Mini exam 6: the nucleus, cell signaling and genomics

Which method revealed that there were many more RNAs transcribed than are accounted for by the protein-coding genes in human cells?

RNA-seq

Importins are recycled to the cytoplasm attached to

RanGDP

Cargo to come into the nucleus includes all except options: ribosomal subunits histones DNA and RNA polymerases ribosomal proteins with snRNA

Ribosomal subunits

The most common method of DNA sequencing is based on premature termination of DNA synthesis by inclusion of

dideoxynucleotides

NO, nitric oxide, causes what reaction to occur?

increases in cGMP

The experimental inactivation of a gene by homologous recombination with an inactive mutant to assess function of the normal genes in intact organisms is often referred to as what type of experiment?

knockout

Hutchinson-Guilford Progeria is caused by mutations in

lamin proteins

MAP kinase is an abbreviation for _______ protein kinase.

mitogen-activated

SDS-polyacrylamide gel electrophoresis (SDS-PAGE) separates proteins by

size

The Ras protein is activated by

GTP binding

The alpha subunit of the G protein that is associated with the epinephrine receptor, Gs,

activates adenylyl cyclase

In performing PCR there are several steps. Match these steps to the process involved. options: -primers attach to the denatured dna strands -separating all double stranded DNA -taq polymerase replicates the DNA match to: -denaturation -annealing -extension

-denaturation- separating all double stranded DNA -annealing-primers attach to the denatured dna strands -extension-taq polymerase replicates the DNA

In plants, cytokinins stimulate

cell division

The first step in growth factor pathway activation is

receptor dimerization

The first enzymatic step in making a cDNA from mRNA uses

reverse transcriptase

Most snoRNAs

splice cleaved rRNAs.

Which method requires the experimental construction of two fusion proteins to assess protein-protein interactions?

yeast two-hybrid system

The eukaryotic 45S pre-rRNA transcript codes for the

28S, 18S, and 5.8S rRNAs.

Eukaryotic ribosomes leave the nucleus as

40S and 60S ribosomal subunits.

Which statement correctly describes how protein kinase A can activate genes?

Cytosolic protein kinase A is activated by cAMP to release the catalytic subunits, which move into the nucleus and phosphorylate general transcription factors

The nuclear localization signal is recognized by and binds to which protein in the process of nuclear protein import?

Importin

Match the detection method to the correct description. [ Choose ] cDNA probe to detect levels of cellular mRNA expresses=d DNA probe to detect cellular mRNA target DNA probe to detect genomic DNA target Antibody probe to detect a protein target Northern blotting Southern blotting Western blotting Microarray

Northern blotting-DNA probe to detect cellular mRNA target Southern blotting-DNA probe to detect genomic DNA target Western blotting-Antibody probe to detect a protein target Microarray-cDNA probe to detect levels of cellular mRNA expresses=d

Which is not a systems biology approach? -The computational overlay of data from both genomic and proteomic experiments -The use of global experimental data for quantitative modeling of integrated cellular processes -The comparative analysis of large datasets from multiple cell types, tissues, and/or organs -The systematic analysis of individual molecules and pathways

The systematic analysis of individual molecules and pathways

Which statement about snRNAs is true? -They are synthesized in the nucleus and function in the nucleus without passing into the cytoplasm. -They are synthesized in the cytoplasm and function in the nucleus. -They are synthesized in the nucleus, move to the cytoplasm to form functional complexes with proteins, and then return to the nucleus. -They are synthesized in the nucleus and function in the cytoplasm.

They are synthesized in the nucleus, move to the cytoplasm to form functional complexes with proteins, and then return to the nucleus.

Which of these features are required to select recombinant bacteria?

a plasmid with an antibiotic resistance gene

The CRISPR/Cas system has revolutionized the efficiency with which scientists can mutate a gene in vivo to investigate the functional role of the protein it encodes. Which component is not essential in the CRISPR/Cas system?

access to target mRNA

Match the class of signaling that is occurring. [ Choose ] synaptic communication T cell stimulation growth hormone plasmodesmata Group of answer choices autocrine endocrine paracrine cell- cell contact

autocrine -t cell stimulation endocrine -growth hormone paracrine -synaptic communication cell- cell contact-plasmodesmata

Match the description to each signaling category. [ Choose ] signals to a closely neighboring cell blood-born signal cells are physically connected signals to self-stimulate the cell autocrine paracrine cell to cell contact endocrine

autocrine- signals to self-stimulate the cell paracrine-signals to a closely neighboring cell cell to cell contact-cells are physically connected endocrine- blood-born signal

Protein kinase A is activated by

binding of cAMP to its regulatory subunits

The nuclear lamina binds to

both the inner nuclear envelope membrane and the chromatin.

The GTP on the G protein that is linked to adenylyl cyclase is split to GDP and Pi

by the active a subunit.

