carbons
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what are the major elements of life?
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C, H, O, N, S and P
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mechanism
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the view that physical and chemical laws govern all natural phenomena, including the processes of life
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organic chemistry
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the study of carbon compounds, regardless of origin
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what is valence?
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the number of covalent bonds an atom can form (see figure 4.4)
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what is the valence number of hydrogen? oxygen? nitrogen? carbon?
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hydrogen = 1
oxygen = 2
nitrogen = 3
carbon = 4
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what are some different ways carbon skeletons vary?
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length, braching, double bonds (can vary in location), rings
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hydrocarbons
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organic molecules consisting of only carbon and hydrogen - hydrogens attach to carbons wherever covalent bonding is available - not prevalent in most living organisms
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why are fats hydrophobic?
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fat molecules have long hydrocarbon tails - the H atoms on the tails and the H in water repel eachother
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isomers - what are the two types of isomers?
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compounds that have the same number of atoms of the same elements but different structures, hence different properties - cis and trans... cis isomers arrange on the same side of the carbon double bond while trans isomers arrange diagonally
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structural isomers
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differ in the covalent arrangements of their atoms
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enantiomers
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isomers that are mirror images of each other and differ in shape due to the presence of an asymmetric carbon (one that is attached to four different atoms or groups of atoms).
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functional group
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different functional groups that attach to a carbon skeleton (can replace a H on a skeleton) to affect molecular function
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seven most important chemical groups in biology
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hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate and the methyl groups (first six are functional groups and are hydrophilic)
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hydroxyl: alcohol
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-OH and hydrogen is bonded to an oxygen which is bonded to a carbon skeleton of an organic molecule (do not confuse this with a hydroxide ion OH-)
example: ethanol
properties: polar and can form hydrogen bonds with water molecules helping dissolve organic compounds such as sugar, p…
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carbonyl: ketones, aldehydes
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>C=O
ketones: if the carbonyl group is within a carbon skeleton - ex: acetone
aldehydes: if the carbonyl group is on the end of a carbon skeleton - ex: propanal
properties: ketones and aldehyde can be structural isomers with different properties, also found in sugars, polar, hydro…
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carboxyl: carboxylic acids
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-COOH
when an oxygen atom is double bonded to a carbon atom that is also bonded to an -OH group (basically a mix of hydroxyls and carbonyls) - ex: acetic acid
properties: acts as an acid, can donate H+ because the covalent bond between oxygen and hydrogen is so polar, found in cells …
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amino: amines
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nitrogen atom bonded with two hydrogens and also the carbon skeleton - ex: glycine
properties: acts as a base, can pick up H+ ions from surrounding, found in cells in the ionized form with a charge of 1+, polar, hydrophylic
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sulfhydryl: thiols
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-SH
consists of a sulfur atom bonded to an atom of hydrogen (resembles hydroxyl group in shape) - ex: cysteine
properties: 2 sulfhydryl groups can react forming a covalent bond which helps stabilize protein, polar, hydrophylic
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phosphate: organic phosphates
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-OPO3^2-
a phosphorous atom is bonded to four oxybgen aton (one O is bonded to the carbon skeleton, two O carry negative charges) - ex: glycerol phosphate
properties: contributes negative charge to the molecule which it is a part, molecules containing phosphate groups have the potent…
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methyl: methylated compounds
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consists of a carbon bonded to three hydrogen atoms, the carbon of a methyl group may be attached to a carbon or to a different atom - ex: 5methyl cytosine
properties: addition of methyl group to DNA or to molecules bound to DNA affects the expression of genes, arrangement of methyl gr…
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adenosine triphosphate (ATP)
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complex organic phosphate, highly funtional in a cell - it is a an organic molecule called adosine connected to a string of three phosphate groups
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what does the term amino acid signify about the structure of a molecule?
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it has an amino group (-NH2) making it an amine (base)
it also has a carboxyl group (-COOH) making it a carboxylic acid (acid)
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what types of isomers are acetone and propanal?
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acetone and propanal are structural isomers
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in what ways does a methyl group differ from the other 6 important chemical groups?
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methyl group is nonpolar and not reactive (not a functional group)
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what could you replace a carboxyl group with?
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a hydroxyl group and a carbonyl group (the replacement of the -OH of a carboxyl group with a hydrogen)
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what are the four critically important large molecules of all living things?
