MBIO Lecture Exam 1

In what year did Francis Crick propose the scheme that underlies information processing at the level of gene expression?

1958

The protonated amino group of an amino acid will lose a proton when the pHpH approaches

9

Complete the passage about matrix‑assisted laser desorption/ionization time‑of‑flight, or MALDI‑TOF, mass spectrometry.

A MALDI‑TOF mass spectrometer uses a laser beam to vaporize the protein sample, which is embedded in a volatile matrix. Collisions between the gaseous protein molecules ionize the sample. An electrostatic potential accelerates the ions through the flight tube toward the detector, and the lightest ions arrive at the detector first.

Identify the true statements regarding disulfide bridges (disulfide bonds).

A disulfide bridge forms between two cysteine residues. Disulfide bridges have a stabilizing effect on proteins. Disulfide bridges can exist between two amino acid residues on different chains.

Which statements about peptide bonds are true?

A tripeptide contains three amino acid residues. Peptides are polymers of amino acids.

Which statement on the amino acids found in proteins is true?

All contain a central α carbon and the majority are dipolar ions, or zwitterions, at physiologic pH.pH.

Complete the description of Christian Anfinsen's ribonuclease A renaturation experiment.

Anfinsen started with purified ribonuclease A inits native state. To begin, he treated it with β‑mercaptoethanol and 8M urea. This process resulted in denatured ribonuclease A protein. Next, he removed the urea and β‑mercaptoethanol resulting in oxidation of S−H bonds,which allowed ribonuclease A to return to its native state.

Which amino acid would be positively charged at physiological pH?

Arg

What do α helices and β sheets have in common?

Both are stabilized by hydrogen bonding involving carbonyl oxygens and amide nitrogens.

Which statement is yes of carbon‑based molecules and silicon‑based molecules?

Both carbon and silicon can form four covalent bonds.

Which statement describes the central dogma of biology?

DNA is transcribed into RNA. RNA is translated into an amino acid sequence.

What happens during transcription?

DNA serves as the template for a new molecule of RNA.

Replication

DNA to DNA

Transcription

DNA to RNA

Suppose a team of researchers sequences the genome and measures the proteome of a human skin cell and a human kidney cell. Will there be a greater difference between the genome or the proteome between these two cells?

Differences in gene expression and post-transcriptional mRNA processing lead to a greater difference in the proteome than the genome between the two cells.

DNA

Double stranded deoxyribose backbone contains base thymine

What is the main difference between a prokaryotic cell and a eukaryotic cell?

Eukaryotic cells have membrane‑enclosed compartments.

Of the 20 amino acids that make up proteins, which is most likely to be present with its R group in a mixture of ionization states near physiological pH?

His

Certain intrinsically disordered proteins protect tardigrades from desiccation. What property of intrinsically disordered proteins will most likely allow them protect tardigrades from desiccation?

Intrinsically disordered proteins can interact with multiple proteins.

Which statements correctly describe the rough endoplasmic reticulum (rough ER)?

It has ribosomes bound to its membrane. It synthesizes proteins that will be sent out of the cell. It is connected to the membrane of the nucleus.

Which statement is true of the proteome?

It includes the interactions of peptides that yield a functional unit. It varies with cell type. It varies with environmental conditions.

Which statement is no of Brownian motion?

It is independent of temperature.

Which statement is true of the chirality of amino acids found in proteins?

Only L amino acids are found in proteins.

In numerous studies, treatment of prion preparations with ionizing and UV radiation does not reduce transmission of disease; however, treatment with denaturants reduces disease transmission.

Prions are proteins. Prions do not contain genetic information, which is affected by ionizing radiation. Denaturants may affect the tertiary structure of prions.

ELISA

Proteins in native state can be used to detect antibody in sample both: require formation of antibody-antigen complex

Select the true statements about SDS‑PAGE, a method of separating proteins. Assume that SDS‑PAGE is performed under reducing conditions.

Protein‑SDS complexes migrate toward the positive electrode. Smaller proteins migrate faster through the polyacrylamide gel. Protein‑SDS complexes have similar mass to charge ratios; therefore, separation is by size.

Which amino acid contains a guanidinium group?

