PRACTICE QUESTIONS Molecular Biology Final

A segment of DNA in the genome that is not a protein-coding gene a. can be used to regulate gene activity b. is completely unimportant to the cell c. must encode a functional RNA d. is junk DNA left over from mistakes in evolution

A

How does phosphorylation control protein activity? a. the phosphate group induces a change in the protein conformation b. the phosphate group alters the primary structure of the protein c. the phosphate group serves as an added source of energy for the protein d. the phosphate group, with its negative charges, prevents other negatively charged molecules from interacting with the protein

A

Protein structures have several levels of organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. Consider the definitions below. Which best fits the term "protein domain" a. a small cluster of alpha helices, beta sheets, and random coils that provide a function to a protein b. the tertiary structure of a substrate-binding pocket c. a complex of more than one polypeptide chain d. a protein segment that folds and has no function

A

The chromosomes we typically see in images are isolated from mitotic cells. These mitotic chromosomes are in the most highly condensed form. Interphase cells contain chromosomes that are less densely packed and a. occupy discrete territories in the nucleus b. share the same nuclear territory as their homolog c. are restricted to the nucleolus d. are completely tangled with other chromosomes

A

Transporters, in contrast to channels, work by ________________. (a) specific binding to solutes (b) a gating mechanism (c) filtering solutes by charge (d) filtering solutes by size

A

What intermediate step was necessary to convert fibroblasts into neurons? a. converting fibroblasts into induced pluripotent stem cells b. converting fibroblasts into embryonic stem cells via the introduction of transcription factors c. converting fibroblasts into organoids in culture d. converting fibroblasts into embryonic stem cells via introduction of tumor suppressor genes

A

What is the primary purpose of integration of viral DNA into the CRISPR region of a bacterial genome? a. creation of a permanent genetic record of past viral infections for the host bacterium b. drive expression of viral genes under control of host promoter sequences located in the repeat sequences c. disruption of the repeat sequences, which results in down-regulation of gene expression at the CRISPR locus d. epigenetic modification of the viral DNA to facilitate restriction enzyme digestion

A

Which is not specifically targeted for destruction by the proteasome? a. phosphorylated proteins b. misfolded proteins c. damaged proteins d. short-lived, regulatory proteins

A

Which of the following statements about mobile genetic elements is true? a. mobile genetic elements can sometimes rearrange the DNA sequences of the genome in which they are embedded by accidentally excising neighboring chromosomal regions and reinserting these sequences into different places within the genome b. DNA-only transposons do not code for proteins but instead rely on transposases found in cells that are infected by viruses c. the two major families of transposable sequences found in the human genome are DNA-only transposons that move by replicative transposition

A

Your friend learns about splicing and fails to understand the benefit of this "wasteful operation." What reason can you give to convince her of the benefit of splicing? a. splicing can allow different proteins to be produced from the same eukaryotic gene b. splicing can allow different produced from the same prokaryotic gene c. splicing will allow eukaryotes to decrease the coding potential of their genome d. splicing can allow prokaryotes to increase the potential of their genome

A

Maintaining pH and concentration is critical to keeping proteins functional. What is the molecular mechanism by which pH affects a protein function a. the covalent bonds with the polypeptide backbone that form the secondary structures are completely disrupted b. only the primary structure is altered, which changes the folding and function of the protein c. a few of the polar R-groups can change charge and the new attraction or repulsion can alter the shape of the protein d. the N and C terminus amino acids with their amino and carboxyl ends can change the shape of the entire protein

C

Of the following proteins or protein complexes, which one does NOT typically interact with an elongating RNA polymerase 2? a. histone-modifying enzymes b. capping enzymes c. mediator complexes

C

Suppose a mRNA's 3' splice site is mutated from AGG to ACG. Predict the consequence of the mutation. a. splicing would occur as normal but there would be a point mutation in the mRNA and final protein sequences b. splicing would begin but not be properly completed if the 3' splice site is altered c. splicing would not begin if the 3' splice site is altered d. splicing would occur as normal because this splice site is less important than the 5' splice site

C

The reason for differences in the sets of proteins expressed in a nerve and a pancreatic cell of the same individual is that nerve and pancreatic cells contain different a. genes b. regulatory sequences c. sets of regulatory proteins d. promoters

C

The retinoblastoma (Rb) protein blocks cells from entering the cell cycle by a. phosphorylating Cdk b. marking cyclins for destruction by proteolysis c. inhibiting cyclin transcription d. activating apoptosis

