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Block 1 - MBOD - 8/31/06


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What is an essential component of energy usage and metabolism?
ATP's production linked to the _________ of food.
What is NAD?
What is another name for what NAD serves as?
Enzyme Cofactor
When NAD is reduced you get what?
What is NAD involved in primarily?
Electron transport chain
What is produced via the ETC?
What is the name of another version of NAD that has a phosphate added, and what is this other compounds primary function?
NADP is the compound, and its primary involvement is as a reducing agent, which means it gets oxidized
What else is NADP involved in?
It is involved in biosynthesis
FAD is what?
Another important compound that gets reduced
NAD and FAD have adenine and sugar ________ connections.
What does FAD do?
It is a compound that we reduce via NAD and then it transfers its electrons.
ATP is involved in many different things. Name 3 ATPases that in part produce ATP
Sodium ATPase, Calcium ATPase, and Myosin ATPase
These ATPases function where (99% of the time)?
In the mitochondria
If you are measuring oxygen consumption, what are you really measuring?
ATP production
Where does most ATP production occur, and is oxygen involved?
Most occurs inside the mitochondria. This occurs aerobically
Is ATP produced anywhere outside the mitochondria, and if so, is oxygen involved?
ATP is produced outside the mitochondria, and when this occurs it is done anaerobically
What are all enzymes?
Catalysts are or are not consumed in a reaction?
They are not consumed in reaction
What is the major function of catalysts?
To allow things to occur very rapidly
Could most reactions that occur with enzymes work without enzymes, and if they could, how would they do this?
Most could occur, but many would take weeks to months to occur without enzymes
Are all enzymes proteins?
The vast majority are, but there is evidence now that ribozymes work catalytically and are not proteins
How do enzymes work?
They lower the activation energy, and in doing so this increases the rate of reaction
So what's the difference between bioenergetics and kinetics?
Bioenergetics says if the reaction will occur, while kinetics says how fast it will occur
Do enzymes change the equilibrium constant?
Will a reaction that is irreversible become reversible if an enzyme is used?
Do enzymes have high or low specificity?
Very high specificity
Specificity refers to what do things?
The kinds of reactions enzymes catalyze as well as how substrate specific they are
Do enzymes require anything else to function?
Oftentimes, they require coenzymes
What are coenzymes?
Many are vitamins
What are 3 examples of coenzymes?
NAD and FAD are examples, as well ATP, which is thought of as a vitamin
Is allosteric regulation used in enzymes?
Yes. For example, hormones use this type of regulation
What are Ribozymes?
They are one of the few if not only things that are enzymes but not proteins, and they act as enzymes
How do they work?
They are bits of RNA's that have the ability to catalyze a limited number of reactions
On the surface of the enzyme, what is the region called that the substrate binds to?
The active site
What is this new thing called once they've hooked up?
Enzyme-substrate complex
Now what happens?
The ES complex catalyzes the reaction
What are enzyme inhibitors?
They are things that bind to the enzyme to prevent it from working
What is an example of an enzyme inhibitor?
Many drugs are enzyme inhibitors
Once the substrate binds, then the _______ occurs.
After the catalysis occurs, you form what?
A product, known as an enzyme substrate complex (EP)
What happens to these two things?
The product is released and the enzyme is released
Can the enzyme be used over again?
Yes, in fact, what often happens in metabolism is you can have one compound converted into another, and then a second, into a third, and fourth, until you get the product you want
What happens if you heat a molecule kinetically?
It can allow the molecule to obtain enough energy to reach over the energy barrier. It doesn't lower it though.
What are the 6 major classes of reactions?
Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, and Ligases
What are oxidoreductases?
They involve oxidations and reductions, and with these are a transfer of electrons
How common are oxidoreductases?
They are very common
What are transferases?
They transfer functional groups
What are hydrolases?
They catalyze cleavages via water
Lyases do?
They are responsible for the addition of a group across a double bond, ie. forms a double bond.
What are isomerases?
They allow production of isomers
What are ligases responsible for?
They form bonds between things using energy derived from ATP
What is the surface element called on enzymes that the substrate binds to?
Active site
Once its bound, what does it form?
An enzyme substrate complex
How does the substrate know to bind there?
The site has a 3D conformation to allow it to bind
This site is made up of what?
Amino acid sidechains
When a protein folds up, and it brings the amino acid sidechains together, what does it form?
A pocket or active site
The kinds of residues found on the active are dependent on what?
They are dependent on the nature of the substrate
If we have a positively charged substrate, what we will have somewhere on the active site?
An electrically charged residue
Is binding dependent on pH?
What is an alternative to the lock and key theory?
It is clear that very often when a substrate binds to the enzyme, it may cause a conformation change in the enzyme
How is it supposed glucose does this?
Once glucose binds to the active site, parts of the chain (on active site) will move
How is the idea of conformation change in enzyme function related to mutation?
Any mutation in a protein, which changes an amino acid, may affect folding, ability of the substrate to bind, and the conformation, and this may lead to a prevention of the correct conformation, so it may look like minor changes in the amino acid may mess up the ability of the acid to function
Where do cofactors bind if they exist?
They bind where the enzyme substrate complex is
When the substrate is bound with cofactors, what does the enzyme do?
It catalyzes the change in substract to the product
Where is glucokinase found, and what does it do?
It is found in the liver and pancreas, and is responsible for converting glucose to glucose-6-phosphate
Whats the difference between glucokinase interacting with glucose and interacting with galactose
Glucokinase does not react with galactose because it has an added hydroxyl group at carbon 4 which is oriented towards where galactose would hydrogen bond with glucokinase
What does trypsin do?
It hydrolizes peptide bonds in digestion
What does trypsin work on?
Lysine or arginine
What does this show?
It is highly specific, an dhydrolizes many proteins, and is highly specific for the type of bond in a protein
What is a model classical curve for a pH curve?
It shows there is no activity at low or high pH, but in the middle you have maximum activity
What is the top activity level called?
pH optima
What are high ends to this maximum pH range?
Some go as high as 10, and some are lower
What is a functional example of why this doesnt work pertaining to carboxyl groups and low pH?
If an enzyme required charge from a carboxyl group, it wouldn't function at low pH because the carboxyl would be deprotonated

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