mechanism linking a mechanical/chemical stimulus to a specific cellular response
Describe the basic signal-transduction pathway used for mating in yeast.
-2 sexes (mating types) called a & alpha
-a cells secrete a signaling molecule: a factor that binds to specific receptor protiens on nearby alpha cells
-alpha cells secret alpha factor that binds to receptors on a cells
-result=mating of 2 cells of opposite type
Explain the evidence that signal-transduction pathways evolved before the first multicellular organisms appeared on Earth.
-molecular details of signal transduction in yeast and mammals are strikingly similar
-these similarities and others suggest that early versions of the cell-signaling mechanisms used today evolved well before the first multicellular creatures appeared on Earth
Define "paracrine signaling" and give an example.
-a secreting cell acts on nearby target cells by discharging molecules of a local regulator (a growth factor, for example) into the extracellular fluid
What are hormones and how do they travel to target cells?
-one of many types of secreted chemicals that are formed in specialized cells
-travel in body fluids
-act on specific target cells in other parts of the body to change their functioning
List the three stages of cell signaling.
What is reception in cell signaling?
target cell's detection of a signaling molecule coming from outside the cell, detection occurs when signaling molecule binds to a receptor protein located at cell's surface or inside cell
What is transduction in cell signaling?
binding of signaling molecule changes receptor protein in some way, initiating process of transduction, it converts signal to a form that can bring about a specific cellular response
What is response in cell signaling?
triggers a specific cellular response, it can be any cellular activity
What is a local regulator?
a secreted molecule that influences cells in the vicinity
What is a ligand?
molecule that specifically binds to another molecule
Describe the nature of a ligand-receptor interaction and state how such interactions initiate a signal-transduction system.
receptor protein on/in target cell allows cell to "hear" signal & respond to it, signaling molecule is complementary in shape to a specific site on the receptor and attaches there (key in lock), signaling molecule= ligand.
-binding of a specific signaling molecule to a receptor in plasma membrane triggers first step in chain of molecular interactions (signal transduction pathway)
What is a G-protein-coupled receptor?
-plasma membrane receptor that works w/ help of a G protein, a protein that binds the energy-rich molecule GTP
-these receptors vary in binding sites for both their signaling molecules and for different G proteins inside cell, proteins each have 7 alpha helices
What are receptor tyrosine kinases?
-belong to major class of plasma membrane receptors characterized by having enzymatic activity
-kinase: enzyme that catalyzes transfer of phosphate groups
-tyrosine kinase: part of receptor protiein extending into cytoplasm, enzyme that catalyzes transfer of a phosphate group from ATP to amino cid tyrosine on a substrate protein
Define a ligand-gated ion channel.
-type of membrane receptor containing a region that can act as a "gate" when receptor changes shape
-when signaling molecule binds as ligand to receptor protein, gate opens or closes, allowing or blocking flow of specific ions through channel in receptor
What are intracellular receptors?
-found in either cytoplasm or nucleus of target cells
List two advantages of using a multistep pathway in the transduction stage of cell signaling.
-the possibility of greatly amplifying a signal, if some of the molecules in a pathway transmit the signal to numerous molecules in the next step in the series, the result can be a large number of activated molecules at the end of the pathway
-provide more opportunities for coordination and regulation than simpler systems, this allows for fine-tuning of response
Explain how an original signal molecule can produce a cellular response when it may not even enter the target cell.
-original signaling molecule is not physically passed along a signaling pathway
-when we say that signal is relayed along pathway, we mean that certain info is passed on
-at each step, signal is transduced into a different form
Describe how phosphorylation propagates signal information.
-phosphorylation cascade: series of different molecules in a pathway are phosphorylated in turn, each molecule adding a phosphate group to the next one in line
-phosphorylation activates each molecule, & dephosphorylation returns it to its inactive form
What is a protein kinase?
general name for enzyme that transfers phosphate group s from ATP to a protein
Explain why a single cell may require hundreds of different protein kinases.
