65 Cards in this Set
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Hydrophoic interactions drive proteins to fold.
A.) What does hydrophobic mean?
B.) Explain why why hydrophobic amino acids drive folding.
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A.) Water-hating
B.)Hydrophobic amino acids like to interact with one another and move away from water. They then fold into the core and hydrophillic residues point towards and interact with water.
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Primary Structure
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linear order of amino acids in chain
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Secondary Structure
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local structure that includes helices and beta sheets
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Tertiary Structure
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Whole protein fold
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Quaternary Structure
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Two or more proteins form dimers and other multimeric complexes
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Four shape determining interactions in proteins
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Hydrogen Bonds: O-H or N-H interacting with a lone pair on N or O
Disulfide Bonds: Two cytesine connect in a disulfide bond after oxidation
Hydrophobic Effect: Interactions between hydrophobic residues
Salt Bridges: interactions between charged side chains
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List the amino acids whose R-groups(side chains) form hydrogen bonds with water.
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Trp,The,Ser,Tyr,Asp,Glu,Asn,Gln,His,Lys and Arg
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List the amino acids involved in hydrophobic interactions.
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Ala, Val, Leu, Ile, Met, Pro and Phe
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What is catalysis in terms of energy changes?
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Free energy change between reactants and products stays the same, while activation energy is lowered.
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What are the 4 different ways enzymes catalyze reactions.
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a. Bring substrate and catalytic sites together
b.Hold substrate at an exact distance and position for reaction
c.Provide acidic, basic or other groups required for catalysis
d.Lower the activation energy by straining bonds in the substrate
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What is the active site of an enzyme?
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Place that substrates bind and undergo chemical change
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What is a cofactor with respect to enzymes?
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A compound used by the enzyme to help catalyze the reaction.
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What is the major way that drugs work in our bodies?
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Drugs are inhibitors of enzymes. Inhibiting an enzyme causes a biological response.
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What is the main purpose of the water-soluble b vitamins?
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They are cofactors used by enzymes to catalyze reactions.
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What is an antioxidant and how do they work?
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The are compounds like vit. A,C and E that react with free radicals in our body. Most of their reactions can be initiated by reactive oxygen species such as hydrogen peroxide.
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How are the reactions (stages) that break down food organized?
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Digestion
Production of acetyl-CoA from glucose, fats or protiens
Citric acid cycle
Electron Transport Chain produces ATP
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What is the main purpose of the citric acid cycle?
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To oxidize Acetyl-CoA to CO2 and produce redcued NADH and FADH2
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Explain how coupled reaction can drive an unfavorable step in a metabolic pathway.
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Coupling an endergonic and exergonic reaction drives the reaction since the exergonic reaction uses extra energy to make the endergonic reaction happen.
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Why is it good that ATP does not store more than 7.3 kcal/mol of energy?
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If it stored more it would be hard to use the energy efficiently and it would be lost to heat.
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What does heat do to enzymes?
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To much heat will make enzymes not function correctly and can denature proteins.
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What is the purpose of the Electron transport chain?
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Pumps protons into the intermembrane space of the mitochondria so the proton gradient can be used to drive ATP synthase making ATP.
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In what organelle in the cell does ATP synthesis happen?
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Mitochondria
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What is the driving force for ATP synthase?
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The proton gradient.
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What is the important difference in the structures of starch and fiber?
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Starch has individual glucose units that are joined by (alpha)-1,4 links rather than by the B-1,4 links of cellulose. This is why starch is digestable by humans while fiber is not.
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What is glycogen and why is it important?
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Glycogen is how animals store glucose. Glucose levels are highly regulated in the body and glycogen provide means to store and access glucose.
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Sucrose is a disaccharide made up of what two monosaccharides?
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Glucose and fructose.
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Hydrolysis of glycogen leads to what molecule?
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Glucose
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Define and give an example of an amphiphilic molecule.
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An amphiphilic molecule has both a hydrophilic and hydrophobic part.
Examples: Fatty acids and phospholipids.
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List and describe the three different ways that molecules cross the cell membrane.
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Passive Diffusion: Uncharged hydrophobic molecule can cross lipid bilayer driven by concentration gradient. (Charged ions such as Cl- moving through small pores)
Facilitated Diffusion: Complex molecule requires a protein to carry it across membrane (glucose). ( Does not require energy …
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Describe how bile acids aid in the digestion of fat.
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They break into small micelles. Miscelles provide access to ester bonds of the triacylglyceride so it can be hydrolyzed by lipases.
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Describe the different fates of pyruvate in mammals and yeast.
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1. Can form acetyl-CoA and go into the citric acid cycle (aerobic)
2.Go to lactic acid and NAD+ (anerarobic).
Yeast- instead of lactate it forms ethanol and NAD+ without oxygen.