C

To crack the genetic code, researchers introduced synthetic messenger RNAs in vitro translation systems and determined which proteins were produced from these synthetic mRNAs. mRNAs consisting of poly-UUC led to the production of three different proteins: poly-Phe, poly-Ser, and poly-Leu. What best explains this result? a. each amino acid is specified by several codons b. each codon codes for several different amino acids c. the synthetic mRNA was read in all three reading frames d. transcription started at three different places

C

Which of the following descriptions is consistent with the behavior of a cell that lacks a protein required for a checkpoint mechanism that operates in G2? a. the cell would be unable to enter the M phase b. the cell would be unable to enter G2 c. the cell would enter M phase under conditions when normal cells would not d. the cell would pass through M phase more slowly than normal cells

C

Which of the following has the lowest rate of diffusion across an artificial membrane? a. water b. glycerol c. glucose d. ethanol

C

Which of the following statements is true? a. ribosomes are large RNA structures composed solely of RNA b. ribosomes are synthesized entirely in the cytoplasm c. rRNA contains the catalytic activity that joins amino acids together d. only one ribosome binds to a mENA at a time

C

Which organelle must hyper fuse in late G1/early S phase and then undergo fission during late G2/ early M phase? a. the endoplasmic reticulum b. the golgi apparatus / body c. the mitochondria

C

You engineer yeast cells that express the M cyclin during S phase by replacing the gene regulatory sequences of the M cyclin gene with those of the S cyclin gene. Keeping in mind that yeast cells have one common Cdk that binds to all cyclins, which of the following outcomes is LEAST likely during this experiment? a. there will be both M cyclin-Cdk and S cyclin-Cdk complexes in the cell during S phase b. some substrates that are normally phosphorylated in M phase will now be phosphorylated in S phase c. G1 cyclin-Cdks will be activated in earlier G1 d. S-Cdk targets will be phosphorylated during S phase

C

The majority of transcription regulators make sequence-specific contacts with DNA. What represents the primary site of contact for the transcription regulators?

the major groove

How do most motor proteins ensure that their movements are unidirectional? a. they hydrolyze their bound GTP, effectively preventing movement in the reverse direction b. their asymmetrical structures support movement in only one direction c. they couple a conformational change to the hydrolysis of an ATP molecule d. they couple a conformational change to the formation of an ATP molecule from ADP and phosphate

C

How does an allosteric inhibitor work? a. it outcompetes the substrate molecule and binds to the active site, preventing substrate molecules from binding there b. it binds to a site other than the active site, causing a conformational change in the enzyme that forces the product to leave the active site c. it binds to a site other than the active site, causing a conformational change in the enzyme that makes the active site less accommodating to the substrate d. it interacts covalently with the substrate, preventing it from fitting into the enzyme's active site

C

Modifications of chromatin can lead to increases or decreases of local or global gene expression. For each situation, state whether the following modifications increase transcription, decrease transcription, or could increase or decrease transcription depending on the context. a. chromatin-remodeling complex uses ATP energy to alter chromatin b. histone acetyltransferase adds acetyl groups to histone tails. c. histone acetyltransferase removes acetyl groups from histone tails. d. methyltransferases add methyl groups to histone tails

A. could increase or decrease B. increase C. decrease D. idk

How do cyclin-Cdk complexes trigger different stages of the cell cycle? a. the concentration of the Cdk subunit increases at different stages of the cycle b. the Cdk subunits are degraded at different stages of the cycle c. the kinase activity of the Cdk subunit increases at different stages of the cycle d. all of the above are correct

C

Match the type of phenotypic change with what type of genetic change is most likely to cause it. a. a mutation within a gene b. gene duplication c. mutation in a regulatory region d. exon shuffling e. horizontal gene transfer ___a protein normally localized in the nucleus is now located in the cytoplasm ___a protein acquires a DNA-binding domain ___tandem copies of a gene are found in the genome ___a copy of a bacterial gene is now found integrated on a human chromosome ___a protein become much more unstable ___a protein normally expressed only in the liver is now expressed in blood cells

A___a protein normally localized in the nucleus is now located in the cytoplasm D___a protein acquires a DNA-binding domain B___tandem copies of a gene are found in the genome E___a copy of a bacterial gene is now found integrated on a human chromosome A___a protein become much more unstable C___a protein normally expressed only in the liver is now expressed in blood cells

Why do you suppose that amino-acid-altering mutations in histone genes are deleterious?

Amino-acid-altering mutations in histone genes are deleterious. This is because the four histones in the octomer (H2A, H2B, H3, and H4) are universal and are critical to the organism. A mutation would decrease this consistency and would cause many problems throughout transcription like the binding of the histone to the DNA backbone.

