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220 Cards in this Set
- Front
- Back
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What is the defining feature of lipids?
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Their insolubility in water due to long fatty acid chains and no double bonds
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What are some functions of lipids?
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Energy storage lipids, structural lipids in membranes, lipids as cofactors, signals and pigments
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What do the fats and oils used as stored forms of energy in living organisms contain?
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Fatty acids
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What are fatty acids?
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Carboxylic acids with hydrocarbon chains ranging from 4-36 carbons long
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When fatty acid hydrocarbon chains are oxidized to CO2 and H2O, what occurs?
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Energy is released
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Name the three types of fatty acids
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Saturated, Monosaturated, Polysaturated
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Describe what a saturated fatty acid is
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Carboxylic acid with hydrocarbon chain that contains no double bonds
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Describe what a monounsaturated fatty acid is
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Carboxylic acid with hydrocarbon that contains one double bond
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Describe what a polyunsaturated double bond is
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Carboxylic acid with hydrocarbon chain that contains multiple double bonds
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In fatty acid nomenclature, what do the two numbers separated by a colon represent
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The two numbers represent chain length and and number of double bonds
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Name two characteristics of the most commonly occuring fatty acids
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Even numbers of carbon atoms, in an unbranched chain of 12-24 carbons
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Where is the double bond located in most monounsaturated fatty acids?
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Between C-9 and C-10
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True or False:
Double bonds on polyunsaturated fatty acids have alternating single and double bonds |
False
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What usually separates double bonds in polyunsaturated fatty acids?
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A methylene group
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What configuration are the double bonds in nearly all naturally occuring unsaturated fatty acids?
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Cis configuration
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How are trans fatty acids produced?
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By fermentation in the rumen of dairy animals. Obtained from dairy products and meat
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Describe an omega-3 fatty acid
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It's polyunsaturated with a double bond between C-3 and C-4, near methyl end of hydrocarbon chain
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Describe an omega-6 fatty acid
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It's polyunsaturated with a double bond between C-6 and C-7, near methyl end of hydrocarbon chain
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True or False:
Humans require but cannot enzymatically produce the omega-3 fatty acid alpha linolenic acid (ALA)? |
True
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What other two omega-3 fatty acids can humans synthesize from ALA?
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Eicosapentaenoic acid and docosahexaenoic acid
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What is the optimal dietary ration of omega-6 and omega-3 fatty acids?
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Between 1:1 and 4:1
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Where can omega-3s be obtained?
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Leafy vegetables and fish oils
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What largely determines the physical properties of fatty acids and the compounds that contain them?
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Length and degree of unsaturation of hydrocarbon chain
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What causes fatty acids to have lower solubility in water?
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The longer the nonpolar hydrocarbon chain is and the fewer double bonds it contains
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The carboxylic acid group in the fatty acid is _________ at neutral pH?
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Polar and ionized
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True or False:
Carboxylic acid group in fatty acids account for a slight solubility of short-chain fatty acids in water |
True
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What is the physical property of saturated fatty acids at room temperature from 12:0 to 24:0?
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Have a waxy consistency
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What is the physical property of unsaturated fatty acids that are 12-24 carbons long?
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Oily liquid
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What accounts for the difference in melting point between saturated and unsaturated fatty acids?
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Different degrees of packing in the fatty acid molecules. Unsaturated fatty acids have kinks and therefore cannot be packed tightly together
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In fully saturated compounds, where does free rotation occur and what does it do?
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Free rotation occurs around each carbon-carbon bond and gives the hydrocarbon chain great flexibility
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Define Gibb's free energy
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It is the amount energy capable of doing work during a reaction (of constant temperature and pressure)
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When the progression of a reaction causes a release of free energy (system goes to a lower energy state), what is the free energy change?
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The free energy change is negative
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Define enthalpy
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Enthalpy describes the change in heat in a reacting system
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What is enthalpy when the progression of a reaction causes a release of heat?
