MCAT Section 1A - Proteins

What is the key distinction between acid hydrolysis and protease treatment of polypeptides

Acid hydrolysis (heat added) is non specific and will generate many random fragments while proteases are highly specific digestion enzymes

What is the only way to increase vmax (the velocity at saturation point)

Add more enzyme to the solution

Which of these is not a way in which an enzyme can be covalently modified I) Phosphorylation 2) Glycosylation 3) Methylation 4) Dephosphorylation

All ways are correct (Trick question!)

What carboxylic acid derivative does a peptide bond form

An amide functional group

Which amino acids are easily phosphorylated and which are commonly glycosylated

Any am. acids with a hydroxyl group can be phosphorylated (serine, threonine, tyrosine), while the amide groups of glutamine and asparganine can be glycosylated

DHFR is reductase enzyme that catalyzes the production of THF from folate. The addition of what cofactors could be helpful in this reaction

Any reducing agents would be useful in complementing DHFR's function. NADH or NADPH can donate a source of electrons to reduce folate.

Given the difference in Km of Glut 2 and Glut 4 (19.4 and 4.3) respectively, what are the assumed reaction orders at physiological glucose level (7.8 mM)

Because Glut 2 Km >>> Gluc concentration it will behave like a first order reaction dependent on glucose conc while Glut 4 Km << Gluc concentration it will behave like a zero order reaction

A kinase is an example of what broad subgroup of enzymes

Because kinases transfer a phosphate group from ATP to another molecules, so therefore they are transferases

What is the difference in cooperativities of hemoglobin and myoglobin

Because myoglobin can only uptake 1 oxygen substrate molecule it can only exhibit noncooperative binding while hemoglobin exhibits positive cooperative binding

Would proline be likely to be found at the start or middle of an alpha helix

Because proline has a kinked shape, it is more likely to be found at the beginning of the alpha helix

What would likely occur to a protein that had a mutation that prevented it from forming its normal Quaternary structure?

Because the Quaternary structure stabilizes the protein by reducing surface area of the protein and bringing catalytic sites closer together, the normal function of the protein would be hindered

At intermediate pH, how do zwitterions exist in water

Because the negative and positive charges on the termini cancel, they will exist as salts in an aqueous solution

What happens to ionizable groups in amino acid under acidic conditions

Because there is an excess of H+ floating around, these groups will tend to get protonated (adding charge to basic species and removing charge from acidic species)

How do cadherin cell adhesion molecules (CAMs) differ from integrins and selectins

Cadherins are a group of glycoproteins that mediate Ca-dependent cell adhesion (and often hold similar cell types together - ie. epithelium). Integrins are proteins that have two chains called alpha and beta and are useful in stabilizing cell processes. Selectrins bind to carb molecules are are expressed on endothelial and white blood cells

What does coenzyme A specifically hold

CoA which appears in metabolism tends to bind to acyl groups

What is the difference between cofactors and conenzymes

Coenzymes tend to be vitamin derived molecules (Nad+, FAD) that help by donating functional groups or electrons while cofactors are usually inorganic minerals or ions that work to stabilize the reaction (Mg2+ ion)

What is the one L amino acid that is R in the CI - prelog system

Cysteine because its R group has higher priority than COOH

What attractive forces hold the heavy and light chains together in an IgG molecule

Disulfide linkages (tertiary structure) and non covalent interactions

What is important about the free ligand approximation for Michaelis Menten Kinetics

During calculations of initial velocity of the reaction [S] must be relatively constant. To ensure that the ES complex isn't impacting this value, the [E] should be much lower than the [S].

How does a graph of a competitive inhibitor vs. no inhibitor compare to a graph of uncompetitive inhibitor vs. no inhibitor

For competitive inhibitor, the y intercept will not change due to vmax being the same. However, the increasing Km value will increase the slope. Uncompetitive inhibitor will both decrease vmax and km which will give a constant slope but a higher y intercept

What is the difference between Gs and Gi and their signaling pathways

Gs stimulates adenylate cyclase which increases levels of cAMP while Gi inhibits adenylate cyclase

What are the advantages of an enzyme having a histidine residue?

Histidine has a pKa very close to physiological pH, which means that it frequently exists as both protonated and deprotonated and can both serve an acid/base function (ie. RNAse)

How do hydrolases and lyases differ?

