Biochem Test 2 Flashcards
Which of the following would be the best definition of the primary structure of a protein?
- Repetitive arrangement of amino acids that are near each other in the linear sequence.
- Association of protein subunits.
-Overall folding of a single chain that can include α-helical and β sheet structures.
- Linear amino acid sequence.
Linear AA sequence.
What would be the best definition of the tertiary structure of a protein?
Overall folding of a single chain that can include alpha helical and beta sheet structures.
According to Anfinsen’s experiment, although ribonuclease has enzymatic activity after the removal of urea and BME, the renatured ribonuclease molecules can be distinguished from the native ribonuclease.
True or False?
False
Because renaturated ribonuclease CANNOT BE DISTINGUISHED from the native form after refolding.
It would regain the same structure and enzymatic activity as the native form.
Tell me about Peptide bonds
Tell me about the Alpha helix structure of proteins
It can serve a mechanical forming stiff bundles of fibers in some proteins, such as keratin.
Alpha helices are stabilized by hydrogen bonds between nearby residues.
(Pro and Gly break up the alpha helices because they do not readily fit into the regular helical arrangement).
The α helix found in fibrous proteins is right-handed, while the α helix found in globular proteins is left-handed?
True or false
False.
the α helix found in both fibrous and globular proteins is typically right-handed. left handed alpha helices are very rare in nature.
What is the secondary structure of Protein?
The hydrogen bonds formed between atoms of the polypeptide backbone.
In parallel β sheets the H-bonded strands run in opposite directions resulting in linear, stronger H-bonds.
True or False
FALSE
parallel beta sheets run in the same direction, makes them bent, weaker H Bonds
anti parallel beta sheets run in opposite direction, makes them linear, stronger H bonds.
α -helix has
3.6 amino acid residues/ turn.
3.4 amino acid residues/ turn.
3.8 amino acid residues/ turn.
3.0 amino acid residues/ turn.
3.6 AA residues/turn
Chaperone proteins facilitate correct folding pathways or provide a micro environment in which folding can occur.
TRUE or FALSE
TRUE!!!
Which binds most tightly to the iron of a heme-containing protein?
one CO molecule
which about hemoglobin is incorrect?
The binding site in the deoxy-form of hemoglobin contains Fe(II).
Hemoglobin has both a quaternary structure and prosthetic groups.
Hemoglobin irreversibly binds O2.
Hemoglobin is a heme-protein.
Hemoglobin irreversibly binds O2
Which of the following statements about myoglobin is incorrect?
- The P50 of myoglobin is lower than the P50 of hemoglobin.
- Myoglobin possess a complex secondary and tertiary conformation.
- The primary sequence of myoglobin is almost identical to the primary sequence of the hemoglobin polypeptides.
- Myoglobin is a main oxygen storage protein.
The primary sequence of myoglobin is almost identical to the primary sequence of the hemoglobin polypeptides.
What is the binding of Myoglobin?
myoglobin can either be bound to oxygen (oxymyoglobin) or not (deoxymyoglobin).
What is not true regarding hemoglobin?
At high altitudes, cells produce more 2,3-BPG to promote the unloading of more O2 to the tissues.
As pO2 increases, the probability that remaining binding sites will have O2 bound also increases.
The sigmoidal shape is a consequence of the 4 subunits of the hemoglobin “cooperating” in the binding of O2.
Hemoglobin affinity for O2 is independent of pH.
Binding of hemoglobin to O2 is a typical example of a positive homotropic regulation.
Hemoglobin affinity for O2 is independent of pH. This is not true
“hemoglobin’s affinity for oxygen is directly affected by pH levels”
In the binding of oxygen to myoglobin, the relationship between the concentration of oxygen and the fraction of binding sites occupied can best be described as:
Hyperbolic
In the binding of oxygen to hemoglobin, the relationship between the concentration of oxygen and the fraction of binding sites occupied can best be described as:
Sigmoidal.
Decreased elimination of CO2 from the body causes pH to __________ and can result in __________ .
Decrease, acidosis
How many possible coordination bonds can the Fe2+ in the heme group form?
