exam 2 cell bio terms

Minor Groove of DNA

Area where bases are closer together and not easily accessed

Major groove of DNA

is the main site of protein binding

B-DNA

Right-handed helical structure of DNA that exists when water is abundant; the secondary structure described by Watson and Crick and probably the most common DNA structure in cells.

Z-DNA

Secondary structure of DNA characterized by 12 bases per turn, a left-handed helix, and a sugar-phosphate backbone that zigzags back and forth.

Topoisomerase

A protein that functions in DNA replication, helping to relieve strain in the double helix ahead of the replication fork.

Supercoiled DNA

DNA is further twisted to save space, describes a higher-order DNA structure. The double-helical structure of DNA entails the interwinding of two complementary strands around. one another and around a common helical axis

Karotype

A picture of all the chromosomes in a cell arranged in pairs

chromosome painting

chromosomes hybridized with fluorescent dye to show their origins

replication origin

Specific sequence of DNA where DNA synthesis begins.

centromere

Region of a chromosome where the two sister chromatids attach

Telomere

DNA at the tips of chromosomes

nuclease

A DNA cutting enzyme that excises damaged DNA.

Histones

Globular protein that assist in DNA packaging in eukaryotes. Histones form octamers around which DNA is wound to form a nucleosome.

Nucleosome

repeating subunit of chromatin fibers, consisting of DNA coiled around histones

agarose gel electrophoresis

Type of Chromatography, used to separate nucleic acids based on size/length of chain. The media serves as the stationary phase and the nucleic acid as the mobile phase. Negatively charged nucleic acids travel toward the anode (positive end). Smaller strands travel faster than larger chains.

Importin

receptor protein that binds to the nuclear localization signal of proteins in the cytosol and then transports the bound protein through the nuclear pore complex and into the nucleus

Ran-GTP

binds importin causing it to dissociate from the cargo

Euchromatin

loosely packed chromatin

Heterochromatin

Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed.

histone code hypothesis

proposes that specific combinations of modifications help determine chromatin configuration and influence transcription

double helix

Shape of DNA

template strand

The DNA strand that provides the template for ordering the sequence of nucleotides in an mRNA transcript.

semi-conservative replication

in each new DNA double helix, one strand is from the original molecule, and one strand is new

replication fork

a Y-shaped point that results when the two strands of a DNA double helix separate so that the DNA molecule can be replicated

origin of replication

Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.

lagging strand

A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.

leading strand

the new complementary DNA strand synthesized continuously along the template strand toward the replication fork in the mandatory 5' to 3' direction

Primers

starting point for DNA synthesis, short structures of nucleotides

Primase

An enzyme that joins RNA nucleotides to make the primer.

Helicase

An enzyme that untwists the double helix of DNA at the replication forks.

Ligase

An enzyme that connects two fragments of DNA to make a single fragment, joining of molecules uses ATP

Proofreading

function of DNA pol in which it reads the newly added base before adding the next one

Nuclease

An enzyme that cuts DNA or RNA, either removing one or a few bases or hydrolyzing the DNA or RNA completely into its component nucleotides.

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

polymerase chain reaction (PCR)

A technique for amplifying DNA in vitro by incubating with special primers, DNA polymerase molecules, and nucleotides.

Anneal DNA

cool to hybridize with primers and build DNA (extension)

Hybridization of DNA

joining of complementary base pair sequences

DNA repair

The removal and replacement of damaged DNA by the correct sequence

Depurination

the loss of a purine base from a nucleotide

Nuclease

An enzyme that cuts DNA or RNA, either removing one or a few bases or hydrolyzing the DNA or RNA completely into its component nucleotides.

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

polymerase chain reaction (PCR)

A technique for amplifying DNA in vitro by incubating with special primers, DNA polymerase molecules, and nucleotides.

Anneal DNA

cool to hybridize with primers and build DNA (extension)

retrotransportation

Mesenger RNA is reverse-transcribed to DNA and then integrated into the genome Resulting in duplicate gene Lack interons (so, can be distinguished from regular gene) Often found on a different chromosome

reverse transcriptase

a polymerase (enzyme) that catalyzes the formation of DNA using RNA as a template

Fixed angle rotor

angle doesn't change as centrifuge spins

differential centrifugation

separates the cellular components by size and density

swing bucket rotor

allows the tube to change angle during the run

density gradient centrifugation

A method of separating particles by centrifugation through a gradient of a dense substance, such as sucrose or cesium chloride.

supernatant

The liquid on top of material deposited by settling or centrifugation.

pellet

a small, rounded, compressed mass of a substance.

signal sequence

The sequence within a protein that directs the protein to a particular organelle.

catalase

An enzyme produced in all cells to decompose hydrogen peroxide, a by-product of cell respiration

signal recognition particle (SRP)

A protein-RNA complex that recognizes a signal peptide as it emerges from a ribosome and helps direct the ribosome to the endoplasmic reticulum (ER) by binding to a receptor protein on the ER.

