Biochemistry Exam two

What is the function of a protein kinase?

A kinase is an enzyme that phosphorylates a protein using a high-energy phosphate, such as ATP, as the phosphate donor.

what level is shown by double-stranded DNA?

Double-stranded DNA is usually thought of a shaving secondary structure, unless we consider its supercoiling (tertiary) or association with proteins (quarternary).

Of what benefit is it for DNA to have thymine rather than uracil?

In DNA, cytosine spontaneously deaminates to uracil. The presence of the extra methyl group is a clear indication that a thymine really belongs in that position, not a cytosine that has be deaminated.

Give a reason for the toxicity that can be caused by overdoses of lipid-soluble vitamins.

Lipid-soluble vitamins accumulate in fatty tissue, leading to toxic effects. Water-soluble vitamins are excreted, drastically reducing the chances of an overdose.

What effect does a catalyst have on the activation energy of a reaction?

The presence of a catalyst lowers the activation energy of a reaction.

Why does a competitive inhibitor not change Vmax?

A competitive inhibitor blocks binding, not catalysis.

Why does a noncompetitive inhibitor not change the observed KM?

A noncompetitive inhibitor does not change the affinity of the enzyme for its substrate.

What is a replication fork? Why is it important in replication?

A replication fork is the site of formation of new DNA. The two strands of the original DNA separate, and a new strand is formed on each original strand.

Why does DNA with a high A—T content have a lower transition temperature, Tm, than DNA with a high G—C content?

A-T base pairs have two hydrogen bonds, whereas G-C base pairs have three. It takes more energy and higher temperature to disrupt the structure of DNA rich in G-C base pairs.

What is the difference between ATP and dATP?

ATP is made from adenine, ribose, and three phosphates linked to the 5'-hydroxyl of the ribose. dATP is the same, except that the sugar is deoxyribose.

Does the behavior of allosteric enzymes become more or less cooperative in the presence of activators?

Activators make the shape of the curve less sigmoidal.

Would you expect to find adenine-guanine or cytosine-thymine base pairs in DNA? Why?

Adenine-guanine base pairs occupy more space than is available in the interior of the double helix, whereas cytosine-thymine base pairs are too small to span the distance between the sites to which complementary bases are bonded. One would not normally expect to find such base pairs in DNA.

List the substances required for replication of DNA catalyzed by DNA polymerase.

All four deoxyribonucleoside triphosphates, template DNA, DNA polymerase, all four ribonucleoside triphosphates, primase, helicase, single-strand binding protein, DNA gyrase, DNA ligase.

What features distinguish enzymes that undergo allosteric control from those that obey the Michaelis-Menten equation?

Allosteric enzymes display sigmoidal kinetics when rates are plotted versus substrate concentration. Michaelis-Menten enzymes exhibit hyperbolic kinetics. Allosteric enzymes usually have multiple subunits, and the binding of substrates or effector molecules to one subunit changes the binding behavior of the other subunits.

Amino acids that are far apart in the amino acid sequence of an enzyme can be essential for its catalytic activity. What does this suggest about its active site?

Amino acids that are far apart in the amino acid sequence can be close to each other in three dimensions because of protein folding. The critical amino acids are in the active site.

Would you expect an irreversible inhibitor of an enzyme to be bound by covalent or by noncovalent interactions? Why?

An irreversible inhibitor is bound by covalent bonds. Noncovalent interactions are relatively weak and easily broken.

Explain how phosphorylation is involved in the function of the sodium-potassium ATPase.

As part of the mechanism, the sodium-potassium ATPase has an aspartate residue that becomes phosphorylated. This phosphorylation alters the conformation of the enzyme and causes it to close on one side of the membrane and open on the other, moving ions in the process.

What is the difference between B-DNA and Z-DNA?

B-DNA is a right-handed helix with specified dimensions (10 base pairs per turn, significant differences between major and minor groove, etc). Z-DNA is a left-handed double helix with different dimensions (12 base pairs per turn, similar major and minor grooves, etc).

Can enzyme inhibition be reversed in all cases?

Competitive inhibition can be overcome by adding enough substrate, but this is not true for all forms of enzyme inhibition.

What are the functions of the gyrase, primase, and ligase enzymes in DNA replication?

DNA gyrase introduces a swivel point in advance of the replication fork. Primase synthesizes the RNA primer. DNA ligase links small, newly formed strands to produce longer ones.

How can breakdown in DNA repair play a role in the development of human cancers?

DNA is constantly being damaged by environmental factors and by spontaneous mutations. If these mistakes accumulate, deleterious amino acid changes or deletions can arise. As a result, essential proteins, including those that control cell division and programmed cell death, are inactive or overactive, eventually leading to cancer.

