Biochem test 3

Describe the structure 18:1delta9cis

18 refers to the amount o carbons in the molecule
1 refers to there only being 1 double bond present
delta 9 refers to the double bond being on the 9th carbon
cis tells us that the direction of the bend

How would you rank the melting points of lipids based on their structures and explain the rankings using non-covalent interactions

I would first rank saturated lipids to have the highest melting point bc they have more carbons making them the largest with the most surface area.
- Larger molecules have stronger induced dipoles and the harder it is to brea them apart

Explain why lipids clump together in water using the principles of thermodynamics

Lipids clump together in water because it increases the entropy of the water. This does decrease the entropy of the lipids but together the overall system's entropy is increased.

What is a micelle?

fatty acids found in micelle tend to have a conical shape - the polar head group is the "fat" part of the cone and the hydrocarbon tail is the point(of the cone)

What is a vesicle?

Membrane lipids found in vesicles have 2 fatty acid "tails" and this gives them a cylindrical shape

Predict whether lipids will form micelles, bilayers, or neither and justify the prediction based on the structure and properties of the lipids

Would you expect soap molecules to form a micelle or a vesicle?
Remember soap is used to dissolve nonpolar substances like butter in water.

Soap molecules would be a micelle bc the center of a micelle is nonpolar which can trap the nonpolar substance in it while interacting with the water with its polar outside
- Vesicles have polar centers and polar exteriors so they would non work for soap.

which membrane would have more fluid characteristics- the one with more saturated fatty acids or the one with more unsaturated fatty acids?

Unsaturated fatty acids will have more fluid like characteristics bc the double bond is going to present the acid from getting close enough to form induced dipole forces (london dispersion) with another unsaturaed fatty acid

what is unique about cholesterol?

At low temps, cholesterol helps to prevent packing of the tails and keeps the membrane from freezing solid.
At high temps, cholesterol's rigid structure continues to interact with nearby lipids, keeping the membrane from melting completely

· Predict whether lipids will be used for storage or structure and justify the prediction based on the structure and properties of the lipids

· Interpret kinetic data and graphs and use the data to draw conclusions.

· Explain the principles and importance of membrane transport, including symport, and use that knowledge to interpret other types of transport.

Review Amino Acids

Do It

What is Kd?

dissociation constant for the substrate on the enzyme

What is Ki?

dissociation constant for the inhibitor to the enzyme

What is an occluded state?

one door closes before the next door opens

Figure out how to read eadie hofstie plot

What structure is this and what type of glycosidic bond does it have?

maltose (alpha 1,4 glycosidic bond)(made up of 2 glucose molecules)

lactose (beta 1,4 glycosidic bond)
- Galactose and Glucose

What structure is this and what type of glycosidic bond does it have?

Sucrose (alpha 1,2 glycosidic bond)
- Glucose and Fructose

What structure is this and what type of glycosidic bond does it have?

amylose (alpha 1,4 glycosidic bond)
- Glucose and glucose

What structure is this and what type of glycosidic bond does it have?

cellulose

What structure is this and what type of glycosidic bond does it have?

put numbers 8-15 from carbs structure activity in here

·Use the structures and properties of cellulose and amylose to propose properties and uses for other polysaccharides.

· Explain why carbohydrates are useful signaling molecules and use the examples from the Inner Life of the Cell to illustrate your answer. Apply this knowledge to other cell signaling pathways that include glycosylated proteins.

Desrcribe biochemical standard state

Temp ; 25C (298K)
Pressure: 1atm
Reactant COncentration: 1M
pH 7

What is Keq

-the equilibrium constant
-[products]/[reactants]

What is Q?

reaction quotient

reaction quotient

-measures concentrations of reactants and products at any point in time during a reaction

-looks identical to the equation for Keq

-if the rates of the forward reaction and baward reaction are equal than Q will equal Keq

What is R

gas constant (8.31)

What is delta G when a reaction is in equalibrium?

delta G is 0

What is equilibrium?

condition in the course of a reversible chemical reaction in which no net change in the amounts of reactants and products occurs.

What are the units for delta G?

J/mol

What are the units for E(reduction potential)?

V

what is n in the delta G reaction?

number of electrons transfered

competitive inhibition

inhibitor that resembles the normal substrate competes with the substrate for the active siteVmax stays the sameKm increases

Why does Vmax stay the same in the presence of a competitive inhibitor?

At high substrate concentrations, the inhibitor doesn't compete well.