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Enthalpy is negative and the reaction is exothermic
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Define entropy
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A quantitative expression for the randomness or disorder in a system
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What happens when the products of a reaction are less ordered or complex than the reactants?
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There is a gain in entropy (positive)
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For any physical or chemical change, the total amount of energy in the universe _______ _______ (1st law of thermodynamics)
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Remains constant
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Restate the 1st law of thermodynamics
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Energy can change form or be transported from one region to another, but it cannot be created or destroyed
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The universe always tends toward _________ disorder. In all natural processes, the entropy of the universe _________
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Increasing; increases
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Define a reacting system
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The collection of matter that is undergoing a particular chemical or physical process
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Give examples of a reacting system
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A cell, an organism, or two reacting compounds
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Define an open system
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An open system can exchange matter and energy with its surroundings
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Give an example of an open system
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Living cells and organisms, since they take up nutrients, release waste products, generate work and heat
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Define a closed system
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A closed system cannot exchange matter and energy with its surroundings
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Give an example of a closed system
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A chemical reaction happening in a perfectly insulated beaker
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If the entropy of the universe is always increasing, how do living systems create more ordered structures (protein, DNA, etc.) out of less structured components?
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The reactions that are happening in a living organism never go to their equilibrium state, which means less entropy due to the constant influx of energy from nutrients
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What defines the equilibrium constant?
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The concentrations of the reactants and products at equilibrium
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Free energy change is ________ related to the equilibrium constant
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Directly
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The composition of a reacting system tends to _________ _________ until equilibrium is reached
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Continue changing
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When a reacting system is not at equilibrium, the tendency to move toward equilibrium is quantified by what?
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The free energy change
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If a reaction is occurring at conditions other than the standard, what depends on reactant and product concentrations?
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Actual free energy change
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What happens when actual free energy change of any reaction proceeds spontaneously towards its equilibrium?
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It is dynamic and becomes less negative as the reaction proceeds and is zero at equilibrium
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In living cells, reactions that would be extremely slow if uncatalyzed are caused to proceed by the use of an ________
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Enzyme
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What is an enzyme?
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It provides an alternative reaction pathway with a lower activation energy
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The toral free energy change for a reaction is _________ of the pathway by which it occurs
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Independent
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What does the total free energy change for a reaction depend on?
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The nature and concentrations of the reactants and products
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Enzymes cannot change __________ __________, but they increase the ______ at which a reaction proceeds in the direction directed by thermodynamics
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Equilibrium constants; rate
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Standard free energy changes are _________, since each reaction has its own free energy change and equilibrium constant
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Additive
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What principle explains how a thermodynamically unfavorable reaction can be driven in the forward direction?
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Standard free energy changes are additive, which couples an unfavorable reaction to a highly exergonic reaction through a common intermediate
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What does a higher equilibrium constant indicate?
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That it is more likely for a reaction to proceed in a forward direction
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Enzymes have a high degree of _________ for their substrates
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Specificity
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What affect do enzymes have on chemical reactions?
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They tremendously accelerate them
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What type of reactions are enzymes are central to?
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Degrade nutrient molecules, transform chemical energy, and make macromolecules from simple precursors
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Most enzymes are _________
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Protein
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What are the additional chemical component called that some enzymes require for their chemical activity?
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Cofactors and coenzymes
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What are cofactors?
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Either one or more inorganic ions, such as Fe2+, Mg2+, Mn2+ or Zn2+
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What are coenzymes?
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Complex organic or metalloorganic molecules
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What do coenzymes act as?
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Transient carriers of specific functional groups
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Most coenzymes are derived from ___________
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Vitamins
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Define a prosthetic group
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A coenzyme or metal ion that is very tightly or even covalently bound to the enzyme of a protein
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Define a holoenzyme
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A complete, catalytically active enzyme together with its bound coenzyme and/or metal ions
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Define an apoenzyme
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It is the protein part of the holoenzyme, also known as the apoprotein
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Name the enzyme that catalyzes this reaction ATP + D-glucose---> ADP + D-glucose 6-phosphate
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ATP-glucose phosphotransferase
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What does ATP-glucose phosphotransferase's name indicate?
