BME 201 EXAM 1

In a typical eukaryotic cell the pH is usually around 7.4. What is the [H+] in a typical eukaryotic cell?

4e-8 M

When the ligand concentration is equivalent to Kd, what percentage ligand binding sites are occupied

50%

What is a prosthetic group of a protein?

A nonprotein structure that is permanently associated with the protein

Which one of the 20 standard amino acids is not optically active & why?

Glycine, its side chain is a hydrogen atom

Which amino acid in hemoglobin is involved in coordinating iron in addition to the heme prosthetic group?

Histidine

What is true about living systems?

can convert chemical energy from one form to another maintain a more-or-less constant composition exist in a dynamic steady-state (NOT necessarily in equilibrium with their surroundings)

Prosthetic groups of glycoproteins are composed of:

carbohydrates

Conversion of CO2 in the blood into the more soluble form of HCO3- is catalyzed by which enzyme?

carbonic anhydrase

The formation of a peptide bond between two amino acids is an example of a(n) _____ reaction.

condensation

The fundamental cause of sickle-cell disease is a change in the structure of:

hemoglobin

What does a protein's function depend on that can be experimentally determined?

its primary structure

Primary structure

sequence of amino acids

Which organelle is NOT found in plant cells?

lysosome

Proteins may be isolated and purified on the basis of:

solubility size and shape charge

Myoglobin and the subunits of hemoglobin have:

very similar tertiary structures, but different primary structures

Which structural level is MOST important to protein structure and function

primary

For the study of a protein in detail, an effort is usually made to first:

purify the protein

Highly elongated cells usually have lengths and diameters in the range of:

0.3 um to 100 um

steps for protein sequence determination

1. Cleave disulfide bonds and separate polypeptide chains 2. Apply chemical or enzymatic methods to generate small peptides 3. Determine the sequence of each peptide 4. Use the overlapping sequences to reconstruct the sequence of each polypeptide

Roughly how many amino acids are there in one turn of an α helix?

3.6

What is true about amino acids?

All of the 20 common amino acids are α−amino acids Amino acids differ from each other in their side chains

The interactions of ligands with proteins:

Are usually transient (short/impermanent)

Which statement comparing hemoglobin and myoglobin is NOT correct? A. Hemoglobin and myoglobin both contain the heme prosthetic group. B. Hemoglobin binds to O2 cooperatively, while myoglobin does not. C. Hemoglobin has a stronger binding affinity for O2 than myoglobin does. D. Hemoglobin is a multisubunit protein, while myoglobin is not. E. Hemoglobin and myoglobin are both primarily composed of α helices.

C.

Which molecule binds MOST strongly to the heme iron?

CO

Which reagent cleaves proteins on the carboxyl side of methionine?

Cyanogen Bromide

True or false: Proteins always consist of a single polypeptide chain

False

True or false: Proteins that have similar functions in different species usually have different amino acid sequences.

False

True or false: For a cell placed in a hypertonic solution one would expect water to move into the cell and the cell to swell and/or burst.

False

True or false: The amino acid residues in protein molecules exist as both D or L stereoisomers.

False

True or false: H bonds can form only between water molecules

False

True or false: Both myoglobin and hemoglobin are equally suited to serve as oxygen carrying (transport) proteins in the bloodstream.

False (describe functions of each)

True or false: Electrospray ionization generates positively charged protein ions from the protonation of amino acids with acidic side chains, which are aspartate and glutamate.

False (find out what is true)

Formic acid has a pKa of 3.75; acetic acid has a pKa of 4.76. Which is the stronger acid? Which has a greater tendancy to lose its proton?

Formic acid has a greater tendency to lose its proton than acetic acid, and formic acid is the stronger acid (lower pKa = stronger acid --> higher tendency to lose proton)

How is an amino acid sequence of a protein or peptide generally reported?

From the N-terminal end to the C-terminal end

Which fractioning procedures separate proteins according to their molecular weight?

Gel filtration chromatography & SDS-PAGE

Why is carbon monoxide toxic to humans?

It binds to the Fe in hemoglobin and prevents the binding of O2.

What does the molecule SDS do to proteins?

It denatures large portions of proteins and distributes a large negative charge throughout the protein.