6
Which of the following is true regarding the binding of hemoglobin to O2?
The T state has a higher affinity for O2.
Conformational change from the T state to the R state involves breaking ion pairs between the α1-β2 interface.
Oxygen binding triggers the R to T conformational change.
The R state has a lower affinity for O2.
The binding of O2 to hemoglobin is non-specific.
Conformational change from the T state to the R state involves breaking ion pairs between the α1-β2 interface.
A decrease in pH causes a greater release of O2 from hemoglobin. This is due to a change in conformation in the molecule of hemoglobin and a “left-shifting” of the O2-hemoglobin binding curve.
True or False
False
A decrease in pH actually causes a RIGHT-SHIFT of the oxygen-hemoglobin binding curve, leading to a greater release of oxygen from hemoglobin, NOT A LEFT SHIFT, this phenomenon is known as the Bohr Effect
What is the role of an enzyme-catalyzed reaction?
To increase the rate at which substrate is converted into product by decreasing Delta G
Which one of the following statements is true of enzyme catalysts?
Their catalytic activity is independent of pH.
They are generally equally active on D and L isomers of a given substrate.
They can increase the equilibrium constant for a given reaction by a thousand fold or more.
They can increase the reaction rate for a given reaction by a thousand-fold or more.
They can increase the reaction rate for a given reaction by a thousand-fold or more.
NAD+, FAD+ are
coenzyme
Which of the following will be true regarding enzymes saturated with substrate?
Increasing the substrate concentration will appreciably increase the reaction rate.
An enzyme with lower Km is more easily saturated than an enzyme with high Km.
An ideal enzyme would have a very low Kcat
Any excess substrate will shift the equilibrium towards the product end of the reaction.
An enzyme with lower Km is more easily saturated than an enzyme with high Km.
BECAUSE
a lower km indicates a higher affinity for the substrate
The number of molecules of substrates converted to product per enzyme molecule per second is called the…
Turnover number (kcat)
Enzymes __________________ the free energies of reactants/products therefore ___________________ the equilibrium of the reaction.
do not change/ do not change
Which of the following is true about Michaelis-Menten kinetics?
It assumes covalent binding occurs between enzyme and substrate.
It describes single substrate enzymes.
Km, the Michaelis constant, is defined as that concentration of substrate at which enzyme is working at maximum velocity.
Km, the Michaelis constant is defined as the dissociation constant of the enzyme-substrate complex
It describes single substrate enzymes.
Put the steps of an enzymatic reaction in the right sequence of events
- Substrate approaches active site
- Enzyme-substrate complex forms
- Substrate transformed into products
- Products released
- Enzyme recycled
In a Lineweaver-burk plot, the Y-intercept is …
1/Vmax
Zn2+, Mg2+, Mn2+, and Fe2+ are
Co factors
What are the classification of Enzymes
- Oxidoreductases: Transfer of electrons
- Transferases: group transfer reactions
- Hydrolases: Hydrolysis reactions (transfer of functional groups to water)
- Isomerases: transfer of groups within molecules to yield isomeric forms
- Lyases: Cleavage of c-c, C-O, C-N, or other bonds by elimination, leaving double bonds or rings, or addition of groups to double bonds.
- Ligases: formation of C-C, C-S, C-O, and C-N bonds by condensation reactions coupled to cleavage of ATP or similar cofactor
Tell me about enzymatic catalysis
- They do not effect equilibrium
- Slow reactions are slow because of large Delta G (energies of activation)
- Enzymes increase reaction rates (k(small k)) by decreasing Delta G. The enzymes helps get to the equilibrium faster!
About Eznymes…
-They lower aE
-They catalyze reversible reactions
-They do not change overall energy
-They do not change equilibrium concentrations
-They speed up a chemical rxn by decreasing the aE of a reaction.
Difference between the two models
Lock & Key Model
- Binding is favorable
- must bend both E & S
- poor enzyme
Induced Fit Model
- Binding still favored
- transition state is least costly
- non covalent interactions btwn transition state S & E pay for this.
