Biol 3140 Exam 3 | Iowa State University

Cell Biology

signal transduction

Conversion of an impulse or stimulus from one physical or chemical form to another. In cell biology, the process by which a cell responds to an extracellular signal.

cell signaling

The molecular mechanisms by which cells detect and respond to external stimuli and send messages to other cells.

extracellular signal molecule

Any molecule present outside the cell that can elicit a response inside the cell when the molecule binds to a receptor.

hormone

Extracellular signal molecule that is secreted and transported via the bloodstream (in animals) or the sap (in plants) to target tissues on which it exerts a specific effect.

local mediator

Secreted signal molecule that acts at a short range on adjacent cells.

neurotransmitter

Small signaling molecule secreted by a nerve cell at a synapse to transmit information to a postsynaptic cell. Examples include acetylcholine, glutamate, GABA, and glycine.

receptor

Protein that recognizes and responds to a specific signal molecule.

intracellular signaling pathway

A set of proteins and small-molecule second messengers that interact with each other to relay a signal from the cell membrane to its final destination in the cytoplasm or nucleus.

molecular switch

Intracellular signaling protein that toggles between an active and inactive state in response to receiving a signal.

protein kinase

Enzyme that catalyzes the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein.

protein phosphatase

Enzyme that catalyzes the removal of a phosphate group from a protein, often with high specificity for the phosphorylated site.

serine/threonine kinase

Enzyme that phosphorylates target proteins on serines or threonines.

tyrosine kinase

Enzyme that phosphorylates target proteins on tyrosines.

GTP-binding protein

Intracellular signaling protein whose activity is determined by its association with either GTP or GDP. Includes both trimeric G proteins and monomeric GTPases, such as Ras.

ion-channel-coupled receptor

Transmembrane receptor protein or protein complex that opens in response to the binding of a ligand to its external face, allowing the passage of a specific inorganic ion.

G-protein-coupled receptor (GPCR)

Cell-surface receptor that associates with an intracellular trimeric GTP-binding protein (G protein) after activation by an extracellular ligand. These receptors are embedded in the membrane by seven transmembrane α helices.

G protein

A membrane-bound GTP-binding protein involved in intracellular signaling; composed of three subunits, this intermediary is usually activated by the binding of a hormone or other ligand to a transmembrane receptor.

adenylyl cyclase

Enzyme that catalyzes the formation of cyclic AMP from ATP; an important component in some intracellular signaling pathways.

cyclic AMP

Small intracellular signaling molecule generated from ATP in response to hormonal stimulation of cell-surface receptors.

cyclic-AMP-dependent protein kinase (PKA)

Enzyme that phosphorylates target proteins in response to a rise in intracellular cyclic AMP concentration.

phospholipase C

Enzyme associated with the plasma membrane that generates two small messenger molecules in response to activation.

inositol phospholipid

Minor lipid component of plasma membranes that plays a part in signal transduction in eukaryotic cells; cleavage yields two small messenger molecules, IP₃ and diacylglycerol.

inositol 1,4,5-trisphosphate (IP₃)

Small intracellular signaling molecule that triggers the release of Ca²⁺ from the endoplasmic reticulum into the cytosol; produced when a signal molecule activates a membrane-bound protein called phospholipase C.

diacylglycerol (DAG)

Small messenger molecule produced by the cleavage of membrane inositol phospholipids in response to extracellular signals. Helps activate protein kinase C.

protein kinase C (PKC)

Enzyme that phosphorylates target proteins in response to a rise in diacylglycerol and Ca²⁺ ions.

calmodulin

Small Ca²⁺-binding protein that modifies the activity of many target proteins in response to changes in Ca²⁺ concentration.

Ca²⁺/calmodulin-dependent protein kinase (CaM-kinase)

Enzyme that phosphorylates target proteins in response to an increase in Ca²⁺ ion concentration through its interaction with the Ca²⁺-binding protein calmodulin.

nitric oxide (NO)

Locally acting gaseous signal molecule that diffuses across cell membranes to affect the activity of intracellular proteins.

adaptation

Adjustment of sensitivity following repeated stimulation; allows a cell or organism to register small changes in a signal despite a high background level of stimulation.

enzyme-coupled receptor

Transmembrane protein that, when stimulated by the binding of a ligand, activates an intracellular enzyme (either a separate enzyme or part of the receptor itself).

receptor tyrosine kinase (RTK)

Enzyme-coupled receptor in which the intracellular domain has a tyrosine kinase activity, which is activated by ligand binding to the receptor's extracellular domain.

Ras

One of a large family of small GTP-binding proteins (the monomeric GTPases) that helps relay signals from cell-surface receptors to the nucleus. Many human cancers contain an overactive mutant form of the protein.

monomeric GTPase

Small, single-subunit GTP-binding protein. Proteins of this family, such as Ras and Rho, are part of many different signaling pathways.

