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60 Cards in this Set
- Front
- Back
Which amino acids favours helixes? |
Alanine, Methionine, Glutamic Acid |
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Which amino acids add a bend, are not helical, and destabilize helixes? |
Proline adds bend Lysine/Arginine and Glutamic Acid/Asparagine are not helical because of helical charge Glycine adds flexibility and destabilizes helix |
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What is the function of myoglobin? |
Oxygen storage in t muscle. Gene bonds the oxygen and is buried inside |
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What is the water entropy effect? or the hydrophobic effect? What protein is this effect common in? |
Hydrophobic side chains point into the interior. Hydrophilic side chains are on the outside and are in contact with the water. Common in globular proteins |
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What structure is involved in electron transfer and also binds to heme? It has no beta strands |
Cytochrome c, needs heme to function. 39% alpha helices, 0% beta strands |
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What is involved in vertebrate defense against foreign invaders? |
Immunoglobulin fold 47% beta stands, 5% alpha helices |
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What does ribonuclease do? What time of bonds stabilize this structure in particular? |
Breaks down(hydrolyses) RNA 26% alpha helix, 35% beta strands Disulphide bonds stabilizes this structure. |
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What are the 4 Weak Interactions? |
1. Hydrophobic effect 2. H-bonding 3. Electrostatic Interactions 4. van der Waals Interactions 5. desulphide bonds (covalent bonds) 6. binding of metals and other ligands |
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True or False: proteins are static |
False, proteins function via changes in conformation. They are dynamic and their atoms are constantly in motion |
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Ways to loss biological activity by protein denaturation |
1. heat breaks the weak interactions 2. cold, the water entropy difference at low temperature is smaller and this causes the protein to unfold 3. pH, charge repulsion at pH extremes 4. mechanical, beating egg whites 5. urea disrupts h bonding and hydrophobic interactions 6. detergents, interferes with hydrophobic effect and exposes them 7. organic solvents |
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What prevents unfolding and helps with refolding proteins? |
molecular chaperones |
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What structure is insulin? |
Quaternary |
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What proteins are not globular proteins? |
fibrous proteins |
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Where is alpha keratin found? is it soluble? |
Found in hair, feathers, and nails. It is insoluble |
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True or False: one basic and one acidic right handed helices form a left handed supercoiled rope |
True |
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What fibrous structure is found in tendons and bone matrix and has a high tensile strength? |
collagen |
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In collagen, which amino acid is found every third residue? |
glycine |
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what type of helix is found in collagen? is it right or left handed? |
Collagen helix, which is more extended. psi =-60 and phi is 160 degrees |
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what is tropocollagen? where is glycine found in this structure? |
3 left handed polypeptides form a right handed triple helix glycine is found where the 3 polypeptides meet, therefore no steric clashes |
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What is silk fibroin made up of? |
stacked antiparallel beta sheets |
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Which amino acids are found in silk fibroin? |
glycine and alanine, allows for close packing of the sheets |
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What is the difference between apoenzyme and holoenzyme? |
apoenzyme is a protein (no coenzyme) holoenzyme is a protein and a coenzyme |
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What is a catalyst? |
a substance that speeds up the rate of a chemical reaction but is not itself consumed |
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What are the six enzyme classes? |
1. oxidoreductases, transfers electrons as H or H+ 2. Transferases, group transfer from one molecule to another 3. Hydrolases, bond breakage through addition of a water 4. Lyases, addition to a double bond or helps formation of a double bond 5. Isomerases, takes a group from one molecule and put it somewhere else which creates an isomer 6. Ligases, uses ATP to form covalent bonds between carbons, sulfur, oxygen, nitogen |
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True or False: There are side reactions in enzymes Enzymes can be turned on and off |
False: no enzymes are specific and there are no side reactions True: enzymes can be regulated |
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what does a -kinase transfer? |
the transfer of a phosphate group. |
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What do proteolytic enzymes do? give examples |
Break (hydrolyze) peptide bonds in proteins Trypsin, chymotrypsin, and elastase, bind different classes of amino acids according to the size, shape and charge properties of their binding site. |
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What do chymotrypsin, trypsin and elastase recognize? |
chymotrypisn: recognizes the large aromatice amino acids, Tyr, Trp, and Phe trypsin: recognizes Lys and Arg positive charges elastase: recognize small side chains |
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True or False: hexokinase phosphorylates glucose, frustose and mannose |
true |
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Why does the free engery increase when going from substrate to product? |