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That it catalyzes the transfer of a phosphoryl group from ATP to glucose
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How do enzymes work?
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They facilitate the transient formation of unstable charged intermediates. They bring together molecules in the proper orientation required for a reaction. They provide a specific environment where the reaction can occur more quickly, some sequester a substrate
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Define active site
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The pocket of the enzyme where the reaction takes place
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Define reaction intermediates
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Transient complexes of the enzyme with the substrate and the product, often denoted as ES, EP
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Define a reaction coordinate diagram
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A picture of how energy changes during the reaction
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The starting point for either the forward or reverse reaction is the ____________
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Ground state
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What does the equilibrium between S and P reflect?
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The difference in the free energy of their ground states
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What is the rate of a reaction dependent on?
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The activation energy
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Define activation energy
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Energy required for the transformations required for the reaction to proceed in either direction. It is also the difference between the energy levels of the ground state and the transition state
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To undergo reaction, molecules must be _________ to a ________ energy level
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Raised, higher
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At the top of the energy "hill" decay to S or P is ________ ________ because ________________
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Equally likely, it is downhill either way
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Activation energy is the energy required to attain the __________ _______
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Transition state
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True or False:
The transition state is a chemical species with significant stability |
False, it is the most energetically unstable position and is VERY transient
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Describe what the transition state is
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A fleeting moment in which events such as bond breakage, bond formation and charge development have proceeded to the precise point at which decay to either substrate or product is equally likely
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Higher activation energy results in a ________ reaction
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Slower
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Enzyme catalysts enhance reaction rates by _________ activation energy
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Lowering
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True or False:
The reaction reaches equilibrium much faster when catalyst is present |
True
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True or False:
The enzyme is used up in the process |
False
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The equilibrium constant K'eq is ___________
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Multiplicative K'eq=K'eq1 x K'eq2
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Define standard free energy change
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Energy change between start, where each reactant and product has a 1M concentration, and end, where reaction is at equilibrium
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Define actual free energy change
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Energy change between start, which are actual conditions of [S] & [P] at a given point in time (not necessarily "standard conditions" and end, where reaction is at equilibrium
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What are the standard conditions of temperature, pressure, pH and concentration of both reactants and products?
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Temperature=25 degrees
Pressure=1 atm pH=7.0 [S] & [P]=1M |
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When several steps occur in a reaction, the overall rate is determined by the step(s) with the __________ activation energy, called the ____-________ ______
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Highest, rate-limiting step
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The rate of any reaction is determined by what two things?
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The concentration of the reactant(s) and by rate constant, k
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What does the rate of reaction (V) represent?
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The amount of S that reacts per unit time V=k[S]
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What does the rate constant k reflect?
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The probability of reaction under a certain set of conditions (temperature, pH, etc.)
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The larger the k, the _________ the reaction
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Faster
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If it is a second-order reaction, what does the reaction rate depend on?
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The concentration of two different compounds or two molecules of the same compound
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What is the rate equation of a second-order reaction?
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V=k[S1][S2]
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What is the relationship between the rate constant and activation energy?
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It is inverse and exponential
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How do enzymes lower activation energy enough to cause huge rate enhancements?
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Rearrangement of covalent bonds and non-covalent interactions between substrate and enzyme
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When an enzyme is present, reactions can take place between a substrates' and enzymes' _____________ ________
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Functional groups
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What forces do the substrate and enzyme interact through? Give examples
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Weak forces such as hydrogen bonds and hydrophobic and ionic interactions
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What occurs when an enzyme and substrate form a specific ES complex?
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A small amount of free energy is released
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Define binding energy
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The free energy released by all weak interactions formed between enzyme and substrate
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Binding energy is a _______ source of free energy used by enzymes to lower activation energies of reactions
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Major
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What causes the weak interactions to form in an ES complex?
