BioChem Exam 2 - Other Tests

evan406's version from 2016-03-23 19:26

Test Questions

Question Answer
Describe the concept of “induced fit” in ligand-protein binding.-Induced fit refers to the structural adaptations that occur when a ligand binds to a protein.

-This often involves a conformational change in the protein that alters the binding site to make it more complementary to the ligand.
Describe in detail the three different ways enzymes function as catalyst.1) Binding energy: Small interactions that are formed upon substrate binding and transitions state formation lower the free energy barrier.

2) Covalent interaction: Covalent binding of the substrate or reaction intermediates provide the possibility of an alternative reaction mechanism with a lower free energy barrier.

-The metal site is distorted to resemble the transition state and is already higher in energy.

-only the substrate binding is needed to complete the transitions state structure.

-This has now become a step with a very low energy barrier.
One of the post-translational modifications that can happen to a protein is proteolytic cleavage. Explain in detail why this is an important process.There are two main reasons why parts of proteins are removed.

- Several groups of proteins contain signal sequences that help with targeting these proteins to the different locations in higher cells.

- most of the time the signal sequence is removed when the protein arrives at its destination.

2) It is a way to activate enzymes.


Question Answer
Some proteins fold spontaneously, others need help with the folding, which is known as assisted folding. Describe shortly the different processes and/or systems involved in assisted folding.-The protein disulfide isomerase catalyzes the interchange or shuffling of disulfide bonds

-Peptide prolyl cis-trans isomerase catalyzes the interconversion of the cis and trans isomers of Pro peptide bonds

-Chaperones bind to the unfolded amino acid chain and prevent folding of these parts of the chain until the whole chain has been synthesized

-Chaperonins are large barrel shape protein complexes that when the unfolded protein is inserted a protected environment is provided for the protein to fold properly
Different steps for the ubiquitination of proteins to be degraded1) ubiquitin-activating enzyme (E1) attaches via ATP-dependent formation of thioester bond to C-termini of ubiquitin

2) ubiquitin-carrier protein (E2) picks up ubiquitin

3) E3 selects a protein for degradation by the nature of the N-terminal amino acid

4) ubiquitin-protein ligase (E3) transfers ubiquitin to free amino groups on the protein

5) multiple ubiquitinations may occur on a protein substrate

Use the curves to estimate the partial pressure of oxygen at 50% saturation for hemoglobin and myoglobin.

Which protein has a higher affinity for oxygen?

hemoglobin: KM = 28 pO2;
myoglobin: KM = 2 pO2

Myoglobin has a smaller KM. This means that 50% saturation is achieved at lower pO2 and therefore myoglobin has a higher affinity for oxygen.


Question Answer
Explain how a person with the sickle cell trait is protected from dying after a malaria infectionThere are two effects.

-The oxygen level in infected blood cells goes down due to the metabolism of the malaria parasite.
-hemoglobin S molecules bind to each other and form long fibers that deform the cell (sickle shape).
-cells are removed from the blood stream and destroyed.

-Hemoglobin S is more prone to form super oxide radicals than hemoglobin A.
-The super oxide radicals and other reactive oxygen species are lethal for the malaria parasites
Describe in detail the role of the GroEL/GroES complex in protein folding1) The cycle starts with the binding of the substrate protein to the rim of the cavity on one ring of the GroEL complex (this becomes the ‘cis-ring’)

2) ATP is bound to the equatorial domains of the same ring

3) GroES binds to the cis-ring and the substrate protein is transferred into the ring cavity

4) ATP is hydrolyzed, causing the conformational change in the ring proteins exposing the hydrophilic surfaces

5) The substrate proteins is (partially) folded

6) A new substrate molecule binds to the trans-ring

7) ATP binds

8) Folded products and ADP are released from cis-ring

9) A new reaction cycle starts

Remaining topics on study guide

Question Answer
Post-translational modifications at the C-terminus1. Amidation
Common in peptides/peptide hormones
-Enabling full activity
-Protects against breakdown

2. Prenylation
-Attachement of an isoprenoid: farnesyl diphosphate or geranylgeranyl diphosphate
-Anchor for membrane proteins

3. GPI anchor
-Glycosyl Phosphatidylinositol
-Anchor for membrane proteins
Post-translational modifications of individual amino acids1.Glycosylation

2. Phosphorylation
-Controls the activity of many proteins by switching them on and off via conformational changes

3. Hydroxylation

4. Sulfation
-In membrane and secreted proteins
-Strengthening protein-protein interaction by the
introduction of a negatively charged highly polar group

5. Attachment of lipids

6. Attachments of prosthetic groups


Question Answer
What is Tm?
The midpoint of the curve corresponds to the melting temperature Tm, where [Folded] = [Unfolded]
Function of proteasomedeubiquitination
Lock-key modelThe protein acts as a lock and the ligand acts as the key. In this model The ligand fits perfectly into the protein. The induced-fit model is more accurate.
What is θ?θ=binding sites occupied/total binding sites
What is Kd?Kd=1/Ka


Question Answer
Why can’t we transport O2 freely in the blood?Oxygen is poorly soluble in aqueous solutions and cannot be carried to tissues in sufficient amounts if it is simply dissolved in blood serum.

Diffusion of oxygen through tissues is also ineffective over distances greater than a few millimeters.
Reactive oxygen speciesex: highly reactive hydroxyl radical (OH)
excessive formation can cause damage and mutations to cells and DNA
ΔG'° and equilibriumΔ𝐺′°=−𝑅𝑇𝑙𝑛𝐾𝑒𝑞′
biochemical standard free energy change at pH 7.0
difference in energy levels between the reactant and product
ΔG‡change in energy between ground state of reactant and transition state


Question Answer
What is a catalyst?Catalysts enhance reaction rates by lowering activation energies
Transition state vs. reaction intermediateTransition state - At the top of the energy hill is a point at which decay to the S or P state is equally probable

Reaction intermediate - is any species on the reaction pathway that has a finite chemical lifetime
kcat and catalytic efficiencykcat=k value of rate limiting step
Catalytic efficiency= kcat/Km
Irreversible inhibitioninhibitors that bind covalently with or destroy a functional group on an enzyme that is essential for the enzyme’s activity.