Signal peptidase

An enzyme that removes the signal sequence of a polypeptide chain by proteolysis.

dolichol

Membrane lipid on which an N-linked oligosaccharide precursor is first assembled before being transferred to the asparigine residue of an ER protein. A sugar carrier

chaperone

(also, chaperonin) protein that helps nascent protein in the folding process

glycosyl transferase (glycosylase)

enzymes that catalyze the transfer of glycosyl residues from their specific donor to an acceptor molecule

Mannose 6-phosphate

Enzymes meant for lysosomes have this marker. It marks proteins targeted for destruction. Deficiency in this marker can lead to junk protein piling up.

Deamination

the removal of an amino group from an amino acid

Thymine dimer

a molecule formed when two adjacent thymine molecules in the same strand of DNA covalently bond to one another

homologous recombination

process that results in genetic exchange between homologous DNA from two different sources

Holliday junction

Special structure resulting from homologous recombination that is initiated by single-strand breaks in a DNA molecule.

Transposons

(jumping genes) short strands of DNA capable of moving from one location to another within a cell's genetic material

Depurination

the loss of a purine base from a nucleotide

GTPase

an enzyme that hydrolyses the GTP to GDP

Arf (ADP-ribosylation factor)

regulate vesicular traffic and organelle structure by recruiting coat proteins, regulating phospholipid metabolism and modulating the structure of actin at membrane surfaces

Sar (systemic acquired resistance)

a mechanism of induced defense that confers long-lasting protection against a broad spectrum of microorganisms

Uncoating

enzymes in the vacuole dissolve the envelope and capsid, releasing the virus into the cytoplasm

Adaptin

mediates binding between the cytosolic end of the cargo receptor and clathrin

Transcytosis

transport into, across, and then out of cell

constitutive secretion

Materials are transported in secretory vesicles and discharged in a continual manner

regulated secretion

specialized protein anchored to the presynaptic "target" membrane to bind v-SNAREs to dock vesicles, making them ready for release (target-snare)

Rab

A family of small GTP-binding proteins that play key roles in vesicular transport.

Low density lipoprotein (LDL)

bad cholesterol

COP II

vesicular trafficking protein ER --> cis-golgi (anterograde)

clatherin

receptor protein on surface of a cell-aids in receptor mediated endocytosis-when a membrane receptor binds certain substrates that the cell wants to internalize, the recptore signals for clathrin lattice formation

paracrine

Referring to a secreted molecule that acts on a neighboring cell.

target protein

Generally a transcription factor that regulates the response.

trimeric G-proteins

A large family of GTPases, consisting of three subunits (α, β and γ). The Gβ and Gγ subunits bind to each other very tightly but bind reversibly to Gα. The association of Gα with Gβγ and the activity of these subunits depend on whether GTP or GDP is bound to Gα. These proteins transduce signals from a family of receptor proteins known as 7-helix transmembrane receptors.

Cyclic GMP (cGMP)

Discharge of materials synthesized in the cell that have been stored in membrane-bound secretory granules in the peripheral regions of the cytoplasm, occurring in response to an appropriate stimulus

coatomer

Coat protiens called _____________ bind with outer surface of membrane, causing vesicle to bud off. (Exocytosis within golgi)

COP I

retrograde: golgi --> ER

Phosphodiesterase

enzyme that degrades cAMP, producing AMP, to terminate signaling

Protein kinase A

a serine/threonine kinase which is activated by cAMP (immediate effect)

Phosphoinositol Triphosphate

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

V-snare

specialized protein anchored to vesicles to aid their fusing to the presynaptic membrane to release neurotransmitter (vesicle-snare)

T-snare

specialized protein anchored to the presynaptic "target" membrane to bind v-SNAREs to dock vesicles, making them ready for release (target-snare)

Rab

A family of small GTP-binding proteins that play key roles in vesicular transport.

Cyclase

An enzyme that produces many cAMP molecules (from ATP) when activated by a G-protein. (Another enzyme breaks down cAMP).

Phosphodiesterase

enzyme that degrades cAMP, producing AMP, to terminate signaling

epidermal growth factor

Abbreviated EGF; stimulates cells to reproduce and heal.

ras

One of a large family of GTP binding proteins (the monomeric GTPases) that help relay a signal from surface cell receptor to nucleus. Many human cancers have an overactive mutant form of the protein.

MAPK cascade

a chain of proteins in the cell that communicates a signal from a receptor on the surface of the cell to the DNA in the nucleus of the cell; mediate signaling initiated by a variety of growth factors, such as platelet-derived growth factor (PDGF) and epidermal growth factor (EGF).

STAT (signal transducers and activator of transcription)

a group of latent cytoplasmic transcription factors that play a central role in transmitting signals from the cytoplasmic membrane to the nucleus

SMAD

Protein that relays signals from serine/threonine kinases

Apoptosis

programmed cell death

DNA laddering

Sensitive indicator of apoptosis. Laddering occurs during karyorrhexis when endonucleases break up DNA resulting in intervals of 180 base pairs.

Caspase

A "killer enzyme" that plays a role in apoptosis, or programmed cell death

Bax

promotes apoptosis