MAP-kinase signaling module

Set of three functionally interlinked protein kinases that allows cells to respond to extracellular signal molecules that stimulate proliferation; includes a mitogen-activated protein kinase (MAP kinase), a MAP kinase kinase, and a MAP kinase kinase kinase.

MAP kinase

Mitogen-activated protein kinase. Signaling molecule that is the final kinase in a three-kinase sequence called the MAP-kinase signaling module.

phosphoinositide 3-kinase (PI 3-kinase)

Enzyme that phosphorylates inositol phospholipids in the plasma membrane, generating docking sites for intracellular signaling proteins that promote cell growth and survival.

steroid hormone

Hydrophobic signal molecule related to cholesterol; can pass through the plasma membrane to interact with intracellular receptors that affect gene expression in the target cell. Examples include estrogen and testosterone.

nuclear receptor

Protein inside a eukaryotic cell that, on binding to a signal molecule, enters the nucleus and regulates transcription.

receptor serine/threonine kinase

Enzyme-coupled receptor that phosphorylates target proteins on serine or threonine.

deoxyribonucleic acid (DNA)

Double-stranded polynucleotide formed from two separate chains of covalently linked deoxyribonucleotides. It serves as the cell's store of genetic information that is transmitted from generation to generation.

double helix

The typical structure of a DNA molecule in which the two complementary polynucleotide strands are wound around each other with base-pairing between the strands.

base pair

Two complementary nucleotides in an RNA or a DNA molecule that are held together by hydrogen bonds—normally G with C, and A with T or U.

complementary

Describes two molecular surfaces that fit together closely and form noncovalent bonds with each other. Examples include complementary base pairs, such as A and T, and the two complementary strands of a DNA molecule.

genetic code

Set of rules by which the information contained in the nucleotide sequence of a gene and its corresponding RNA molecule is translated into the amino acid sequence of a protein.

gene expression

The process by which a gene makes a product that is useful to the cell or organism by directing the synthesis of a protein or an RNA molecule with a characteristic activity.

chromatography

Technique used to separate the individual molecules in a complex mixture on the basis of their size, charge, or their ability to bind to a particular chemical group. In a common form of the technique, the mixture is run through a column filled.

karyotype

An ordered display of the full set of chromosomes of a cell, arranged with respect to size and number.

gene

Unit of heredity containing the instructions that dictate the characteristics or phenotype of an organism; in molecular terms, a segment of DNA that directs the production of a particular protein or functional RNA molecule.

genome

The total genetic information carried by all the chromosomes of a cell or organism; in humans, the total number of nucleotide pairs in the 22 autosomes plus the X and Y chromosomes.

cell cycle

The orderly sequence of events by which a cell duplicates its contents and divides into two.

replication origin

Nucleotide sequence at which DNA replication is initiated.

telomere

Repetitive nucleotide sequence that caps the ends of linear chromosomes. Counteracts the tendency of the chromosome otherwise to shorten with each round of replication.

centromere

Specialized DNA sequence that allows duplicated chromosomes to be separated during M phase; can be seen as the constricted region of a mitotic chromosome.

nucleolus

Large structure within the nucleus where ribosomal RNA is transcribed and ribosomal subunits are assembled.

histone

One of a small group of abundant, highly conserved proteins around which DNA wraps to form nucleosomes, structures that represent the most fundamental level of chromatin packing.

chromatin

Complex of DNA and proteins that makes up the chromosomes in a eukaryotic cell.

nucleosome

Beadlike structural unit of a eukaryotic chromosome composed of a short length of DNA wrapped around an octameric core of histone proteins; includes a nucleosomal core particle (DNA plus histone protein) along with a segment of linker DNA that ties the core particles together.

SMC ring complex

a large ring-shaped structure that contains two Structural Maintenance of Chromosomes (SMC) protein subunits at its core; the ring these proteins form is large enough for nucleosomes to pass easily through it. Cohesins and condensins are two major

cohesin

a ring-shaped SMC protein complex that organizes interphase chromosomes into a long series of large chromatin loops; in addition, a special subset of cohesins holds together the sister chromatids after DNA has been replicated.

ATP

Activated carrier that serves as the principal carrier of energy in cells; a nucleoside triphosphate composed of adenine, ribose, and three phosphate groups.

histone-modifying enzyme

Enzyme that catalyzes the covalent addition of a small molecule, such as a methyl or acetate group, to a specific amino acid side chain on a histone.

heterochromatin

Highly condensed region of an interphase chromosome; generally gene-poor and transcriptionally inactive.

euchromatin

One of the two main states in which chromatin exists within an interphase cell. Prevalent in gene-rich areas, its less compact structure allows access for proteins involved in transcription.

epigenetic inheritance

The transmission of a heritable pattern of gene expression from one cell to its progeny that does not involve altering the nucleotide sequence of the DNA.