Why does Km increase in the presence of a competitive inhibitor?

the apparent Km (Km') for the substrate is increased since a higher concentration of substrate is required to overcome inhibitory effects of the competitor.

uncompetitive inhibition

the inhibitor binds only to the enzyme-substrate complextemporarily locks substrate in enzyme preventing its release (increasing affinity b/w enzyme and substrate so it lowers Km)Lower Km and vmax

Why do both Km and Vmax lower when an uncompetitive inhibitor is present?

Uncompetitive inhibitors can only bind to the ES complex. Therefore, these inhibitors decrease Km because of increased binding efficiency and decrease Vmax because they interfere with substrate binding and hamper catalysis in the ES complex.

mixed inhibition

inhibitor binds to allosteric site in either enzyme or enzyme-substrate complex

vmax decreases

If inhibitor binds to enzyme, it increases Km (lowers affinity)

If inhibitor binds to enzyme-substrate complex, it lowers Km (increases affinity)

So overall the Km stays the same

A noncompetitive has ----- affinity for both free enzyme and the ES complex?

equal

How do you know when an inhibitor is competitive or not competitive?

If it looks like the substrate than its competitiveIf it doesn't look like the substrate than its not competitive

How can you identify the substrate, enzyme, and the active site on a wierd picture like #1 on the enzyme catalysis skill excercise?

Where you have the most interactios to a spot. The spot is the substrate. The others are the active site and the lines is the enzyme

Why does the Km decrease in the presence of an uncompetitive inhibitor?

Km decreases with increased presence of ES complex. Uncompetitive inhibitors bind only to the ES compexes, locking them in place and preventing them from seperating. This means that there are more ES complexes present in the presence of an uncompetitive inhibitor at any given time, then if there was no inhibitor*Drawing with substrate in enzyme and inhibitor blocking substrate to leave like jail bars

M-M and Lineweaver-Burke plot for competitive inhibition

Lineweaver-Burke plot for mixed inhibition

Lineweaver-Burke plot for uncompetitive inhibition

what is delta G knot'?

delta G at standard conditions
- It is measured at eq. concentration of reactants and products

What is delta G

Delta G is the free energy change associated with something.
- Not measured at eq. concentrationsof eactants and products

What is the relationship between K and Q?

Q>K is a reverse reaction
Q

What is glycolysis?

the breakdown of glucose by enzymes, releasing energy and pyruvic acid.

What is gluconeogenesis?

synthesis of glucose

Phosphylation

addition of a phosphate group

dephosphorylation

removal of a phosphate group

Tautomerism or isomerism

Compounds with the same chemical formula that differ in the arrangement of their atoms.

Decarboxylation

the removal of CO2.

kinase

an enzyme that catalyzes the transfer of a phosphate group from ATP to a specified molecule.

What are isozymes or isoforms?

Enzymes that are not the same but catalyze the same reaction

What is Km?

Substrate concentration at 1/2 Vmax

Where does pyruvate produced by glycolysis go?

pyruvate dehydrogenase to form acetyl coA
or it makes lactate in the muscles

· Explain the mechanism of complementary regulation of glycolysis and gluconeogenesis by fructose-2,6-bisphosphate

PFK-1 turns ATP into ADP which results in FPBase-1 in glycolysis and in gluconeogenesis FPBase-1 continues the reverse reaction without PFK-1. They are coordinated becasue PFK-1 is an irreversible reaction but FPBase-1 can bypass this reaction in gluconeogenesis with the help of the "new" enzyeme PFK-1.

· Explain why regulation occurs at the irreversible (far-from-equilibrium) steps of glycolysis and gluconeogenesis

Regulation occurs at irreversible steps to ensure whichever product is needed is produced. If glycolysis and gluconeogenesis were completley reversible reactions than no real product would be produced.

Predict the effects of cellular concentrations of glucose, glucose-6-phosphate, ATP, ADP, and AMP on glycogen metabolism

Insulin Function

lowers blood glucose levels

Identify near-equilibrium and far-from-equilibrium reactions in glycolysis and explain, using thermodynamics, why far-from-equilibrium reactions do not run in reverse

Far from equilibrium reactions do not run in reverse because their products are quickly becoming reactants for the next step of glycolysis

Alpha is

both up or both down

Beta is

one up and one down

Symport

A membrane transport process that carries two substances in the same direction across the membrane.

Antiport

A membrane transport process that carries one substance in one direction and another in the opposite direction.

Competitive Inhibition

What type of inhibition is this

Competitive inhibition

What type of inhibition is this?

Uncompetitive inhibition

Uncompetitive inhibition

What type of inhibition is this?

Mixed Inhibition

Mixed Inhibition