Restriction endonucleases are enzymes that

cleave DNA only at specific sequences

Match the type of plasmid with the use for the plasmid. [ Choose ] make large amounts of protein make protein when gene regulation allows it make large amounts of DNA cloning plasmid expression plasmid reporter plasmid

cloning plasmid-make large amounts of DNA expression plasmid-make large amounts of protein reporter plasmid-make protein when gene regulation allows it

Nitric oxide is a signal molecule that can

diffuse across cell membranes and directly alter the activity of intracellular enzymes

Steroids, like estrogen and testosterone, work through which signaling mechanism?

diffuse into the cell, bind a nuclear receptor, stimulate gene expression

Nucleic acid hybridization is the

formation of a double-stranded molecule from the interaction of two complementary-sequence single-stranded molecules

A glucocorticoid binding to its receptor stimulates

formation of a receptor dimer that binds to and activates a gene

A trimeric G protein

has three subunits: alpha, beta and gamma

Polycomb proteins promote

heterochromatin formation and gene silencing

The G protein that activates adenylyl cyclase is a

heterotrimeric G protein that separates into alpha and beta-gamma subunits

The directionality of nuclear transport is determined by _______ in the nucleus and _______ in the cytosol.

high Ran/GTP; high Ran/GDP

Hormones that signal through "second messengers" tend to be

hydrophilic signaling molecules

Mass spectrometers are used to

identify proteins by mass/ratio peptide analysis as part of proteomic procedures.

Which method uses an antibody that recognizes cellular proteins to investigate protein-protein interactions?

immunoprecipitation

Nuclear proteins that are stripped of their nuclear localization signal and injected into the cytoplasm of cultured cells will localize

in the cytoplasm

Transgenic mice are usually produced by

injecting DNA containing the gene into the pronucleus of a fertilized egg.

Enkephalins and endorphins bind to the same receptors in the brain as

morphine

The major pathway for molecules to pass into and out of the nucleus is through

nuclear pore complexes.

Small molecules (< 20 kd) enter nuclei by way of

passive diffusion through nuclear pore complexes

Consider a hypothetical signaling pathway where the initiating signal is A, the terminal response is E, and there are three intermediate components, B, C, and D, such that the complete pathway is A-B-C-D-E. Experimentally, you determine that E acts to simulate A. This is an example of

positive feedback

A major function of cAMP in animal cells is to activate

protein kinase A

The nucleolus is the site where _______ is(are) assembled.

ribosomal subunits

The nuclear envelope is continuous with the

rough endoplasmic reticulum

Export of RNAs from the nucleus occurs primarily by

selective transport through nuclear pore complexes

Ras is a membrane-bound _______ when activated.

small monomeric G protein that binds GTP

Cajal bodies are thought to represent sites of

snRNA processing and assembly.

Match the technique to the description. [ Choose ] CRISPR/Cas technology insert DNA is integrated into the genome plasmid DNA is expressed in eukaryotes plasmid DNA is replicated and expressed in bacteria stable transfection transient transfection transformation gene editing

stable transfection-insert DNA is integrated into the genome transient transfection-plasmid DNA is expressed in eukaryotes transformation-plasmid DNA is replicated and expressed in bacteria gene editing-CRISPR/Cas technology

Match the hormone to the mechanism of signaling. [ Choose ] -opens a ligand-gated ion channel in skeletal muscle -binds to a receptor tyrosine kinase, causing dimerization and activation -binds a nuclear receptor which is a DNA binding protein - binds to a histone acetylase to activate transcription steroid like progesterone neurotransmitter Acetylcholine thyroid hormone growth hormone

steroid like progesterone-binds a nuclear receptor which is a DNA binding protein neurotransmitter Acetylcholine-opens a ligand-gated ion channel in skeletal muscle thyroid hormone- binds to a histone acetylase to activate transcription growth hormone-binds to a receptor tyrosine kinase, causing dimerization and activation

What is best described as an engineering approach to understanding and manipulating biological systems?

synthetic biology

In tandem mass spectrometry the unique second phase is characterized by

the addition of a collision based fragmentation step to the first phase sample to determine amino acid sequence

What reaction does adenylyl cyclase catalyze?

the conversion of ATP to cAMP

When putting an insert into a plasmid

the insert and plasmid have to have compatible ends

On an agarose gel to separate DNA fragments, Group of answer choices -the samples need to be denatured to run and load in the gel -the largest DNA fragments migrate the slowest -the current moves from cathode (+) to anode (-) -the smallest DNA fragments migrate the slowest

the largest DNA fragments migrate the slowest

Heterochromatin is normally associated with

the nuclear envelope.

Newly replicated DNA is located in a few hundred spots (in replication factories) in the nucleus because

there are a few thousand origins of replication active at any one time, but they are located in a few hundred discrete clusters

When introduced into living cells, antisense RNA molecules bind

to complementary mRNA sequences and block protein synthesis.

Microarrays are used to look at a cancer cell and normal cell's

transcriptomes