Foods are broken down into simple molecular subunits for distribution and use throughout the body. Which type of simple subunits, listen below, is used preferentially as an energy source? a. proteins b. simple sugars c. free fatty acids d. glycerol

B

How are most eukaryotic transcription regulators able to affect transcription when their binding sites are far from the promoter? a. by binding to their binding site and sliding to the site of the RNA polymerase assembly c. by unwinding the DNA between their binding site and the promoter d. by attracting RNA polymerase and modifying it before it can bind to the promoter

B

Sister chromatid separation occurs because ___ are destroyed by the APC/C? a. kinetochores b. securins c. cohesins d. condensins

B

The N-terminal take of histone H3 can be extensively modified, and depending on the number, location, and combination of these modifications, these changes may promote the formation of heterochromatin. What is the result of heterochromatin formation? a. an increase in gene expression b. gene silencing c. recruitment of remodeling complexes d. dis placement of histone H1

B

UV radiation is a 'negative signal' which can indicue apoptosis in cells as a result of various forms of cell damage. If DNA damage is irreparable which of the following is activated as a part of the apoptotic cascade> a. Bid b. p53 c. Fas ligand d. nuclear lamins

B

What is a plausible explanation as to why A. thaliana, a plant, has a similarly size genome as the fruit fly, but twice the number of protein coding genes? a. flies are more complex organisms with neural behaviors b. plants have more genes that were duplicated during evolution c. flies are motile and must need more genes for movement d. plants have more repeated noncoding DNA sequences

B

Which of the following DNA sequences is LEAST likely to accommodate mutations? a. regulatory DNA sequences b. ribosomal RNA sequences c. DNA sequences found between genes d. the coding sequence of a duplicated gene

B

Which of the following is NOT a chemical group commonly found on core histone N-terminal tails for chromatin regulation? a. methyl b. sulfhydryl c. phosphate d. acetyl

B

Which of the following is not a mobile DNA element? a. transposon b. long terminal repeats (LTR) c. long interspersed elements (LINES) d. insertion sequence (IS) elements

B

Which of the following is not involved in post-transcriptional control a. dicer b. mediator c. RISC

B

Which statement is true about the association of histone proteins and DNA? a. Histone proteins form hydrogen bonds with the nucleotide bases of DNA. b. Histone proteins have a high proportion of positively changed amino acids, which bind tightly to the negatively charged DNA backbone. c. each histone protein has a deep groove into which a DNA double helix tightly fits. d. histone proteins have a high proportion of negatively charged amino acids, which bind tightly to the positively charged DNA backbone.

B

HIV is a human retrovirus that integrates into the host cell's genome and will eventually replicate, produce viral proteins, and ultimately escape from the host cell. Which of the following proteins is NOT encoded in the HIV genome? a. reverse transcriptase b. envelope protein c. RNA polymerase d. capsid protein

C

A key step in activating eukaryotic RNA polymerase 2 is the addition of what groups to its tail? a. methyl b. acetyl c. phosphate d. hydroxyl

C

Although the chromatin structure of interphase and mitotic chromosomes is very compact, DNA-binding proteins and protein complexes must be able to gain access to the DNA molecule. Chromatin-remodeling complexes provide this access by a. recruiting other enzymes b. modifying the N-terminal tails of core histones c. using the energy of ATP hydrolysis to move nucleosomes d. denaturing the DNA by interfering with the hydrogen bonding between base pairs

C

An adult hematopoietic stem cell found in the bone marrow a. will occasionally produce epidermal cells when necessary b. can produce only red blood cells c. can undergo self-renewing division for the lifetime of the healthy animal d. will express all the same transcription factors as those found in an unfertilized egg

C

Glyceraldehyde-3-phosphate dehydrogenase operates by stripping a hydride ion from its substrate. Which molecule is the recipient of the proton and two electrons during this transfer. a. oxygen b. acetyl CoA c. NAD+ d. FADH

C

What are some ways cells can ensure that their daughters remember what kind of cells they need to be?

Cell memory- remember so daughter cells look alike Each daughter cell receives 1/2 of the parents' histone with modifications. The enzymes in the daughter cells recognize the patterns on the mRNA and let histone specific proteins surround the histone. This leads the daughter cell to have similar euchromatin to one of the parent cells.