Qualities of 2,3-bisphosphoglycerate (BPG)

It is an allosteric modulator. It binds at a distance from the heme groups of hemoglobin. It binds with lower affinity to fetal hemoglobin than to adult hemoglobin. It is normally found associated with the hemoglobin extracted from red blood cells. (It does NOT increase the affinity of hemoglobin for oxygen.)

What is true of the process of spontaneous folding of proteins?

It may involve... initial formation of local secondary structure; initial formation of a highly compact state. a gradually decreasing range of conformational species. be defective in some human diseases. It is NOT an essentially random process.

Which bonds have freedom of rotation?

N - Cα Cα - C R - Cα (C - N does not because it doesn't have an alpha carbon)

What partial charge does the oxygen atom in water have?

Negative

What amino acids have negatively charged side groups? Which have positively charged side groups?

Negative: aspartate (Asp, D) & glutamate (Glu, E) Positive: lysine (Lys, K), arginine (Arg, R) & histidine (His, H)

When energy is used by a system, can it be "used up"?

No, energy can be converted into kinetic and potential energy.

Why can only some amino acids be used to measure protein concentration based on absorption of UV light?

Only some amino acids are aromatic.

What is the major reason that antiparallel β-stranded protein structures are more stable than parallel β-stranded structures?

Parallel β-stranded structures have weaker hydrogen bonds laterally between adjacent strands.

Which interactions are NOT considered to be "weak" in proteins?

Peptide bonds

How does specific activity differ from activity?

Specific activity is the activity per total amount of protein (e.g. enzyme units per mg of protein)

As Kd decreases, what happens to the binding affinity between the receptor and ligand?

The binding affinity increases

Describe the Bohr effect

The change in hemoglobin-binding affinity for oxygen due to changing pH and CO2 concentration in the blood

True or false: Amino acid side chains (R groups) within a beta sheet configuration protrude outward from the sheet alternating in an up and down direction.

True

True or false: Each hydrogen atom water bears a partial positive charge

True

True or false: H bonds are relatively weak compared to covalent bonds

True

Why is severe dehydration potentially life-threatening?

Water . . . is a solvent for many biomolecules is a chemical participant in many biological reactions is necessary for buffering action in the body its attraction to itself drives hydrophobic interactions

Does Hemoglobin's affinity for oxygen decrease with decreasing pH yielding a rightward shift in the oxygen binding curve?

Yes

Is a tertiary structure described for all proteins?

Yes

All of the 20 common amino acids contain an R-group that is attached to the:

alpha carbon

Proteins are polymers made up of monomers known as:

amino acids

Selective precipitation of a protein from a crude extract is MOST effective by which molecule?

ammonium sulfate

An allosteric interaction between a ligand and a protein is one in which:

binding of a molecule to a binding site affects binding properties of another site on the protein.

An increase in the entropy of a system can be described as an increase in the total amount of ________ of a system.

disorder

If heat energy is absorbed by the system during a chemical reaction, the reaction is said to be:

endothermic

The major difference between prokaryotes and eukaryotes is that:

eukaryotes have a nucleus, while prokaryotes do not

If the free energy change ΔG for a reaction is -46.11 kJ/mol, the reaction is:

exergonic

The amino acid substitution of Val for Glu in Hemoglobin S results in aggregation of the protein because of _____ interactions between molecules.

hydrophobic

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

The chirality of an amino acid results from the fact that its alpha carbon...

is bonded to four different chemical groups

In hemoglobin, the transition from T state to R state (low to high affinity) is triggered by:

oxygen binding

Secondary structure

particular stable arrangements of amino acid residues

Water derives all its special properties from its:

polarity and hydrogen-bonding capacity

Long-range interactions between residues on a single polypeptide chain could BEST be classified as _____ structure.

tertiary

Quaternary structure

the arrangement of component polypeptide chains in space for a protein that has two or more polypeptide subunits

What are the two major factor that determine protein conformation?

the formation of the maximum number of hydrogen bonds and ionic interactions the placement of hydrophobic amino acid residues within the interior of the protein

Where are the R groups on the amino acid residues in an α helix found?

the outside of the helix spiral

A Hill coefficient (nH) of 2 indicates that:

there is positive cooperativity in ligand binding.

Tertiary structure

three-dimensional folding of a polypeptide chain