Question | Answer |
constitutive | a gene that is on all the time and thus does not respond much to the environment |
inducible | enzymes are produced only if substrate is present (e.g. lac) |
repressing | if the substrate exists, no need to produce the enzyme (e.g. tryptophan) |
negative control | gene expression (GE) occurs unless regulator molecule shuts it off |
positive control | GE occurs only if regulator directly stimulates it (CAP/cAMP in lac operon) |
I+ gene in lac operon | needed for lock-and-key fit of repressor and operator; if bacteria is I-, lac genes will undergo transcription/translation WITHOUT lactose
constitutive |
O+ gene in lac operon | affects repressor chape; if gene is mutated (Oc), then no lock-and-key fit --> makes enzymes w/o lactose |
I^s mutation in lac operon | causes the inducer to lack lactose binding site --> doesn't make enzymes
repressed |
effect of glucose on lac operon | represses lac operon by CAP-cAMP complex binding at promoter
inducible condition
cAMP exerts positive control |
tryptophan operon | attenuator
biosynthesis
when trp absent, the cell needs to make it |
cellular localization pattern | where the protein goes after it is produced |
Dscam gene | encodes protein that giudes axon growth, uses alt. splicing |
types of regulatory RNA | short RNA
RNA interference, RNAi (animals)
post transcriptional gene silencing, PTGS (plants)
short interfering RNA, siRNA (plants) |
short RNA | regulates CYTOPLASMIC gene expression by repressing translation or degrading mRNA |
post transcriptional gene silencing (PTGS, plants) | dsRNA is cut every 21 nucleotides by DICER to make short interfering RNA (siRNA), which unwinds to sense and antisense strands; the antisense strand combines with a protein coplex (RISC), which recognizes, binds, and cleaves mRNA |
microRNA | ssRNA that binds w/ internal or 3' untranslated mRNA and either
-blocks translation
-targets RNA for degradation |
cyclin | a protein that checks conformation before cell enters next phase of cell cycle
cyclin B must be bound to CDK1 for mitosis to continue |
G1/S | CDK4-cyclin D |
G2/M | CDK1-cyclin B |
tumor suppressor genes | halt passage through cell cycle |
proto-oncogenes | promote cell division |
RB1 | retinoblastoma
85% of those born with mutation get it (fam)
55-60% who develop mutation -> tumor (sporadic) |
TF, EF2 | normally tell cell to stop, but in mutated form, cell cycle always on -->retinoblastoma |
WT1 | Wilms tumor gene
kidney cancer, child
gene on HSA11p encodes TF |
p53 | tumor suppressor gene
TF for 20 genes
normal action shut down by carcinogens
negatively regulated by MDM2
Li-Fraumeni disease |
BRCA1-HSA17 | predisposition inherited as a dominant trait
85% w/ one mutation develop another
increased risk of breast and ovarian cancer |
BRCA2-HSA13 | autosomal dominant
breast cancer ONLY |
Rous sarcoma | 1st oncovirus described
SRC gene encodes for tyrosine kinase |
Ras proteins | signal transduction proteins that reg. cell growth/division; transmit extracellular signals to cytoplasm
single aa substitution to -> mutation
30% of cancers have mutation |
HRAS | on chromosome 11
regulates cell division in response to growth factor |
NRAS | chromosome 1
control of cell growth |
Philadelphia chromosome | result of reciprocal translocation between 9&22
Chronic Myelogenous Leukemia |
metalloproteins | encode matrix cutting enzymes for metastasis to occur |
colon cancer | -benign->malignant (95%)
-familial
1.Familial adenomatous polyposis
2.Hereditary non-polyposis colorectal cancer |
Familial adenomatous polyposis | related genes: FAP, APC, HSA5
slow progression, rapid initiation
many polyps |
Hereditary non-polyposis coleorectal cancer | related genes:HSA2, HSA3, MSH6, MLH3
slow initiation, rapid progression
few polyps |
top cancer killers, men and women | men: lung, prostate, colon/rectum
women: lung, breast, colon/rectum |
solid tumors | derived from epithelium |
requirements for good vector | -independently replicate
-restriction enzyme cleavage site
-selectable marker (antibiotic resistance, lac)
-easy to recover |
pUC18 | commonly used plasmid vector
has polylinker site, lac Z gene as selectable marker for blue-white screening |
BACs | Bacterial artificial chromosome
200Kb |
YACs | yeast artificial chromosome
230-1900Kb |
Southern blotting | allows us to determine which DNA clones contain the DNA fragment of interest |
roche 454 pyrosequencing | relies on detection of phosphate release during nucleotide incorporation |
categories of genomics | -structural
-functional
-comparative |
shot-gun sequencing | isolate genome->fragment by sonication->clone fragments into vectors->prepare clone library->clones selected at random and sequenced |
c-value paradox | genome size (in eukaryotes) does NOT correlate with genome complexity (polyploidic plants) |
human genome | first discovered by Venter (2007)
50% transposable elements (LINEs, SINEs) |
chimp vs. us | differences:
-indels
-regulation of gene expression
-recombination hot spots |
paralogs | arise from single gene duplication in SAME spp |
orthologs | homologous genes in DIFFERENT spp |
alpha and betablobin | sequances are similar, reflecting some common elolutionary history |
HSA 14 | heavy chains |
HSA2, HSA22 | light chains |
break-nibble-add mechanism | joining of V (variable region) and J (joining region) is imprecise, subject to adding or removing a few bases (rearranging the gene) |
proteomic tech | -2D electrophoresis: separate by charge then MW
-mass spec |
FGF-10 | component of signal pathway controlling outgrowth in turtles |
development, basic | 1. maternal effect genes establish gradient
2. gap genes, pair-rule genes, and segment polarity genes divide organism into segments (determination)
3. homeotic/selector genes specify the identity of each segment (differentiation) |
runx2 | pair-rule gene
mutation in this causes 'runt', cleidocranial dysplasia |
HOMEOBOX | shared sequence of selector/homeotic genes among many spp. |
things that activate responsible hox genes | -retinoic acid
-fibroblast growth factors
-Wnt proteins
-bone morphogenic proteins (deer antler)
-hedgehog proteins |
HOX-D13, HSA2q | cause synpolydactyly in humans
autosomal dominant |
HOX-A13 | autosomal imcomplete dominance
frameshift |
PAX | paired box genes
nervous system
mutations -> cancer, 'splotch', Waardenburg syndrome (autodom) |
ced 3, 4, 9, 1
bcl2 | cell death genes
3&4 -> cell death in many ways
9 -> protects cell from destruction
1 -> activates 9
bcl2 -> prevents apoptosis (cancer causing gene) |