-a single cell may have hundreds of different kinds, each specific for a different substrate protein
-together, they probably regulate a large proportion of the thousands of proteins in a cell
What is a protein phosphate?
enzyme that can rapidly remove phosphate groups from proteins
Explain how protein phosphatases turn off signal-transduction pathways.
by dephosphorylating and thus inactivating protein kinases, phosphatases provide the mechanism for turning off the signal transduction pathway when the initial signal is no longer present
Define the term "second messenger." Briefly describe the role of these molecules in signaling pathways.
-small, nonprotein water-soluble molecules or ions involved in many signaling pathways
-they can readily spread throughout the cell by diffusion
-2 most widely used: cyclic AMP, Ca2+
What is cyclic AMP?
-cyclic adenosine monophosphate: a ring shaped molecule made from ATP that is a common intracellular signaling molecule
How is cyclic AMP formed?
epinephrine outside the cell binds to a specific receptor protein, the protein activates adenylyl cyclase, which in turn can catalyze the synthesis of many molecules of cAMP.
What is adenylyl cyclase?
an enzyme embedded in plasma membrane that converts ATP to cAMP in response to an extracellular signal
Explain how the cholera bacterium causes the symptoms of cholera by disrupting G-protein signaling pathways.
-cholera toxin is an enzyme that chemically modifies a G protein involved in regulating salt & water secretion
-modified G protein is unable to hydrolyze GTP to GDP & remains stuck in active form, continuously stimulating adenylyl cyclase to make cAMP
-high [ ] of cAMP causes intestinal cells to secrete large amounts of salts, w/ water following by osmosis, into intestines
What is cell division?
reproduction of cells
Describe the cell cycle.
life of a cell from the time it is first formed from a dividing parent cell until its own division into two cells
cells' endowment of DNA, its genetic info
What are chromosomes?
carry genetic material, one consists of one very long DNA molecule and its associated proteins
What is chromatin? What is its composition?
-makes up eukaryotic chromosomes
-it's a complex of DNA and associated molecules
What are nucleosomes? What is their relation to histone proteins?
basic bead-like unit of DNA packing in eukaryotes, consisting of a segment of DNA wound around a protein core composed of two copies of each for types of histone
What is a histone?
a small protein w/ a high proportion of positively charged amino acids that binds to the negatively charged DNA and plays a key role in its chromatin structure
What is the mitotic (M) phase?
includes both mitosis and cytokinesis, which are the shortest part of the cell cycle
-accounts for 90% of the cycle
-the cell grows and copies its chromosomes in preparation for cell division
-can be divided into subphases:
*G1 phase ("first gap")
*S phase (synthesis)
*G2 phase ("second gap")
^during all 3, cell grows by producing proteins and cytoplasmic organelles such as mitochondria and endoplastic reticulum
Describe the three subphases in interphase.
cell grows (G1), continues to grow as it copies chromosomes (S), grows more as it completes preparations for cell division (G2), & divides (M)
What occurs in prophase? (mitosis)
-chromatin fibers more tightly coiled, condense into discrete chromosomes
-each duplicated chromosome appears as 2 identical sister chromatids joined at centromere
-mitotic spindle begins to form
-centrosomes move away from each other, propelled by lengthening microtubules between them
What occurs in metaphase? (mitosis)
-longest stage, 20 minutes
-centrosomes at opposite poles of cell
-chromosomes convene on metaphase plate, an imaginary plane that is equidistant between spindle's two poles
-for each chromosome, kinetochores of sister chromatids are attached to kinetochore microtubules coming from opposite poles
What occurs in anaphase? (mitosis)
-cehesin proteins are cleaved
-2 sister chromatids part suddenly, each chromatid becomes a full-fledged chromosome
-2 chromosomes begin moving toward opposite ends of the cell as microtubules shorten
-cell elongates as nonkinetochore microtubules lengthen
-by end: 2 ends of cell have equivalent collections of chromosomes
What occurs in telophase? (mitosis)
-2 daughter nuclei form in cell
-nuclear envelopes arise from fragments of parent cell's nuclear envelope
-chromosomes become less condensed
Describe cytokinesis in plants and animals.