For yeast and mammals it is important to form NAD+ since this is needed to continue the glycolysis pathway i…
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How do coupled reactions drive the glycolysis pathway?
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The process is exergonic, but many steps are endergonic. Steps from both couple together to pull the reaction along.
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Explain what happens when you have high blood glucose levels.
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High blood glucose causes the pancreas to release insulin. Insulin increases the number of glucose transporters in the cell wall and the gradient pushes glucose into the cell.
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What happens in the cell when there are high levels of glucose?
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Leads to glycogen and triacylglyceride synthesis for energy storage.
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What happens when you have low blood glucose levels?
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Causes the release of glucagon. Glucagon signals for the breakdown of triacylglycerides to fatty acids and glycerol and glycogen to glucose for energy production.
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Describe energy use over time while exercising. (Example, what is your energy source for the first couple seconds? The next minute? Hour?
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First energy source is ATP (a couple seconds)
Second you make ATP from creatine phosphate ( 30 seconds)
Third consume free glucose (1-2 minutes)
Fourth consume glycogen (2-3 hours)
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Describe energy use when starving.
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When most of glucose and glycogen is consumed you use protein and lipids as energy.
Ketone bodies from lipid metabolism are used by heart and muscles while remaining glucose is used by brain.
When all glucose is used ketones make up brains energy requirements.
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What are the major products of the oxidation of lipids that are used to produce energy?
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Acetyl-CoA, NADH and FADH2
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Name the molecules involved in glycogenesis. B) What are their sources? C) Under what conditions does glycogenesis occur?
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Glycogenesis is the synthesis of glycogen.
A. Glucose, ATP and UTP.
B. Glucose is from diet, ATP is from the ETC and UTP is synthesized from ATP.
C.Glycogenesis occurs when glucose concentration is high like after eating.
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Molecular oxygen plays an important role in whether the glycolysis products enter the citric acid cycle. A.)During what stage of metabolism is oxygen used? B.)What are the products of glycolysis when no oxygen is present? C.)What is the significance of these products?
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A.) ETC
B.) Lactate and NAD+.
C.) Production of lactate provides NAD+ so glycolysis can continue w/o oxygen. This allows prodution of ATP from glycolysis pathway.
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Under what conditions do you produce ketone bodies?
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WHen Acetyl-CoA levels are high they overwhelm the citric acid cycle leading to ketone bodies.
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What is the purpose of ketone body formation?
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Provide a water soluable energy source for muscles, heart, and brain when glucose levels are very low.
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Describe Type I diabetes and how its treated.
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(Insulin-dependent) caused by failure of pancreatic cells to produce enough insulin.
-Injection of insulin.
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Describe Type II diabetes and how its treated.
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(Non-insulin dependent) insulin is plentiful, but fails to promote passage of glucose across cell membranes.
-Diet modification, exercise and treatment with drugs that increase insulin or insulin receptor levels.
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Protein
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Large biological molecule made of amino acids linked by peptide bonds.
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Amino acid
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Molecule that contains an amino group and carboxylic acid
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Side chain
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R-group bonded to central carbon atom
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Peptide bond
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Links two amino acids together
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Zwitterion
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Neutral dipolar ion has one + and one - charge.
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Substrate
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Reactant in an enzyme catalyzed reaction
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Coenzyme
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molecule that acts as an enzyme cofactor
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Induced fit model
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enzyme action in which enzyme has flexible active site that changes shape to best fit the substrate and catalyze reaction
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Activation
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Process that initiates or increases action of enzyme
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Inhibitor
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Process that slows or stops the action of enzyme
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Allosteric control
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interaction in which binding of a regulator at one site affects the proteins ability to bind at a different site
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Allosteric enzyme
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enzyme whos activity is controlled by the binding of an activator or inhibitor at a location other than the active site
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Uncompetitive inhibition
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Enzyme regulation in which an inhibitor binds reversibly ot the enzyme substrate complex blockin the binding of the second substrate to the active site
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Competitive inhibition
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Enzyme regulation in which an inhibitor competes witha substrate for binding to the enzyme active site.
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Irreversible inhibition
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Ezyme deactivation in which an inhibitor forms covalent bonds to the active site permanentaly blocking it.
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Zymogen
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Compound that becomes an active enzyme after undergoing a chemical change.
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Endergonic reaction
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Nonspontaneous reaction that absorbs free energy has positive G
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Exergonic reaction
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Spontaneous reaction that releases free energy and has negative G
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Cytoplasm
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Region between cell membrane and nuclear membrane
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Cytosol
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Fluid part of cytoplasm surrounding organelles
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Oxidative phosphorylation
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Syntheis of ATP form ADP using energy released in the ETC
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Chem 102: Final