Hydrolases break down a compound into two molecules with the addition of water (peptidases are one example) while lyases don't require water to break down a compound often needing to generate a double bond or ringed structure in order to work

Whats the main reason for hydrophobic residues going to the interior of the protein

Hydrophobic residues are not easily solubilized by surrounding water molecules (the solvation layer), which rearrange themselves in a specific state to maximize hydrogen bonding. Thus the entropy decreases (enthalpy not the right reason)

How are receptor tyrosine kinases an example of enzyme linked receptors

In addition to a ligand binding domain and a membrane spanning domain, RTK also has a catalytic domain that phosphorylates additional cellular enzymes (can also phosphorylate itself like with Ras pathway)

How does a beta sheet form a pleated structure?

In order to accommodate as many H-bonds as possible, residues point above or below the plane of the beta sheet

A researcher hypothesizes that Enzyme A binds the carboxylic acid moieties on an substrate. If this is valid they should see the Km (increase/decrease) from adding glutamate to the system

Increase. This would mean that the glutamate (which also has a carboxylic acid moiety) will compete with the substrate to bind to Enzyme A, raising the Km.

What is the difference between the lock and key model of enzymes and the induced fit model

Induced fit says that the shape of the active site in the enzyme becomes complimentary once the substrate begins binding most tightly at the transition state (more accepted). Lock and key says that the configuration is already predetermined beforehand

What is the mechadnism of GABA as an inhibitory neurotransmitter

It binds to ligand gated chloride channels and induces a conformational change that opens the channel

What structural protein does myosin normally interact with

It interacts with actin during sarcomere contraction but can also be involved in cellular transport

What is the kcat value measuring qualitatively speaking

It measures the number of substrate molecules turned over into product per enzyme molecule per second of time (quantitatively kcat = vmax / [E]

Does aspirin's therapeutic effects take advantage of the properties of reversible or irreversible inhibition

It permanently alters an enzyme (cyclooxygenase-1) to prevent it from making prostaglandins products that cause pain.

If a specific protein extract is purified will the specific activty increase or decrease.

It will increase because there is less "junk" around. Total activity can be calculated as mass of extract x specific activity

What is a fundamental way in which pH denatures proteins

It will interfere with ionic bonding and affect the tertiary and quatenary structure of proteins

How would the affinity of a binding protein vary that must maintain steady state concentrations by rapid binding and unbinding

It will likely have different affinities based on environmental conditions

If Enzyme A lacked an integral cofactor/coenzyme B what would it be called

It would be an apoenzyme if it was an inactive enzyme without the necessary cofactor

What is the advantage of the body secreting potentially dangerous enzymes as inactive zymogens

It's a protective measure since the zymogens (like trypsinogen which is only needed in the intenstines) have a regulatory site that must be removed or altered to expose the active site

What secondary structure does keratin have?

Keratin is a molecule arranged in the form of an alpha helix

What type of enzyme would likely be responsible for catalyzing a nucleic acid synthesis reaction

Ligases catalyze synthesis reactions generally between large similar groups

An enzyme that has a higher Km value has a lower or higher affinity to its substrate?

Lower affinity because it requires a higher substrate concentration for enzymes to be half saturated

Would we expect to find eukaryotic organisms having D amino acids

No, all amino acids used in biological organisms are found to be in the L configuration, with the amino group on the left in a fischer projection

Would trypsin be able to cleave a polypeptide if it only had negatively charged and hydrophobic residues

No, because trypsin is highly specific in cleaving positively charged amino acids such as K and R

Is collagen the structural protein commonly found in hair and nails

No, that would be keratin. Collagen is normally found as fibers in the extracellular matrix of connective tissue.

What is the subtle difference between noncompetitive and mixed inhibitors

Noncompetitive inhibitors bind equally well to the enzyme and ES complex, while mixed have different affinities for both (if inhibitor binds to ES complex more it will lower Km value by increasing affinity). Both still bind to allosteric sites

How is it possible to tell whether an effector is an inhibitor or an activator on a Lineweaver-Burke plot

Only need to look at the y-intercept. A higher Y-intercept indicates that the vmax has decreased and its an inhibitor, while a lower Y-intercept indicates the vmax has increased and its an activator

What is the difference between the pH environments where pepsin and pancreatic enzymes operate

Pepsin which works in the acidic stomach requires a pH of around 2 while pancreatic enzymes function best at a pH of around 8.5

How many dalton is 1 amino acid. What's the size of a 500 residue protein?

1 amino acid= 110 Dalton. 500 residue protein is roughly 50 kDA

What are the net products from a disulfide bond formation

2 hydrogen ions and 2 electrons

How many residues per turn in an alpha helix?