-division of cytoplasm is usually well under way by late telophase
-animals: formation of a cleavage furrow, which pinches cell in two
-plants: no cleavage furrow, instead, in telophase, vesicles derived from Golgi apparatus move along microtubules to middle of cell, where they coalesce producing a cell plate
What is a mitotic spindle?
begins to form in cytoplasm during prophase, it consists of fibers made of microtubules and associated proteins
subcellular region containing material that functions throughout cell cycle to organize cells' microtubules
What is an aster?
radial array of short microtubules extends from each centrosome
a structure of proteins associated w/ specific sections of chromosomal DNA at the centromere
What is the cell cycle control system?
a cyclically operating set of molecules in the cell that both triggers and coordinates key events in cell cycle, it's regulated at certain checkpoints by both internal & external signals
Describe the cell cycle clock.
-protein kinases are enzymes that activate or inactivate other protiens by phosphorylating them- some of these give the go ahead signals at G1 and G2
- to be an active kinase, it must be attached to a cyclin: a protein that gets its name from its cyclically fluctuating concentration in cell <--these kinases are called cyclin-dependent kinases
-ex. MPF: cyclin-Cdk complex that was discovered first, in frog eggs
What is a growth factor?
a protein released by certain cells that stimulates other cells to divide
What is anchorage dependence?
-requirement that a cell must be attached to the substratum in order to divide
-substratum ex: inside of a culture jar or the extracellular matrix of a tissue
What changes must occur in a cell for it to become cancerous?
-cancer cells don't heed normal signals and divide excessively and invade other tissues
What is a transformed cell?
-transformation: process that converts a normal cell to a cancer cell
-body's immune system recognizes transformed cell as an insurgent & destroys it
-if cell evades destruction, it may proliferate and form a tumor: a mass of abnormal cells w/ normal tissue
Differentiate between a "benign tumor" and a "malignant tumor."
-benign: lump where abnormal cells remain-do not cause serious problems and can be completely removed by surgery
-malignant: becomes invasive enough to impair functions of one or more organs -cancer
What is metastasis?
-metastasis: spread of cancer cells to locations distant from their original site
What is a gene?
a discrete unit of hereditary info consisting of a specific nucleotide sequence in DNA (or RNA, in some viruses)
Distinguish diploid and haploid numbers. Which cells carry haploid sets? Where are haploid cells created?
-haploid: n, gametes made in sex organelles
What is meiosis?
a modified type of cell division in sexually reproducing organisms consisting of 2 rounds of cell division but one round of DNA replication, results in cells with half the number of chromosome sets as original cell
Define karyotype. What kinds of defects can be identified from karyotypes?
-karyotype: display of chromosome pairs of a cell arranged by size and shape
-genetic defects; ex. Down's Syndrome
Describe alternation of generations.
there is both a multicellular diploid form (sporophyte) and a multicellular haploid form (gametophyte)--> characteristic of plants & some algae
What are 3 events unique to meiosis that occur in meiosis 1?
-homologs on metaphase plate
-separation of homologs
What is synapsis?
during prophase 1, replicated homologs pair up and become physically connected along their lengths by a zipper-like protein structure
What is crossing over?
-crossing over: genetic rearrangement between nosister chromatids
-2 homologs pull apart slightly but remain connected by at least one x-shaped region called a chiasma
What is nondisjunction?
an error in meiosis or mitosis in which members of a pair of homologous chromosomes or a pair of sister chromatids fail to separate properly from each other
What is the semiconservative model (of DNA)?
type of DNA replication in which replicated double helix consists of one old strand, derived from the old molecule, and one newly made strand
What is the conservative model (of DNA)?
2 parent strands somehow come back together after process
What is the dispersive model (of DNA)?
all 4 strands of DNA following replication have a mixture of old and new DNA
What are origins of replication?
replication of DNA molecules begins at these special sites, short stretches of DNA having a specific sequence of nucleotides
What is a primer?
a short stretch of RNA w/ a free 3' end, bound by complementary base pairing to template strand, that is elongated w/ DNA nucleotides during DNA replication
Describe the way that proteins initiate DNA replication.
-proteins recognize sequence & attach to DNA, separating 2 strands & opening up a replication "bubble," then entire molecule copied
-at tend of each replication bubble is a replication fork: a Y-shaped region where parental strands of DNA are being unwound
What are helicases?
enzymes that untwist the double helix at the replication forks, separating the 2 parental strands, and making them available as templates
What does the enzyme topoisomerase do?
helps relieve strain of twisting of helix by breaking, swiveling, & rejoining DNA strands
What are DNA polymerases?
enzymes that catalyze the synthesis of new DNA by adding nucleotides to a preexisting chain
Differentiate between a leading strand and a lagging strand.
