TATA binding protein

basal TF that sits DIRECTLY on TATA box of promoter region

kinks DNA to separate strands upon completion of initiation complex (transcription)

final basal TSF to bind initiation complex; 2 fxns:

-helicase actiivty to unwind helix

-kinase activity to phosph. RNA pol II to begin ts

*carried on tail of RNA pol to assist with TRANSCRIPTION COUPLED REPAIR (TCR)

enhancer element, which becomes bound by transcription factors for initiation of tx

5- end= good consensus, 3' end = loose/varied

respond to ENVIRONMENTAL signals

influence transcription rates by facilitating the formation of initiation complex via:

-recruitment of HATs and chromatin remodeling complexes

-direct interaction with general TFs or indirect via mediator proteins

-->Euchromatin Enhances transcription rate!

-acetylation of histones interferes with their (+) charge, lessening its affinity for DNA

Carries a (+) charge that helps it associate with the negatively charged exterior of DNA

DNA wraps twice around histone octamer to make nucleosome; histone H1 binds linker DNA

multi-protein complex that binds TATA box

interacts with RNA pol

same for every gene; NOT controlled by environment

requires TF to begin tx

does NOT require primers, as in DNA pol

no proofreading activity

carries splicing factors, capping proteins, and TFIIH (NUCLEOTIDE EXCISION REPAIR) on its CTD!

methylation--> heterochromatin

inhibits transcription, sim to HDAT

7-methylguanylate (backwards 5' -5' linkage) added to mRNA as it leaves the tx bubble

gives stability, allows mature mRNA to leave nucleus,

and necessary for initiation of TRANSLATION

transcribes all protein-coding genes + micro RNA, siRNA, non-coding genes

-carries pre-mRNA processing proteins on its tail: capping proteins and splicing proteins, in addition to TFIIH (assists in nucleotide excision repair)

4 kinds

combine with more than 80 proteins

70-90 nucleotides

31 kinds

a GEF

Normally binds inactive EIF2 and exchanges GDP for a GTP to activates translation

phosphorylation of EIF2-GDP by a kinase inactivates the eIF2-GDP/eIF2B complex in response to stress

associated with cellular differentiation and tissue-specific patterns of gene expression

-necessary for chromosomal stability by keeping repetitive sequences in non-coding regions in a repressed state

recruits DNA methylase to make the repressed state more stable

reader-writer proteins modify newly synth DNA to match histones already bound

represents a heritable pattern of gene expression that is maintained during REPLICATION

normally NOT methylated;

housekeeper genes, tumor suppressors, DNA repair -inapropriate methylation leads to cancer

proteins made on free ribosomes

default = cytosol

use hyaluronidase to increase spread of solutions injected SC;

catabolizes CT matrix

formation of non-standard bp btw tRNA and mRNA; 5' base of tRNA anticodon undergoes more movement than the other 2

SILENT Mutation

"degeneracy of genetic code"

at 3' end:  hairpin loop in TRANSFERRIN receptor mRNA are stabilized by IRE-BP binding when iron levels are low

at 5' end:  reduces translation of FERRITIN (storage protein)

RNA surveillance

nonsense mediated mRNA decay

-marker proteins placed on exon-exon jxns

-test translation done near the nuclear membrane

-mRNA quickly degraded if it finds:

in-frame stop codon (early nonsense)

unspliced intron, or

extended 3'UTR

RAPIDLY degraded WITHOUT adenylation!

imprinting of maternal chromosome+ microdeletion in paternal DNA--> prader willi; obesity

imprinting of paternal & lack of maternal DNA- angelman syndrome- giddy

Reads/moves in 3' to 5' direction

Synthesizes DNA in 5' to 3' direction

3' to 5' exonuclease proofreading activity

phosphodiester bond created btw 5' PO4 and 3'OH

commonly begins with loss of the poly-A tail; can also trigger decapping

less commonly, some unstable mRNAs have binding sites in 3'UTR that increase/decrease rate of deadenylation and degradation;

others have endonucleases that recognize sites in 3'UTR to cleave the poly A tail