R

Translation

RNA to protein

The steps of protein immunoblotting (commonly called western blotting) are listed. Step 1: Perform SDS-PAGE on protein samples. Step 2: Transfer proteins from gel to membrane Step 3: Probe membrane with labeled antibodies. Select the statement that best describes the purpose of step 1.

Separate proteins by size.

RNA

Single strand ribose backbone contains the base uracil

quaternary structure

The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.

Which statements accurately describe the polarity and electronegativity of water?

The oxygen atom in a water molecule is strongly electronegative. A water molecule is polar, but it has no net charge. The atoms of the water molecule are held together by covalent bonds.

Select the true statements about protein secondary structure.

The α‑helix is held together by hydrogen bonds between the amide N−HN−H and C=OC=O groups. The secondary level of protein structure refers to the spatial arrangements of short segments of the protein. In a β‑pleated sheet, the side chains extend above and below the sheet.

Which statement is false regarding peptide bonds?

They tend to have the amide nitrogen protonated to give a positive charge.

Select all the choices that correctly describe the Golgi apparatus of the cell.

This organelle is made up of flattened sacs of membrane. Proteins are modified by this organelle and repackaged into transport vesicles.

Select the statement that best describes the purpose of step 2.

Transferring proteins to a membrane makes them more accessible to antibody binding.

Instead of using acidic conditions, how could the research team release chymotrypsin from the column?

Treat the column with a concentrated solution of tryptophan.

Select the statement that best describes the purpose of step 3.

Visualize a specific antigen.

Biological membranes are present in all cells, and they make up the endomembrane system of eukaryotic cells. Among other functions, they act as barriers that selectively allow the transport of small molecules and ions into and out of the cell or organelle. Which of the choices best describes a biological membrane?

a bilayer containing lipids with hydrophilic head groups oriented toward the solvent (extracellular fluid and cytosol) and hydrophobic tail groups pointing inward components of membrane: proteins and lipids

Select the descriptions that apply to the ribosome.

a cellular structure that is composed of both RNA and protein a molecular structure that is the site of protein synthesis

Which bond or interaction is considered covalent?

a disulfide bond

The partially positively charged hydrogen atoms of one water molecule can interact with the partially negatively charged oxygen atoms of another water molecule. This interaction between water molecules is called

a hydrogen bond

Select the descriptions that apply to the smooth endoplasmic reticulum

a membranous structure that surrounds the nucleus without attached ribosomes an organelle that synthesizes fatty acids, phospholipids, and steroids

What is the method for ensuring that proteins are separated by size and not be charge during gel electrophoresis?

a negatively charged detergent binds to amino acids and denatures the protein

Secondary Structure

alpha helix and beta pleated sheet

Select all the parameters that can be determined by analyzing a protein sample with tandem mass spectrometry.

amino acid sequence precursor ion mass

The conversion of cysteine to cystine is what kind of reaction?

an oxidation

Which structure represents the secondary structure of a protein?

an α‑helix

How does the hydrophobic effect influence protein folding? In an aqueous environment, nonpolar portions of the molecule

are found in the interior of the protein, away from water, which preserves the entropy of water in solution.

Glycogen

branched glucose polymer

An IgG antibody that specifically recognizes a protein of interest, p50, was used to isolate p50 from a whole‑cell lysate. The resulting protein mixture can undergo SDS-PAGE to separate p50 from IgG. The molecular weight of p50 is 50 kDa,50 kDa, and the protein does not contain any cysteine residues. The molecular weight of IgG is 160 kDa.160 kDa. IgG contains two heavy chains and two light chains that weigh 50 kDa50 kDa and 25 kDa,25 kDa, respectively. Both types of chains contain cysteine residues. Select the components of the SDS‑PAGE loading buffer.

bromophenol blue glycerol sodium dodecyl sulfate

Which of the constituents found in eukaryotic cells are correctly ranked from largest to smallest?

cell nucleus > mitochondrion > ribosome > protein > amino acid > water molecule > proton

Select the phrases that describe the plasma membrane.

creates a barrier between the inside and outside of the cell regulates transport of molecules into and out of the cell

An assay is useful for what during protein purification?

detecting a protein in a sample

What can SDS polyacrylamide electrophoresis be used to do?

determine the molecular weights of subunits of an oligomeric protein

The first step in protein purification is called _______________________.