-leading: new complementary DNA strand synthesized continuously along the template strand toward replication fork in 5'-->3' direction
-lagging: a discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, 5'-->3' direction
What are Okazaki fragments?
segments of the lagging strand of DNA, named after Japanese scientist who discovered them
What is DNA ligase?
linking enzyme essential for DNA replication; catalyzes covalent bonding of the 3' end of one DNA fragment (such as an Okazaki fragment) to the 5' end of another fragment (such as a growing DNA chain)
Describe proofreading DNA.
DNA polymerase proofread each nucleotide against its template as soon as it is added to the growing strand, incorrectly repaired nucleotide gets removed by polymerase and synthesis is resumed
What is nuclease?
enzyme that cuts DNA or RNA, either removing one or a few bases or hydrolyzing the DNA or RNA completely into its component nucleotides
Describe nucleotide excision repair.
repair system that removes and then correctly replaces a damaged segment of DNa using the undamaged strand as a guid
What is telomerase?
catalyzes the lengthening of telomeres in eukaryotic germ cells, thus restoring their original length and compensating for the shortening that occurs during DNA replication
What is a telomere?
tandemly repetitive DNA at the end of a eukaryotic chromosome's DNA molecule that protects the organism's genes from being eroded during successive rounds of replication
Define a nucleoid.
in prokaryotic cells, dense region of DNA in bacterium, not bounded by a membrane
What is chromatin?
complex of DNA and protein
Describe chromatin packing in a eukaryotic chromosome.
1. DNA, double helix
4. 30-nm fiber
5. looped domains
6. metaphase chromosome
Define heterochromatin and euchromatin.
-heterochromatin: interphase chromatin, visible as irregular clumps w/ a light microscope
-euchromatin: less compacted, more dispersed
Define gene expression.
process by which DNA directs the synthesis of proteins
-expression of genes that code for proteins includes 2 stages: transcription & translation
What is transcription?
synthesis of RNA under the direction of DNA, both nucleic acids use same language, info is simply copied from one molecule to the other
-DNA can serve as a template for assembling a complementary sequence of RNA nucleotides
What is mRNA?
-messenger RNA: synthesized using DNA template, attaches to ribosomes in cytoplasm and specifies primary structure of a protein
What is translation?
synthesis of a polypeptide, which occurs under direction of mRNA, there is a change in language, cell must translate base sequence of an mRNA molecule into amino acid sequence of a polypeptide
Where are the sites of translation?
ribosomes: complex particles that facilitate the orderly linking of amino acids into polypeptide chains
Where do transcription and translation occur?
transcription occurs in nucleus, mRNA is transported to cytoplasm, where translation occurs
Describe the central dogma.
-genes program protein synthesis via genetic messages in form of mRNA
What are the codes for amino acids?
triplets of nucleotide bases are smallest units of uniform length that can code for all amino acids
What is a triplet code?
a set of 3-nucleotide-long words that specify amino acids for polypeptide chains
What is a template strand?
DNA strand that provides teh pattern, or template, for ordering the sequence of nucleotides in an RNA transcript
What are codons?
mRNA base triplets, written in 5'-->3' direction
What does RNA polymerase do?
pries 2 strands of DNA apart and joins RNA nucleotides as they base-pair along DNA template, 5'-->3' direction, don't need primer
What is a promoter?
DNA sequence where RNA polymerase attaches and initiates transcription
What is a terminator?
in bacteria-sequence that signals end of transcription
What are the 3 stop codons?
What is the TATA box?
DNA sequence crucial in forming transcription initiation complex
Describe RNA processing.
modification of RNA transcripts, including splicing out introns, joining together of exons, & alteration of 5' and 3' ends
How is each end of a pre-mRNA molecule modified?
-5' end is synthesized first-receives a 5' cap: a modified form of guanine (G) nucleotide added onto 5' end after transcription of first 20-40 nucleotides
-at 3' end, enzyme adds 50-250 more adenine (A) nucleotides, forming a poly-A tail
What are the functions of the 5' cap and the poly-A tail?