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carbohydrates, lipids, proteins and nucleic acids
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macromolecules
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carbohydrates, proteins and nucleic acids - huge of molecular scale (can contain thousands of atoms)
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polymer
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chainlike molecules (the three macromolecules - carbs, proteins and nucleic acids- are polymers)`
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monomer
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the building blocks/small parts of a polymer (like boxcars to a train) - some molecules that serve as monomers have other functions of their own
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enzymes
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a macromolecule servimg as a catalyst, a chemical agent that increases the rate of a reaction without being consumed by the reaccttion - most enzymes are proteins
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dehydration reaction
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the reaction by which monomers are connected to one another covalently with the loss of a water molecule - when a bond forms bw two monomers each monomer contributes part of the water molecule that is released during the reaction (one releases H+ and the other releases OH-)
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hydrolysis (give an example of hydrolysis)
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a process where polymers are disassembled to monomers - reverse of the dehydration reaction (breaking down water)
ex: digestion - the bulk of organic material in our food is in the form of polymers that are much too large to enter our cells... within the digestive tract various enzymes…
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how many molecules of water are needed to completely hydrolyze a polymer that is ten monomers long?
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P[1]P[2]P[]3P[4]P[5]P[6]P[7]P[8]P[9]P
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suppose you eat a serving of fish. what reactions must occur for the amino acid monomers in the protein of the fish to be converted to new proteins in your body?
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the amino acids in the fish protein must be released in hydrolysis reactions and incorporated into other proteins in dehydration reactions
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carbohydrates
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include both sugars and polymers of sugars - the simplest is monosaccharides (simple sugars)
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monosaccharides
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simple sugars - glucose is the most common
trademarks of sugar: a carbonyl group and multiple hydroxyl groups (see figure 5.3)
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disaccharide
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consists of two monosaccharides joined by a glycosidic linkage (a covalent bond bw two monosaccharides by a dehydration reaction) ex: maltose is two glucose bonded together
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glycosidic linkage
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covalent bond between two monosaccharides by a dehydration reaction
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polysaccharides
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macromolecules - polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages
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starch
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a plant polysaccharide - polymer of glucose monomers - synthesizing starch enables the plant to stockpile surplus glucose - represents stored energy
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explain the storage of starch in plants
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plants store starch as granules within cellular structures known as plastids which include chloroplasts - synthesizing starch enable the plant to stockpile surplus glucose - glucose is a major cellular fuel starch represents stored energy - sugar can later e used through hydrolysis which …
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glycogen`
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an animal polysaccharide - polymer of glucose (similar to starch but more branched)
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explain the storage of glycogen in animals
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animal cells stockpile glycogen as dense clusters of granules within liver and muscle cells - mitochondria are cellular organelles that help break down glucose released from glycogen
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cellulose
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polysaccharide - major component of the tough walls that enclose plant cells - polymer of glucose - never branched - can attach together by hydrogen bonding
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cell wall
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in plants is made up of mircofibrils made up of parallel cellulose molecules bonded together
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alpha and beta glucose ring structures
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differ in the placement of the hydroxyl group attached to the number one carbon
in cellulose every beta glucose monomer is upside down with respect to its neighbor (5.7)
glucose is made up of alpha monomers in the same orientation
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chitin
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structural polysaccharide - carbohydrate used by arthropods to build their exoskeletons (also used as a strong flexible surgical thread that will eventually decompose)
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write the formula for a monosaccharide that has three carbons
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C3H6O3
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a dehydration reaction joins two glucose molecules to form maltose - the formula for glucose is C6H12O6 - what is the formula for maltose?
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C12H22O11
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after a cow is given antibiotics to treat an infection, a vet give the animal a drink of "gut culture" containing various prokaryotes. why is this necessary?
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the antibiotic is likely to have killed the cellulose digesting prokaryotes in the cows stomach - the absence of these will hamper the cows ability to obtain energy from food and could lead to weight loss or death - thus the prokaryotic species are reintroduced
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lipids
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are the one class of large biological molecules that does not include true polymers and not big enough to be considered macromolecules - hydrophobic - fats, phosopholipids and steriods
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fat
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not polymers but are large molecules assembled from smaller molecules: glycerol and fatty acids
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fatty acid
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has a long carbon skeleton (usually 16 to 18) - one end is a carboxyl group (which is why it's acidic) and the rest is a hydrocarbon chain - hydrophobic due to nonpolar C-H skeleton
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triglycerol
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three fatty acid molecules each joined to a glycerol molecule by an ester linkage (bond between a hydroxyl group and a carboxyl group)
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saturated fatty acid vs unsaturated fatty acid
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if there is no double bonds between carbons in the fatty tail, then as many hydrogens as possible will bond (the tail is saturated why hydrogen)
if there is one or more double bonds which takes away a hydrogen (most of the time this will creat a cis bond where the tail is bent)
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hydrogenated vegetable oils means what?