A virus... a. is a type of cell b. has genetic materialal made of proteins c. cannot persist in its host for more than one cell generation d. can act as a vector mechanism for gene transfer

D

DNA ligase is an enzyme used when making recombinant DNA molecules in the lab. In what normal cellular process is DNA ligase involved? a. none; it is only found in virtually infected cells b. transcription c. transformation d. DNA replication

D

In the intestine, what do Wnt proteins promote? a. apoptosis of precursor cells in each intestinal crypt b. apoptosis of the stem cells at the base of each intestinal crypt c. secretion of mucus at the base of each intestinal crypt d. proliferation of the stem cells and precursor cells at the base of each intestinal crypt

D

Mobile genetic elements can promote gene duplication and exon shuffling by a. interesting into an exon and destroying its function b. excising themselves from a gene c. explicating genes during the mobilization process d. serving as targets for homologous recombination

D

Several different classes of enzymes are needed for the catabolism of carbohydrates. Which of the following descriptions best matches the function of an isomerase? a. An enzyme that catalyzes a change in the position of a specific chemical group with a single molecule. b. An enzyme that catalyzes the oxidation of a molecule by removing a hydride ion. c. An enzyme that catalyzes the addition of phosphate groups to other molecules. d. An enzyme that catalyzes the rearrangement of bonds within a single molecule

D

Step 3 in glycolysis requires the activity of phosphofructokinase to convert fructose 6-phosphate into fructose 1,6-bisphosphate. Which of the following molecules is an allosteric inhibitor of this enzyme? (a) Pi (inorganic phosphate) (b) AMP (c) ADP (d) ATP

D

The N-terminal tail of histone H3 can be extensively modified, and depending on the number, location, and combination of these modifications, these changes may promote the formation of heterochromatin. What is the result of heterochromatin formation? a. an increase in gene expression b. recruitment of remodeling complexes c. displacement of histone H1 d. gene silencing

D

The octameric histone core is composed of four different histone proteins, assembled in a stepwise manner. Once the core octamer has been formed, DNA wraps around it to form a nucleosome core particle. Which of the following histone proteins does NOT form part of the octameric core? a. H4 b. H2A c. H3 d. H1

D

What happens to disease-causing unfolded proteins? a. they are degraded b. they bind a different target protein c. they form structure filaments d. they form protein aggregates

D

What should designers of artificial chromosomes include to ensure proper kinetochore assembly on the artificial chromosome? a. condensin b. centrosome c. orgin of replication d. centromere

D

Which of the following doubles the Vmax of an enzymatic reaction when performing an enzyme kinetics assay? a. add less competitive inhibitor so that the active site is available to more substrate available b. add ATP so it can bind to the active sight and give the protein more energy c. add double the amount of substrate compared to the original assay d. double the number of enzyme molecules compared to the original assay

D

Which of the following statements is true? a. the mitotic spindle is largely made of intermediate filaments b. the contractile ring is made largely of microtubules and actin filaments c. the contractile ring divides the nucleus into two d. the mitotic spindle helps segregate the chromosomes to the two daughter cells

D

Which statement is true about the association of histone proteins and DNA? a. Histone proteins from hydrogen bonds with the nucleotide bases of DNA. b. Each histone protein has a deep groove into which a DNA double helix tightly fits. c. Histone proteins have a high proportion of negatively charged amino acids, which bid tightly to the positively charged DNA backbone. d. Histone proteins have a high proportion of positively charged amino acids, which bind tightly to the negatively charged DNA backbone.

D

Which substances are used as energy stores within your body? In which organs?

Fats in adipose tissue. Proteins in muscle.

Why can't humans be model organisms?

Good model organisms should reproduce rapidly, which humans do not (we take months per offspring). And unlike humans, model organisms should be easy to introduce genetic mutations to.

What role do non-covalent bonds play in the interactions between proteins and ligands?

The more non-covalent bonds there are, the more stable to proteins/ligands re and the tighter / stronger their bond is.

Why is aminoacyl-tRNA synthetase such an important enzyme for the process of translation?

The tRNA has to be charged in order for it to complete its role. It has to be charged with an amino acid. The aminoacyl-tRNA synthetase is the only enzyme involved in translation. It matches the tRNA with its correct amino acid and double-checks to ensure it did so correctly.

A gene for kanamycin resistance to (kanR) was ligated into a plasmid vector. We want to transform this recombinant plasmid into E. coli cells. What would we expect to observe when we spread the transformed E. coli onto agar containing kanamycin? Explain how these results allow us to determine whether transformation was successful or unseccessful.

We would expect to see colony-forming units (CFUs). By seeing this, we can determine that our transformation was successful. We could also calculate the transformation efficiency to get more precise results as to whether our transformation was successful or not.

If only 2% of the human genome is comprised of protein-coding genes, then what makes up the other 98% of the genome?

non-coding genes like introns and genes that code for regulatory DNA