3.6 residues per turn

What is the difference between a competitive and an uncompetitive inhibitor

A competitive inhibitor competes with substrate to bind to free enzyme preventing formation of the ES substrate. An uncompetitive inhibitor binds only to ES complex. The impact of a competitive inhibitor can be overcome by adding more substrate

What is the difference between a holoenzyme and an apoenzyme

A holoenzyme are enzymes that do contain nonprotein cofactors (organic molecules or metal ions) while apoenzymes do not

What's the difference between a phosphatase and a phosphorylase

A phosphatase is a type of hydrolase that removes a phosphate group using water. A phosphorylase takes a phosphate from an inorganic source and puts it on a substrate.

What CAMs do white blood cells use in migration

Selectins and integrins

Fibroin will have how much distance per residue

Since fibroin is a beta sheet, it will have 3.5 Angstroms per residue

Why are cysteine amino acids prone to oxidation but not serine

The S-H bond is significantly weaker than the O-H bond making disulfide linkage more likely

What is meant by a homotropic inhibitor

The allosteric regulator and the substrate are the same for a particular enzyme (Ie. ATP for phosphofructokinase)

What is most likely to occur if a molecule binds to the enzyme's allosteric site

The allosteric site is away from the active site and is most often used by molecules that serve to regulate the enzyme's acitivity

What does the steady state assumption say as it pertains to enzyme kinetics

The concentration of the ES complex is constant so formation of ES = loss of Es

What is one example of a conjugated protein that forms a prosthetic group with a iron at its core and binds and carries oxygen

The heme group in hemoglobin

A molten globule would indicate what about the proteins stage in the folding process

The molten globule is a highly unstable intermediate state which will likely require more help from chaperone to fold into its proper native state

How do the isoelectric points of basic amino acids compare to negative amino acids

The pI will be much greater for basic acids compared to acidic ones

What are the biological consequences after an antibody binds to a pathogen

The pathogen is marked for destruction (opsonization) by white blood cells. Agglutination can also occur where the pathogen and antibody form large protein complexes that can be digested by macrophages

What coenzyme in DNA polymerase stabilizes the negatively charged DNA

The positively charged magnesium ion

Why would disulfide bridges be found on the exterior of the cell with separated thiol groups on the interior

There is a reducing environment (due to antioxidants) on the interior of the cell that would generate the separated cysteine residues while the exterior lacks these antioxidants

How many peptide bonds in a 20 amino acid molecule

There will be N - 1 peptide bonds for N residues, so there will be 19 amino acids

What are the structural characteristics of a G-protein coupled receptor (GCPR)

They are characterized by seven membrane spanning alpha helices

Enzymes with dehydrogenase or reductase are usually what kind of enzymes

They are typically oxioreductases which catalyze redox reactions with a transfer of electrons

How can motor proteins display enzymatic activity

They can function as ATPases that power conformational change necessary for motor function

How can the cooperativity of an enzyme be quantified

Through a value called Hill's coefficient (n) If n > 1, positive cooperativity, one bound substrate increases affinity of other substrates If n < 1, negative cooperativity, one bound substrate decreases affinity of other substrates If n = 1, no cooperative binding

How do sequences in the variable region of antibodies bind to the epitopes, or corresponding sequences on antigens

Through non covalent interactions (such as hydrogen bonding or electrostatic interactions)

Which amino acid is aromatic but relatively polar

Tyrosine because of the presence of its hydroxyl group

Contrast the ways in which urea and SDS denature proteins?

Urea interferes directly with disulfide bridges and H-bonds, while SDS disrupts noncovalent bonds to promote denaturation

What is a similarity between actin and tubulin

While actin mostly makes up microfilaments and tubulin makes up microtubules, both have a positive and a negative end (negative end usually closer to the nucleus)

At a very high pH, would a glycine molecule be negatively charged

Yes because under basic conditions side chains become deprotonated. The pH will be much greater than the pKa of both N and C termini making the C terminus negatively charged and the N terminus neutral

If we eat an egg, will the primary structure of a protein be lost

Yes, because enzymes in our bodies will digest these proteins, affecting the primary structure, however allowing our bodies to utilize these amino acids to make our own amino acids

Is there a distinction between synthetases and synthases

Yes, synthetases are part of the ligase family and usually require ATP to synthesize bigger molecules. Synthases belong to the lyase family and do not require energy

What is catalytic efficiency referring to in terms of kcat and Km

kcat/Km is the ratio referred to as catalytic efficiency. Higher catalytic efficiency will result in a large kcat or small km value

How can the Km value be found on a lineweaver burk plot

the x intercept is = to -1/km. So a decrease in km will make the x intercept more negative and shift it to the left