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that unsaturated fats have been converted to saturated fats by synthetically adding hydrogen
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cardiovascular disease (atherosclerosis)
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deposits called plaques develop within the walls of blood vessels causing inward bulges that impede blood flow and reduce the resilience of the vessels (saturated fats)
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trans fat
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hydrogenating vegetable oils creates saturated fats and unsaturated fats with trans bonds called trans fats - are worse than unsaturated fats and contribute to cardiovascular disease
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what fatty acid is essential for normal growth in children?
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omega-3 fatty acid (also prevent cardio vascular diesase in adults) ex. fish, nuts
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phospholipids
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essential for cells because they make up the membranes - similar to a fat molecule but only has two tail instead of three - when added to water they form a bilayer protecting their hydrophobic tails with their hydrophilic heads
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bilayer
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made of phospholipids when added to an aqueous solution - protects the hydrophobic tails with the hydrophilic heads - main fabric of biological membranes
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steriods
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lipids characterized by a carbon skeleton consisting of four fused rings
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cholesterol
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crucial molecule in animals - precursor from which other steriods are synthesized - in vertabrates cholesterol is obtained from the diet and synthesized in the liver
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compare the structure of a fat (triglyceride) with that of a phospholipid
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a triglyceride is a carboxyl and hydroxyl head with three hydrophobic fatty acid tails made up of hydrocarbon
a phopholipid has two fatty acid tails and a phosphate group
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why are human sex hormones considered lipids?
human sex hormones are steroids a type of hydrophobic compound
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human sex hormones are steroids a type of hydrophobic compound
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suppose a membrane surrounded an oil droplet as it does in the cells of plant seeds - describe and explain the form it might take
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the oil droplet membrane could consist of a single layer of phospholipids rather than a bilayer because an arrangement in which the hydrophobic tails of the membrane phospholipids were in contact with the hydrocarbon regions of the oil molecules would be more stable
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50% of the dry mass of cell is made up of what?
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protein
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catalysts
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enzymatic proteins regulate metabolism by acting as catalysts, chemical agents that selectively speed up chemical reactions without being consumed by the reaction
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polypeptide
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polymers of amino acids
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protein
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biologically functional molecule that consists of one or more polypeptides, each folded and coiled into a specific three dimensional structure
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list eight different proteins
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enzymatic proteins, defensive proteins, storage proteins, transport proteins, hormonal proteins, receptor proteins, contracctile and motor proteins and structural proteins
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enzymatic proteins
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function: selective acceleration of chemical reactions
example: digestive enzymes catalyze the hydrolysis of bonds in food molecules
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defensive proteins
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function: protection against disease
example: antibodies inactivate and help destroy viruses and bacteria
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storage proteins
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function: storage of amino acids
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transport proteins
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function: transport of substances
example: hemoglobin transports oxygen from the lungs to other parts of the body, other proteins transport molecules across cell membranes
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hormonal proteins
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function: coordination of an organism's activities
example: insulin causes other tissues to take up glucose regulating blood sugar concentration
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receptor proteins
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function: response of cell to chemical stimuli
example: receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells
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contractile and motor proteins
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function: movement
example: motor proteins are responsible for the undulations of cilia and flagella. actin and myosin proteins are responsible for the contraction of muscles
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structural proteins
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function: support
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amino acid
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organic molecule possessing both an amino group and a carboxyl group - the center is a carbon atom with a amino group, carboxyl group, hydrogen atom and a variable group (could be simple like a H or a carbon skeleton)
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MEMORIZE THE 20 AMINO ACIDS OF PROTEINS
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figure 5.16
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9 non polar amino acid side chains
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Gus Always Values Learning In Math Pretending To Pass
-glycine (gly, g)
-alanine (ala, a)
-valine (val, v)
-leucine (leu, l)
-isoleucine (ile, i
-methionine (met, m)
-phenalalanine (phe, f)
-tryptophan (trp, w)
-proline (pro, p)
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6 polar amino acid side chains
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Silly Tim Can't Teach Algebra Well
-serine (ser, s)
-threonine (thr, t)
-cystine (cys, c)
-tyrosine (tyr, y)
-asparagine (asn, N)
-glutamine (gln, q)
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2 acidic, negatively charged amino acid side chains
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Ass Gluts
-aspartic acid (asp, d)
-glutamic acid (glu, e)
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3 basic, positively charged amino acid side chains
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HAL
-histidine (his, h)
-arginine (arg, r)
-lysine (lys, k)
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BIOL 1107: Test 4