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The specificity of an enzyme for a substrate
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Weak interactions between enzyme and substrate are ______ in the transition state
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Optimal
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Enzyme-substrate interaction are like a ______ and ______
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Lock and key
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Why is an enzyme complementary to the substrate so ineffective?
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The stable ES impedes the bending that must occur to reach the transition state, since it has a much lower energy state than S. Thus, from this ES, activation energy is much higher than from S
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Why is an enzyme complementary to the transition state so effective?
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Interactions are maximized at the transition state, which partially offsets the energy that must go into making the bent state
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The weak interactions that are formed only in the __________ ______ are those that make the biggest contribution to lowering activation energy
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Transition state
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Name one reason why enzymes (and some coenzymes) are so large
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The requirement for multiple weak interactions to drive catalysis
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When is optimal binding usually achieved?
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When the substrate is in an active site where it is effectively removed from water
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What occurs if an enzyme active site has functional groups that are arranged so that weak interactions with the substrate are maximized at the transition state
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The enzyme will not be able to interact to the same degree with any other molecule, enzyme is specific
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What energy can be used to to overcome physical and thermodynamic barriers?
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Binding energy
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Name the factors that contribute to the activation energy
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(1) Entropy of molecules in solution (2) Solvation shell of hydrogen-bonded H2O (3) Distortion of substrate molecules (4) Need for proper alignment of catalytic functional groups on enzyme
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How does entropy (freedom of motion) of molecules in solution increase the activation energy?
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It reduces the possibility that molecules will come into contact
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How does the solvation shell of hydrogen-bonded H2O hinder the reaction?
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It surrounds most molecules in aqueous solution
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How is binding energy used to overcome barriers to reaching activation energy?
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Entropy reduction, formation of a desolvation layer, distorting the substrate molecule(s) and changing the conformation of an enzyme all requires energy
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How does decreasing entropy make a reaction much more likely to occur?
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Decreasing entropy allows the substrate(s) to be held in place be the enzyme
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What do enzyme-substrate interactions replace when a desolvation layer is formed?
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They replace many of the hydrogen bonds between the substrate and H2O molecules
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Distortion of the substrate molecule(s), esp _________ _____________ may be necessary to achieve the transition state
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Electron redistribution
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What are enzyme conformation change induced by?
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Weak interactions with substrate: "induced fit"
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What do enzyme conformation changes do?
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They bring enzyme functional groups into the proper position to catalyze the reaction
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Enzyme conformation may also open sites for more ______ ________ with the substrate at the transition state
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Weak bonding
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When can [S] be regarded as constant?
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When the very beginning of a reaction is being monitored, since changes in [S] are limited to a few percent
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When is the increase in initial velocity the highest?
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When [S] is low
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How do we know when Vmax is achieved?
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When increasing the [S] does not increase the Vo anymore
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At any point in time, what two forms do enzymes exist in?
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Free enzyme E and the complex ES
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What does the Michaelis-Menten equation describe?
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A one-substrate enzyme-catalyzed reaction
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Which equation gives a more accurate determination of Vmax?
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The Lineweaver-Burk equation
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The Michaelis-Menten equation show the relationship between Vo and [S] when a reactions is under what type of conditions?
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Steady state
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When does Km=[S]?
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When Vo= 1/2Vmax
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Define Kcat
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It is a more general rate constant that describes the limiting rate of any enzyme-catalyzed reaction at saturation
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What does Kcat incorporate when a reaction doesn't have only one clear rate-limiting step?
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It incorporates rate constants of all partially rate-limiting steps
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Kcat is a useful parameter in comparing ________ _________
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Enzyme activities
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What does a competitive inhibitor do?
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It competes with the substrate for the active site of an enzyme
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How can the competition be biased to favor the substrate?
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By adding more substrate
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What does an uncompetitive inhibitor do?
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It binds at a site distinct from the enzyme active site, and only binds to the ES complex
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What does a mixed inhibitor do?
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It binds at a site distinct from the enzyme active site, but it can bind to E or ES
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What do irreversible inhibitors do?