-facilitate export of mature mRNA from nucleus
-help protect mRNA from degradation by hydrolytic enzymes
-help ribosomes attach to 5' end of mRNA once it reaches cytoplasm
What is RNA splicing?
cut-and-paste job, removal of large portions of RNA molecule that is initially synthesized
What are introns?
-noncoding segments of nucleic acid that lie between coding regions
What are exons?
other regions that are eventually expressed, usually by being translated into amino acid sequences
What is a spliceosome?
several different snRNPs join w/ additional proteins to form an even larger assembly
-it interacts w/ certain sites along an intron, releasing intron and joining together to exons that flanked intron
What are ribozymes?
RNA molecules that function as enzymes
What are 3 properties of RNA that allow it to act as an enzyme?
1. single-stranded, 3-D structure
2. some bases in RNA contain functional groups that may participate in catalysis
3. ability of RNa to hydrogen-bond w/ other nucleic acid molecules adds specificity to its catalytic activity
What is tRNA?
transfer RNA: an RNA molecule that functions as an interpreter between nucleic acid and protein language by picking up specific amino acids and recognizing appropriate codons in mRNA, it transfers amino acids from cytoplasmic pool to ribosome
What is an anticodon?
nucleotide triplet that recognizes a particular complementary codon on an mRNa molecule
Describe aminoacyl-tRNA synthetases.
-correct matching up of tRNa and amino acid is carried out by this family of related enzymes
-synthetase catalyzes covalent attachment of amino acid to its tRNa in a process driven by hydrolysis of ATP
flexible base pairing rules in which nucleotide at 5' end of tRNA anticodon can form hydrogen bonds with first base at the 3' end of a codon
What organelle facilitates specific coupling of tRNA anticodons w/ mRNA codons?
What are the P site, A site, and E site for?
-P site holds tRNA carrying growing polypeptide chain
-A site holds tRNA carrying next amino acid to be added to chain
-E site is where discharged tRNAs leave ribosome
What are polyribosomes (polysomes)?
strings of ribosomes that attach to mRNA, enable a cell to make any copies of a polypeptide very quickly
What is the difference between a bound ribosome and a free ribosome?
-free ribosome: suspended in cytosol and functions there
-bound ribosome: attached to cytosolic side of endoplastic reticulum or to nuclear envelope, they make proteins of endomembrane system as well as proteins secreted from cell
What is a mutation?
a change in the nucleotide sequence of an organism's DNA, ultimately creating genetic diversity, mutations also can occur in the DNA or RNA of a virus
What is a point mutation?
chemical changes in the base pair of a gene
What are insertions and deletions?
additions or losses of nucleotide pairs in genes
What is an operator?
-in bacterial DNA: sequence of nucleotides near start of an operant to which an active repressor can attach, binding of repressor prevents RNA polymerase from attaching to promoter and transcribing genes of operon
What is an operon?
unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway
What is a repressor?
binds to operator and blocks attachment of RNA polymerase to promoter, preventing transcription of genes, it's the product of a regulatory gene
What is a regulatory gene?
located some distance from operon, it controls and has its own promoter
What is an inducible operon?
usually off but can be stimulated (induced) when a specific small molecule interacts w/ a regulatory protein
What is an inducer?
a small molecule that inactivates the repressor
What is a differential gene expression?
expression of different genes by cells w/ same genome
Define histone acetylation.
acetyl groups (-COCH3) are attached to lysines in histone tails
What is genomic imprinting?
methylation permanently regulates expression of either the maternal or paternal allele of particular genes at start of development
What is an enhancer?
segment of eukaryotic DNA containing multiple control elements, usually located far from the gene whose transcription it regulates
What are oncogenes?
cancer causing genes
What are control elements?
segments of noncoding DNA that help regulate transcription by binding certain proteins
What is recombinant DNA?
DNA molecules formed when segments of DNA from 2 different sources-often different species- are combined in vitro
manipulation of organisms or their components to make useful products
What are restriction enzymes?
enzymes that cut DNA molecules at a limited number of specific locations
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