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BCMB 3100 Exam One
Terms in this set (61)
Electrostatic interactions are:
Charge-charge or ionic interactions
Van der waals interactions are:
Reliant on dipoles
Hydrogen bonds between biological molecules are disrupted by water because:
Water will form hydrogen bonds with the molecules
The hydrophobic effect is the primary driving force for protein folding because:
A folded protein maximizes entropy of water
What charged groups are/is present in glycine at pH 7?
-NH3+ & -COO-
Which two amino acids are positively charged at neutral pH?
Lysine and arginine
Enzymes catalyze reactions by:
Reducing the activation energy of a reaction
Enzymes that catalyze the transfer of electrons are called:
What is the primary buffering system in blood?
A reaction will occur spontaneously if delta G is:
An enzyme will specifically bind its substrate primarily because of:
A large number of weak interactions at the active site
When an enzyme catalyzed reaction has reached equilibrium:
Rate of the forward and reverse reaction are the same and there is no net change in the concentrations of substrates and products.
The following parameter(s) of an enzyme-catalyzed reaction depend(s) on enzyme concentration:
Vmax (maximum velocity)
Km is the equivalent of:
Substrate concentration when 1/2 Vmax is reached
The following value is a measure of an enzyme's affinity for its substrate:
When a substrate concentration is MUCH greater than Km, the rate of the catalysis is almost equal to:
In conducting an experiment with a new drug, you find that regardless of the concentration of substrate, the drug is able to inhibit the enzyme activity. You are NOT likely to have a(n):
What conclusion can be drawn concerning an inhibitor if the Km is the same in the presence and absence of the inhibitor?
The inhibitor has a structure that is NOT very similar to the substrate
In this type of inhibition, the inhibitor can only bind to the ES complex to form an ESI complex:
The following type of inhibition can be overcome by increasing substrate concentration:
Identify the atoms in the peptide plane:
Which bonds are rotated to give the phi and psi torsion angles?
N-> C terminus/2,4 and 10,12
What is the charge of the peptide @ pH 10?
Which of the following amino acids is next to the K?
Which serine protease will cleave this peptide?
What is the function of carbonic anhydrase?
To speed up both the formation and decomposition of carbonic acid
Which interaction involves an induced dipole?
Van der waals
What was the significance of fred sanger sequencing insulin?
He showed that proteins had a defined structure
What's the basis of the hydrophobic effect?
Decreasing the order of water molecules, increasing entropy
What did Christian anfinsen's nobel prize-winning work on the spontaneous refolding of RNAse A mean?
That protein folding is directed by the protein amino acid sequence
Based strictly on Pauling's definition of alpha helices and beta sheets, can proline fit in the middle of an alpha helix and why/ why not?
No because proline can't satisfy the strict main-chain hydrogen bonding requirements
An individual born with a mutation that replaces the D amino acid with a N in the bohr salt-bridge. What do you think might be the result?
The individual will adapt by increasing levels of 2,3-BPG to compensate for the reduced bohr effect
The hydration of CO2 to form H2CO3 is thermodynamically uphill, meaning the reverse reaction is favorable (spontaneous). What makes the hydration of CO2 favorable in the blood?
Because of the bohr effect, oxygenated Hb absorbs protons as it releases O2. Thus, the hydration of CO2 is favorable bc of Le Chatelier's Principle.
What did catalytic antibodies prove?
That simply stabilizing the transition state of a rxn can enhance a rxn rate.
On a cold winter morning at cornell university in 1926, Dr. James Sumner noticed his urease purification had produced crystals. How did this lead to his nobel prize?
He showed that the crystals contained only protein and went on to prove that enzymes were proteins
What would be the effect of reducing the Km for an enzyme?
It would create a thermodynamic pit and decrease the rate of the catalyzed rxn
One of your fellow students freaks out and beings to hyperventilate. You try to calm him down by saying:
You are reducing the CO2 conc. In your blood. The histidine of the bohr salt bridge will be deprotonated, making the release of O2 inefficient.
Sickle Cell Anemia is a devastating disease caused by a single point mutation in the B-globin gene. If a sickle cell patient were to try and run a marathon, their cells would sickle, blocking blood flow in capillaries, causing pain and increasing the risk of stroke. Given this observation, you devide to develop a treatment option from the list below. It doesn't have to be an actual, existing treatment.
Develop an inhibitor that reduces 2,3-BPG synthesis in red blood cells
What type of inhibition kinetics would be characteristic of a transition state analog?
What is an enzyme?
An enzyme is usually a protein catalyst, although some types of RNA also function as catalysts. Catalysts enhance the rate of a chemical reaction without themselves being permanently altered.
What is an organelle?
Can be any of a number of membrane-bounded structures inside eukaryotic cells.
Which organelles are surrounded by two membranes?
Mitochondria, chloroplasts, and nuclei
How does the nuclear membrane differ from other membranes?
Nuclear membrane is not continuous. It is a set of closed membranes that come together at pores.
Trace the pathway of the formation of a secretly protein from its gene to its exocytosis from the cell.
The gene is transcribe into RNA, which is translated into the protein on ribosomes bound to the endoplasmic reticulum. The protein enters the lumen of the endoplasmic reticulum, is sequestered into transport vesicles, and moves to the Golgi complex, where the protein is modified. The protein is packaged into secretary vesicles that fuse with the plasma membrane, resulting in the exocytosis of the protein.
Common form of cytoplasmic membrane
Smooth endoplasmic reticulum
Processes exogenous chemicals
Rough endoplasmic reticulum
Membrane with ribosome attached
Site of carbohydrate addition to proteins
Facilitate communication between the rough endoplasmic reticulum and the Golgi complex
Destined for fusion with the plasma membrane
Carries important biochemicals into the cell
Contains digestive enzyme
Site of fuel oxidation
Site of photosynthesis
Location of most of the cell's DNA
Separates the inside of the cell from the outside
All weak interactions can be said to be fundamentally electrostatic interactions. Explain.
Ionic bonds, and van der Waals interactions all depend on the unequal distribution of electrons, resulting in an unequal distribution of charge.
Explain how the following statement applies to biochemistry: Order can be generated by an increase in randomness.
The statement essentially describes the hydrophobic effect. Specific complicated biochemical structures can form, powered by the increase in entropy that results when hydrophobic groups are removed from aqueous solution.
Define hydrophobic effect.
The tendency of non polar molecules to interact with one another in the presence of water. The interaction is powered by the increase in entropy of water molecules when the non polar molecules are removed from the watery environment.
Choose the single best response. Blood bicarbonate can be thought of as:
The deprotonated form of carbonic acid
What is the primary "driving force" behind how the hydrophobic effect stabilizes protein structure?
Increase in overall entropy resulting from disorganization of water.
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