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They bind covalently with or destroy a functional group on an enzyme that is essential for the enzyme's activity
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Suicide inhibitors are relatively ___________ until they bind to the active site of a specific enzyme
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Unreactive
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What happens to a suicide inactivator after it undergoes the first few steps of normal enzymatic reaction?
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It is converted to a very reactive compound that combines irreversibly with the enzyme
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Suicide inhibitor are also known as what?
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Mechanism-based inhibitors
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What do regulatory enzymes exhibit in response to certain signals?
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Increased or decreased catalytic activity
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How do allosteric enzymes function?
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Through reversible, noncovalent binding of regulatory compounds
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Allosteric enzymes generally have one or more __________ _____ for binding modulators
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Regulatory sites
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True or False:
Allosteric enzymes generally have large and multiple subunits |
True
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Describe feedback inhibition
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It occurs when a regulatory enzyme is specifically inhibited by the end product of a pathway
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True or False:
Allosteric enzymes exhibit the same kinetic properties as mixed and uncompetitive inhibitors |
False
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_____________ is a common reversible covalent regulatory modification
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Phosphorylation
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Allosteric enzymes generally have one or more __________ _____ for binding modulators
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Regulatory sites
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True or False:
Allosteric enzymes generally have large and multiple subunits |
True
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Describe feedback inhibition
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It occurs when a regulatory enzyme is specifically inhibited by the end product of a pathway
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True or False:
Allosteric enzymes exhibit the same kinetic properties as mixed and uncompetitive inhibitors |
False
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_____________ is a common reversible covalent regulatory modification
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Phosphorylation
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What does phosphorylation introduce to the regulatory enzyme?
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A bulky negatively charged group, whose oxygen atoms can hydrogen bond with other groups (like amide groups)
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What do multiple phosphorylations allow?
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Tight regulation
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What is the name of the inactive precursor that is cleaved to form the active enzyme?
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Zygomen
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Proteolytic cleavage is an _____________ reaction
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Irreversible
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What kinds of protein bind tightly to the enzyme's active site after it is exposed from cleavage?
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Inhibitor proteins
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Why are carbohydrates important?
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They are the most abundant biomolecules on earth, sugar and starches are dietary staples
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Oxidation of carbohydrates is a central __________-_________ pathway
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Energy-yielding
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Carbohydrate polymers (glycans) serve as structural and protective elements in what?
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The cell walls of bacteria and plants and in connective tissues of animals
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What do monosaccharides consist of?
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A single polyhydroxy (two or more hydroxyl groups) aldehyde or ketone units
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In an aldehyde, where is the carbonyl located?
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At the end of the carbon chain
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In a ketone, where is the carbonyl located?
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Between two carbon atoms
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Describe what type of solid monosaccharides are
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Colorless and crystalline
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Monosaccharides are freely soluble in _____ but insoluble in _______ ___________
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Water, nonpolar solvents
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Describe the backbones of common monosaccharides
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Unbranched carbon chains in which all carbon atoms are linked by single bonds
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When do monosaccharides tend to form a cyclic structure?
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When they have 5 or more carbons in their chains
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True or False:
Many of the carbon atoms to which hydroxyl groups are attached are chiral centers |
True
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Most naturally occurring sugars are in what isomer form?
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D-isomer
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What are two sugars that differ only in the configuration around one carbon called?
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Epimers
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Which group forms a covalent bond with an oxygen of the hydroxyl group for a monosaccharide to have a cyclic structure?
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The carbonyl group
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What is produced when the carbonyl group forms a covalent bond with the oxygen in the hydroxyl group?
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An additional chiral carbon (alpha form and beta form)
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What does the alpha form in cyclic structures indicate?
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That the hydroxyl group at the anomeric center is in the opposite direction (trans) as the hydroxyl on the farthest chiral carbon
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What does the beta form in the cyclic structures indicate?
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That the hydroxyl group at the anomeric center is in the same direction (cis) as the hydroxyl on the farthest chiral carbon
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What are the alpha and beta form of the ring structures called?