DNA replication

The process by which a copy of a DNA molecule is made.

template

A molecular structure that serves as a pattern for the production of other molecules. For example, one strand of DNA directs the synthesis of the complementary DNA strand.

replication origin

Nucleotide sequence at which DNA replication is initiated.

replication fork

Y-shaped DNA junction at the site where DNA is being replicated.

DNA polymerase

Enzyme that catalyzes the synthesis of a DNA molecule from a DNA template using deoxyribonucleoside triphosphate precursors.

Okazaki fragment

Short length of DNA, including an RNA primer, produced on the lagging strand during DNA replication. Following primer removal, adjacent fragments are rapidly joined together by DNA ligase to form a continuous DNA strand.

lagging strand

At a replication fork, the DNA strand that is made discontinuously in short fragments that are later joined together to form one continuous new strand.

leading strand

At a replication fork, the DNA strand that is made by continuous synthesis in the 5_-to-3_ direction.

proofreading

The process by which DNA polymerase corrects its own errors as it moves along DNA.

RNA (ribonucleic acid)

Molecule produced by the transcription of DNA; usually single-stranded, it is a polynucleotide composed of covalently linked ribonucleotide subunits. Serves a variety of informational, structural, catalytic, and regulatory functions in cells.

primase

An RNA polymerase that uses DNA as a template to produce a short RNA fragment that serves as a primer for DNA synthesis.

DNA ligase

Enzyme that seals nicks that arise in the phosphodiester backbone of a DNA molecule; in the laboratory, can be used to join together two DNA fragments.

DNA helicase

Enzyme that pries open the DNA double helix, using energy derived from ATP hydrolysis. Used to expose DNA single strands for DNA replication.

telomere

Repetitive nucleotide sequence that caps the ends of linear chromosomes. Counteracts the tendency of the chromosome otherwise to shorten with each round of replication.

telomerase

Enzyme that elongates telomeres, synthesizing the repetitive nucleotide sequences found at the ends of eukaryotic chromosomes.

DNA repair

Collective term for the many different enzymatic processes that correct damage to DNA.

mismatch repair

Mechanism for recognizing and correcting incorrectly paired nucleotides—those that are noncomplementary.

nonhomologous end joining

An error-prone mechanism for repairing double-strand breaks in DNA by rejoining the two broken ends; often results in a loss of information at the site of repair.

homologous recombination

Mechanism by which double-strand breaks in a DNA molecule can be repaired flawlessly; uses an undamaged, duplicated, or homologous chromosome to guide the repair. During meiosis, the mechanism results in an exchange of genetic information between the maternal and paternal homologs.

mutation

A randomly produced, permanent change in the nucleotide sequence of DNA.

cancer

Disease caused by abnormal and uncontrolled cell proliferation, followed by invasion and colonization of body sites normally reserved for other cells.

gene

Unit of heredity containing the instructions that dictate the characteristics or phenotype of an organism; in molecular terms, a segment of DNA that directs the production of a particular protein or functional RNA molecule.

transcription

Process in which RNA polymerase uses one strand of DNA as a template to synthesize a complementary RNA sequence.

RNA transcript

RNA molecule produced by transcription that is complementary to one strand of DNA.

RNA polymerase

Enzyme that catalyzes the synthesis of an RNA molecule from a DNA template using ribonucleoside triphosphate precursors.

messenger RNA (mRNA)

RNA molecule that specifies the amino acid sequence of a protein.

noncoding RNA

An RNA molecule that is the final product of a gene and does not code for protein. These RNAs serve as enzymatic, structural, and regulatory components for a wide variety of processes in the cell.

gene expression

The process by which a gene makes a product that is useful to the cell or organism by directing the synthesis of a protein or an RNA molecule with a characteristic activity.

promoter

DNA sequence that initiates gene transcription; includes sequences recognized by RNA polymerase and its accessory proteins.

general transcription factors

Proteins that assemble on the promoters of eukaryotic genes near the start site of transcription and load the RNA polymerase in the correct position.

RNA processing

Broad term for the modifications that a precursor mRNA undergoes as it matures into an mRNA. It typically includes 5_ capping, RNA splicing, and 3_ polyadenylation.

RNA capping

The modification of the 5_ end of a maturing RNA transcript by the addition of an atypical nucleotide.

polyadenylation

The addition of multiple adenine nucleotides to the 3_ end of a newly synthesized mRNA molecule.

intron

Noncoding sequence within a eukaryotic gene that is transcribed into an RNA molecule but is then excised by RNA splicing to produce an mRNA.

exon

Segment of a eukaryotic gene that is transcribed into RNA and dictates the amino acid sequence of part of a protein.

RNA splicing

Process in which intron sequences are excised from RNA molecules in the nucleus during the formation of a mature messenger RNA.