Describe the discontinuous synthesis of the lagging strand in DNA replication.

DNA is synthesized from the 5' end to the 3' end, and the new strand is antiparallel to the template strand. One of the strands is exposed from the 5' end to the 3' end as a result of unwinding. Small stretches of new DNA are synthesized, still in an antiparallel direction form the 5' end to the 3' end and are link by DNA ligase.

With the concerted model, what conditions favor greater cooperativity?

Greater cooperativity is favored by having a higher ratio of the T/R form. It is also favored by having a higher dissociation constant for the substrate binding to the T form.

How can competitive and noncompetitive inhibition be distinguished in terms of KM?

In the case of competitive inhibition, the value of KM increases, while the value of KM remains unchanged in noncompetitive inhibition.

Does the behavior of allosteric enzymes become more or less cooperative in the presence of inhibitors?

Inhibitors make the shape of the curve more sigmoidal

Explain what is meant by K0.5.

K0.5 is the substrate concentration that leads to half of the maximal velocity. This term is used with allosteric enzymes, where the term KM is not appropriate.

Suggest a reason why the same protein system moves both sodium and potassium ions into and out of the cell.

Nature chooses what works. This is an efficient use of a large protein and of the energy of ATP.

Do all enzymes display kinetics that obey the Michaelis-Menten equation? Which ones do not?

Not all enzymes follow Michaelis-Menten kinetics. The kinetic behavior of allosteric enzymes does not overy the Michaelis-Menten equation.

DNA synthesis always takes place from the 5' to the 3' end. The template strands have opposite directions. How does nature deal with this situation?

One strand of newly formed DNA uses the 3'-5' strand as a template. The problem arises with the 5'-3' strand. Nature deals with this issue by using short stretches of this strand for a number of chunks of newly formed DNA. They are then linked by DNA ligase.

• Transcription

Production of RNA from a DNA template.

• Replication

Production of new DNA from a DNA template.

Why does propeller-twist occur?

Propeller-twist reduces the strength of the hydrogen bond but moves the hydrophobic region of the base out of the aqueous environment, thus being more entropically favorable.

What is homologous recombination?

Recombination that involves a reaction between homologous sequences.

What amino acids are often phosphorylated by kinases?

Serine, threonine, and tyrosine are the three most often phosphorylated amino acids in proteins that are acted upon by kinases. Aspartate is another one often phosphorylated.

Proteins, nucleic acids, and carbohydrates are grouped by common structural features found within their group. What is the basis for grouping substances as lipids?

Solubility properties (insoluble in aqueous or polar solvent, soluble in nonpolar solvents). Some lipids are not at all structurally related.

How does the structure of steroids differ from that of the other lipids discussed in this chapter?

Steroids contain a characteristic fused-ring structure, which other lipids do not.

• Translation

Synthesis of proteins directed by mRNA, which reflects the base sequence of DNA

Other things being equal, what is a potential disadvantage of an enzyme having a very high affinity for its substrate?

The ES complex would be in an "energy trough," with a consequentially large activation energy to the transition state.

Can the presence of a catalyst increase the amount of product obtained in a reaction?

The amount of product obtained in a reaction depends on the equilibrium constant. A catalyst does not affect that.

Why does the absorbance increase when a DNA sample unwinds?

The bases in a double-stranded chain are partially hidden from the light beam of a spectrophotometer by the other basses in close proximity, as though they were in the shadow of other bases. When the strands unwind, these bases become exposed to the light and absorb it; therefore, the absorbance increases.

How does DNA replication in eukaryotes differ from the process in prokaryotes?

The general features of DNA replication are similar in prokaryotes and eukaryotes. The main differences are that eukaryotic DNA polymerases do not have exonuclease activity. After synthesis, eukaryotic DNA is complexed with proteins; prokaryotic DNA is not.

Suggest a reason why animals that live in cold climates tend to have higher proportions of polyunsaturated fatty acid residues in their lipids than do animals that live in warm climates.

The higher percentage of unsaturated fatty acids in membranes in cold climates is an aid to membrane fluidity.

Why does the enzyme reaction for chymotrypsin proceed in two phases?

The initial phase releases the first product and involves an acylenzyme intermediate. This step is faster than the second part, in which water comes into the active site and breaks the acyl-enzyme intermediate.

The enzyme D-amino acid oxidase has a very high turnover number because the D-amino acids are potentially toxic. The KM for the enzyme is in the range of 1 to 2 mM for the aromatic amino acids and in the range of 15 to 20 mM for such amino acids as serine, alanine, and the acidic amino acids. Which of these amino acids are the preferred substrates for the enzyme?