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Anomers
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What is the difference between conformations and configurations?
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Conformations are interconvertible without the breakage of covalent bonds, while configurations are isomers and covalent bonds would have to be broken
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True or False:
Interconversion of ring structures happen readily because it doesn't stress the ring |
False
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Why is conformation important?
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Important for determining the biological properties and functions of some polysaccharides
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In the synthesis and metabolism of carbohydrates, what are the intermediates?
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Sugars phosphorylated derivatives
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Sugar phosphates are relatively _______ at neutral pH and bear a __________ charge
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Stable, negative
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What is one effect of sugar phosphorylation within cells?
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To trap the sugar inside the cell since most cells do not have plasma membrane transporters for phosphorylated sugars
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What do disaccharides consist of?
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Two monosaccharides joined covalently by an O-glycosidic bond
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What is the end of chain with a free anomeric carbon called when describing disaccharides or polysaccharides?
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Reducing end
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True or False:
Most carbohydrates in nature occur as disaccharides |
False. They occur as polysaccharides
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Describe polysaccharides
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They are polymers of medium to high molecular weight
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How do polysaccharides differ from each other?
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Identity of their recurring monosaccharide units, the length of their chains, and their degree of branching
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What is the difference between homo and heteropolysaccharides?
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Homo contain only a single monomeric species while hetero contain two or more species
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Which polysaccharide serves as a storage form of monosaccharides that are used as fuel?
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Homopolysaccharides
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Which polysaccharide serves as structural elements in plant cell walls and animal exoskeletons?
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Homopolysaccharides
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Which polysaccharide provides extracellular support for organisms of all kinds?
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Heteropolysaccharides
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Why do polysaccharides generally do not have a defined molecular weight?
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There is no template for polysaccharide synthesis and there is no specific stopping point in the synthetic process
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What are the most important storage polysaccharides in pant cells and in animal cells?
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Starch in plant cells and glycogen in animal cells
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Starch and glycogen molecules are heavily _________, because they have many exposed __________ ________ available to hydrogen bond with water
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Hydrated, hydroxyl groups
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Starch contains which two types of glucose polymers?
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Amylose and amylopectin
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Describe amylose
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Consists of long unbranched chains of D-glucose residues
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Describe amylopectin
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Highly branched
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Which starch glucose polymer is glycogen similar to?
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Amylopectin
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Which carbon becomes the anomeric carbon when a ring structure is being formed?
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The former carbonyl carbon
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The alpha and beta anomers of D-glucose can interconvert in a process known as what?
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Mutorotation
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What are glycosaminoglycans?
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Linear polymers of repeating disaccharide units with a helical 3-D structure. Found in ECM
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What are proteoglycans?
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Marcromolecules of the cell surface or ECM in which one or more sulfated glycosaminoglycan chains are joined covalently to a membrane protein or secreted protein
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What are glycoproteins?
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Proteins with one or more oligosaccharides covalently attached
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Where are glycoproteins found?
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On the outer face of the plasma membrane, in specific organelles (golgi), in the ECM, and in blood
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What are glycolipids?
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Membrane sphingolipids with oligosaccharides as their hydrophillic head group
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Where are glycolipids located?
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On the outer face of plasma membrane
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What are lectins?
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They are carbohydrate-binding proteins
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What does the oligosaccharide portion of glyoproteins and glycolipids do?
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They form highly specific sites for lectin recognition
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Cells use specific oligosaccharides for what?
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Intracellular targeting proteins, cell-cell interactions, extracellular signaling and cell differentiation and tissue development
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Lectins are often _________, which enable crosslinking of ligands
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Polyvalent
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Binding of lectins can affect the stability of ___________
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Glycoproteins
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True or False:
Analysis of oligosaccharides is more complicated than for proteins |
True
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How are the positions of glycosidic bonds determined?
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By methylating the free hydroxyl groups and then hydrolyzing the polysaccharide
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