energy is required to break the water so it can attach, and for the double bond to oxygen is stretched(breaking) into a single bond. |
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what is the transition state? |
is the point at which there is an equal probability of the O-H and C=O bonds reforming and new HCO3- bonds forming |
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how do enzyme catalysts speed up reactions? |
by lowering the activation energy so the activation energy of the catalyst is lower then the activation energy of the uncatalyzed |
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how does the reaction rate depend on free energy? |
the rate of the reaction (k) depend on the free energy difference between the substrate and the transition state
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What type of energy can lower the transition state? |
binding energy lowers the transition state |
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What is induced fit? |
substrate induces a conformational change in the enzyme that will bind the transition state more tightly |
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how does substrate binding effect entropy? how does this effect the transition state? |
substrate binding will reduce entropy and thus lower free energy of the transition state |
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What are the side chains in chymotrypsin active site that form a Catalytic Triad |
Histidine, Aspartic acid, Serine |
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Lewis acid-base definition |
acids donate H+ and accept electron pairs bases accept H+ and donate electron pairs |
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what does an oxyanion do? |
stabilized by h-bonding to groups in the enzyme |
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true or false: metals can help bind and orient substrates |
true |
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What does a big Ks or Km mean? What about a small Ks or Km |
Big Ks or Km means weak binding Small Ks or Km means strong binding |
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From the Michaelis Menton equation, what is the Y=mx+b equation |
Y= 1/Vo m= Km/Vmax X= 1/[S] b= 1/Vmax |
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how does pH in enzymes effect the amino acid in the active site? |
the pH might change the ionization states |
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How does the pH in enzymes effect the substrate? |
the pH might change the ionization state of the substrate |
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how does the pH effect enzymes? |
might denature enzymes |
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what are competitive inhibitors? |
inhibitor has a similar structure as the substrate and binds competitively to the same site on the enzyme as the substrate would |
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what are non-competitive inhibitors? |
Inhibitor bides a a different site from the substrate site, usually an allosteric site. Alters the conformation and prevents product from forming. Inhibitor can bind to the free enzyme or the enzyme-substrate complex. |
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what happens to Km when the binding affinities of the inhibitor to enzyme and inhibitor to enzyme-substrate complex are the same? |
There is no effect on Km if they are the same |
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What is feedback inhibition? |
The last product will be an inhibitor to an earlier reaction in a metabolic pathway. This will regulate the entire pathway. |
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What is the different between heterotropic and homotropic regulation in feedback inhibition? |
heterotropic: enzyme is regulated by molecules that are not substrate or product of the enzyme being regulated homotropic: if the substrate or product of the activity of their own enzyme regulation |
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What is the difference between sigmoidal and hyperbolic plots? |
Vo vs [S] is sigmoidal MM plots are hyperbolic (straight line) |
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what are the two conformations for allosteric enzymes? |
the t-state is low affinity the r-state is high affinity |
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Without substrate, what state will equilibrium favour? What happens when small amounts of substrate are added? If more substrate is added? |
the state will favours the T-state. Small amounts of substrate do not bind because the affinity is low. As more substrate is added, the R-state begins to stabilize because its binding |
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Which inhibitors stabilize the T-state? Which activators stabilizes the R-state? |
Allosteric inhibitors, enzyme is less sensitive to substrate Allosteric activators, enzyme is more sensitive to substrate |
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what binds O2 cooperatively? Non-cooperatively? |
hemoglobin binds O2 cooperatively myoglobin binds O2 non-cooperatively |
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True or False: inhibitors and activators bind at the substrate-binding site and do not change the conformation of the protein |
False, they bind at different sites and change the conformation of the protein |
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What is the difference between kinase and phosphatase? |
Kinase adds (or phosphorylates) a phosphate Phosphatase removes a phasphate |
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What is covalent regulation? |
reversible reaction by adding or removing phosphates |
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What are irreversible inhibitors? |
they usually form a covalent bond with an active site amino acid |
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What are zymogens? |
An inactive enzyme, that needs another enzyme for activation. ex. in the pancreas, production of inactive trypsinogen is produced. In the gut, an activating enzyme will activate this and make it into trypsin. |