The low KM for the aromatic amino acids indicates that they will be oxidized preferentially.

Explain why 50S ribosomal subunit and a 30S ribosomal subunit combine to form a 70S subunit, instead of an 80S subunit?

The numbers 50S, 30S, etc refer to a relative rate of sedimentation in an ultracentrifuge and cannot be added directly. Many things besides molecular weight influence the sedimentation characteristics, such as shape and density.

If only a few of the amino acid residues of an enzyme are involved in its catalytic activity, why does the enzyme need such a large number of amino acids?

The overall protein structure is needed to ensure the correct arrangement of amino acids in the active site.

Define processivity, and indicate the importance of this concept in DNA replication.

The processivity of a DNA polymerase is the number of nucleotides incorporated before the enzyme dissociates from the template. The higher this number, the more efficient the replication process.

For the reaction of glucose with oxygen to produce carbon dioxide and water (Glucose + 6 O2 → 6 CO2 + 6 H2O), the ΔG is -2880 kJ/mol, a strongly exergonic reaction. However, a sample of glucose can be maintained indefinitely in an oxygen-containing atmosphere. Reconcile these two statements.

The reaction of glucose with oxygen is thermodynamically favored, as shown by the negative free-energy change. The fact that glucose can be maintained in an oxygen atmosphere is a reflection of the kinetic aspects of the reaction, requiring overcoming an activation-energy barrier.

Why is the replication of DNA referred to as a semiconservative process? What is the experimental evidence for the semiconservative nature of the process? What experimental results would you expect if replication of DNA were a conservative process?

The semiconservative replication of DNA means that a newly formed DNA molecule has one new strand and one strand form the original DNA. The experimental evidence for semiconservative replication comes from density-gradient centrifugation. If replication were a conservative process, the original DNA would have two heavy strands and all newly formed DNA would have light strands.

In lipid bilayers, there is an order-disorder transition similar to the melting of crystal. In a lipid bilayer in which most of the fatty acids are unsaturated, would you expect this transition to occur at a higher temperature, a lower temperature, or the same temperature as it would in a lipid bilayer in which most of the fatty acids are saturated? Why?

The transition temperature is lower in a lipid bilayer with mostly unsaturated fatty acids compared with one with a high percentage of saturated fatty acids. The bilayer with the unsaturated fatty acids is already more disordered than the one with a high percentage of saturated fatty acids.

Succulent plants from arid regions generally have waxy surface coatings. Suggest why such a coating is valuable for the survival of the plant.

The waxy surface coating is a barrier that prevents loss of water.

Are the sequences shown in Q6 those of RNA or DNA? How can you tell?

They are DNA sequences because of the presence of thymine rather than uracil.

Which of the following lipids are not found in animal membranes?

Triacylglycerols are not found in animal membranes.

How is the turnover number of an enzyme related to Vmax?

Turnover number = Vmax / [ET]

Why can some vitamin-K antagonists act as anticoagulants?

Vitamin K plays a role in the blood-clotting process. Blocking its mode of action can have an anticoagulant effect.

What are the structural features of waxes? What are some common uses of compounds of this type?

Waxes are esters of long-chain carboxylic acids and long-chain alcohols. They tend to be found as protective coatings.

what level is shown by mRNA?

mRNA is usually considered a primary structure, as it has little other structure.

what level is shown by tRNA?

tRNA is a tertiary structure with many folds and twists in three dimensions.

In what naturally occurring nucleic acids would you expect to find A-form helices, B-form helices, Z-form helices, nucleosomes, and circular DNA?

• A-form helices: Double-stranded RNA • B-form helices: DNA • Z-form helices: DNA with repeating CGCGCG sequences • Nucleosomes: Eukaryotic chromosomes • Circular DNA: Bacterial, mitochondrial, plasmid DNA

Give the sequence on the opposite strand for ACGTAT, AGATCT, and ATGGTA (all read 5'→3').

• ACGTAT→TGCATA • AGATCT→TCTAGA • ATGGTA→TACCAT

Which of the following statements are consistent with what is known about membranes?

• Membranes contain glycolipids and glycoproteins • Lipid bilayers are an important component of membranes • Covalent bonding between lipids and proteins occurs in some anchoring motifs • Proteins 'float' in the lipid bilayers, rather than being sandwiched between them • Bulkier molecules tend to be found in the outer lipid layer

Which statements are consistent with the fluid-mosaic model of membranes?

• Some proteins and lipids undergo lateral diffusion along the inner or outer surface of the membrane • Carbohydrates are covalently bonded to the outside of the membrane • Peripheral proteins are also considered part of the membrane • Mosaic refers to the pattern of distribution of proteins in the lipid bilayer