Rare form of post-tx regulation

use tissue-specific deaminase enzymes to change a ribonucleotide POST-transcription

ex- apolipoprotein B in the intestine: deaminase enzymes change C to U, resulting in a premature stop codon - shorter version of a protein that lacks LDL receptor binding domain

usu tissue or development stage-specific

-preferred conformation of a protein is expressed in a given cell

1. alternative splicing (60% of genes)

2. regulation of mRNA stability (degradation)

3. RNA editing (rare)

intent is for SYSTEMIC circulation; alveoli of lungs present a large absorbing surface and extensive capillary supply almost immediate calibration due to - high L/W partition coefficients

-small molecular radii

-readily permeable alveolar membranes

very small liquid or solid particles with increased deposition if the patient holds in their breath or with hygroscopic addition;

not intended for systemic absorption, however this can be  appreciable

Transcription factor involved in DNA damage/crisis

tumor suppressor

ACTIVATED by phosphorylation

induces the synthesis of a CDK inhibitor (p21)

type I: makes single stranded nick

type II: double stranded nick

prevents supercoiling

double helical circle, no histones

-mult copies of DNA per mt and multiple mt per cell

-replication is not limited to S phase makes 13 proteins that fxn in the mt; "imports" all other prots

-acidic drugs tend to bind albumin

-basic drugs tend to bind alpha-1-glycoprotein

-possibility of drug interaction producing toxic effects when prot bound fraction > 80%

hepatic dysfunction can decrease the amount of plasma protein binding

E-dependent

can be saturated (has a transport max)

similar compounds compete with one another for a specific tubular excretory process

binds fairly strongly to the R form (active) and also to the T form (inactive)

rxn is pulled to right and response is seen, just not as great as full agonist

enzyme only found in germline cells, stem cells & 85% of cancer cells

NOT normally found in somatic cells- confers 

immortalization

contains an RNA template to extend its paternal 3' end via a reverse transcriptase (TERT)

expt cancer vaccines target telomerase as a tumor-specific antigen

miRNA

3'UTR

one miRNA can regulate MANY mRNAs, but inhibition requires at LEAST 2 miRNAs= combinatoral control

can be tumor supressors or oncogenes

strong match-rapid degradation; mediocre match - sequestration in P (processing bodies) of cytosol

Drosha cleaves pre-miRNA, Dicer complexes miRNA with RISC Complex and argonaute (catalytic subunit)

depends on accessibility of 5' CAP or 3'UTR

occurs more quickly than transcriptional regulation, but has shorter-lived effects

important form of developmental regulation; initiation is most rate limiting step

Form of Translational regulation - eg, Ferritin!

proteins that stabilize structures in the 5' region can REPRESS translation by making the cap less accessible to cap-protein binding

storage protein for iron

accessibilty of 5'cap is form of TRANSLATIONAL regulation

proteins can interfere with binding of eIF (initiation factors )to the 5' cap

usually represses 

proteins bind to 3'UTR sequences can interfere with cap binding complex or the small ribosomal subunit

mRNA may be sequestered to certain regions where translation is more or less likely to occur (ie, no ribosomes) 

critical for regulation of gene expression in early embryo

oocytes have many mRNAs that are not translated until after fertilization; they have short polyA tails that are not translated efficiently

masking proteins bind the 3'UTR until hormonal stimulation signals their release; polyadenylation factors help stabilize the mRNA for proper translation

glycosylation patterns default to secretion, but some proteins will be deposited in the lumen of the ER

localization is dependent upon a signal peptide (short aa on the N-terminus) that is bound by a SRP- signal recognition particle

the SRP finds its receptor on the ER membrane and a translocator pulls the growing polypeptide into the ER membrane

mannose-6-phosphate

traffics proteins for retention in the lysosome

I cell disease:  pts lack the kinase necessary to phopsphorylate the mannose placed on lysosomal enzymes

constitutive secretion sends proteins to the plasma membrane for fusion unless there are specific signals for another destination

regulated secretion recognizes sorting signals and segregates proteins into secretory vesicles where they are retained at plasma membrane until external signal is received

cleavages begin in trans-golgi and continue in secretory vesicles, sometimes even in ECF after secretion

many polypeptide hormones, neuropeptides and hydrolytic enzymes are secreted as inactive precursors - need to be cleaved for activation