differential centrifigation

Antibodies used as regents to quantify proteins is the basis of a lab method called _____________.

enzyme-linked immunosorbant assay

Identify the applications for gel filtration chromatography

estimation of molecular weights separation of components in a mixture by size

Biological macromolecules can be divided into four different classes. Which type of molecule is NOT a major class of biological macromolecules?

fatty acids

Samples of the octapeptide AVGWRVKS are subjected to proteolytic cleavage by either trypsin or chymotrypsin. Select the most appropriate technique for separating the digestion products of AVGWRVKS if cleaved by trypsin.

gel‑filtration chromatography

Which amino acid has the simplest side chain?

glycine

The mitochondrion

has an interior membrane with deep folds where ATP synthesis occurs. contains unique DNA that is different from the cell's nuclear DNA.

Identify the buffer solution that can be used for eluting a transcription factor bound to a DNA affinity column.

high salt concentration

What is the MOST abundant element in human beings by percentage of total atoms?

hydrogen

Water is said to be highly cohesive because water molecules interact with one another through

hydrogen bonds.

Water‑soluble proteins, such as myoglobin, tend to fold such that

hydrophobic amino acid R groups are on the interior of the protein and hydrophilic groups are on the outside.

The second law of thermodynamics states that a spontaneous process

increases the total entropy of a system plus its surroundings.

Cell membranes are composed of phospholipids that have head and tail regions. The phospholipid head is hydrophilic and spontaneously orients toward the environment. Which of the phrases best describes the hydrophilic region of a phospholipid?

interacts with water

Select the most appropriate technique for separating the digestion products of AVGWRVKS if cleaved by chymotrypsin.

ion‑exchange chromatography

The three‑dimensional structure of a protein is specified by

its amino acid sequence and environment.

Proteins

linear amino acid polymer

What characteristics determine the position of a protein on an IPG strip at the end of isoelectric focusing?

local pH in the medium the pI of the protein

What is the best method to precisely determine the mass of a protein?

mass spectrometry

Primary structure

order of amino acids

A biological molecule can serve as a hydrogen bond donor if the hydrogen is attached to

oxygen or nitrogen.

Which pair of terms describes molecules that can dissolve in water?

polar and hydrophilic

Western Blot with SDS Page

proteins have no higher order structure proteins transferred to membrane or sheet both: require formation of antibody-antigen complex

isoelectric focusing

proteins separated by charge carried out in a pH gradient final net protein charge is zero

SDS-Page

proteins separated by mass carried out in detergent solution final net protein charge is negative

What are the characteristics of a secondary antibody used in Western blotting?

recognizes the Fc region of the primary antibody contains a covalently attached tag

Fibrous Proteins

rod-like intermediate filaments insoluble in water primarily function as structural proteins in cell Both: polymers of amino acids, exhibit secondary protein structure

Globular Proteins

some function as enzymes structure somewhat spherical myoglobin soluble in water Both: polymers of amino acids, exhibit secondary protein structure

The dielectric constant of the interior of a protein is considerably smaller than that of water. How would this difference in dielectric constants affect the strength of an electrostatic interaction between two opposite charges with the same distance between them if the charged groups were located in the interior of the protein rather than on its surface? The strength of the electrostatic interaction would be

stronger if the interacting charges were in the interior of the protein

In a typical monomeric protein, which level of structure is most highly conserved?

tertiary structure

The major conclusion of the experiment of C. Anfinsen involving ribonuclease was that

the information dictating how the protein should fold is contained in the amino acid sequence.

Which descriptions apply to a chloroplast?

the main site of photosynthesis in a plant cell a membrane‑bound organelle that contains chlorophyll

tertiary structure

the overall shape of a polypeptide resulting from interactions between the side chains of the various amino acids

The genetic information present in DNA is described by

the sequence of bases along a DNA strand.

Enzyme‑linked immunosorbent assays (ELISA) are useful in biochemistry because

they can be used to detect very small amounts of a specific material.

What are the roles of sodium dodecyl sulfate (SDS) in two‑dimensional electrophoresis?

to denature proteins to cause bound proteins to have a large negative charge

When sequencing a protein, it is necessary to break disulfide bonds within a polypeptide chain. What reagent is used to break the disulfide bonds?

β‑mercaptoethanol