module 2 Flashcards
gene
entire nucleic acid sequence that is necessary for the synthesis of a useful RNA molecule or a functional polypeptide
distal promotor
distant portion of the promoter for a particular gene
region of DNA that may contain additional regulatory elements, often with a weaker influence than the proximal promoter.
proximal promotor
upstream of the gene that tends to contain primary regulatory elements
approximately 250 base pairs or nucleotides, nts upstream of the transcription start site
basal transcription factors
Required to assemble the transcription complex TFII(N).
regulatory transcription factors
regulatory proteins whose function is to activate transcription of DNA by binding to specific DNA sequences
enhancer element
elements which enhance transcription by helping transcription factors bind to promoter. Activators bind to enhancers.
upstream or downstream
activator
proteins which may alter chromatin structure or interact with the Mediator or other transcription factors.
inducible factor
bind to upstream elements that are regulated by an inducer
co-activator
only found in eukaryotes, localized in nucleus
may alter chromatin structure or interact with tf
CpG island
areas rich in CG repeats. Methylation of cytosine can inhibit gene expression due to enhanced chromatin compaction by methyl binding proteins
methyl binding proteins
contain the conserved DNA binding motif methyl-cytosine binding domain
mediating gene silencing via DNA
TATA Box
located upstream of start site
has consensus sequence
required for transcription of many genes
TFIID
multi protein complex made of TATA binding proteins
bind to DNA and bend
Transcription factor binding elements
proteins with DNA binding activity that are involved in the regulation of transcription
TFIIB
bind to DNA at TFIID
TFIIH
bind to res of preinitiation complex
phosphorylates the COO- terminal of RNA polymerase
RNA Polymerase I
Reads Class I genes - rRNA
RNA Polymerase II
Reads Class II genes (genes encoding proteins)–produces mRNA)
RNA Polymerase III
tRNA, small rRNA, small viral
RNAs
Mediator
A multiprotein complex which regulates transcription between activators, coactivators, transcription factors and TFIID.
Silencer
interact with repressor proteins which block activator/coactivator from interacting with transcription factors or the initiation complex
insulator
act as boundaries between genes to ensure the “correct” gene gets transcribed
wildtype
A typical, “normal” form of a given species
mutant
Organisms that contain one or more mutations
Intron
Noncoding DNA
Exon
Coding DNA
PolA tail
Polyadenylation
part of mRNA processing
PABP
recognizes PolyA tail in assembly of mRNA preinitiation complex
mGuanine cap
Guanine methylation
5’ end cap
Recognition of the 5’ mG cap by eIF4E
transcription initiantion/elongation
start of transcription in the nucleus
growing nascent mRNA strand
hnRNA
heterogeneous nuclear RNA
encompasses various types and sizes of RNAs found in the eukaryotic cell nucleus
mRNA
transported to the cytosol for protein synthesis
messenger RNA
Code/sense/codon
double-stranded DNA that carries the translatable code in the 5′ to 3′ direction
anti code/antisense/anti-codon
template stand
template strand
used in its 3’—> 5’ anti-parallel orientation
used to make RNA
HAT/HdAC
part of DNA accessibility
Histone acetyltransferase
transfers an acetyl group to a histone protein allowing euchromatin to form
Euchromatin
non condensed chromatin
Heterochromatin
condensed (transcriptional inactive) chromatin
histone
conserved, small basic (Lys & Arg rich) proteins that condense DNA
nucleosome
Octamer of 2 of each of the core histones complexed with 146 bp of DNA
zinc finger
small protein structural motif that is characterized by the coordination of one or more zinc ions in order to stabilize the fold
helix-loop-helix
found in transcription factors which have DNA binding and protein interaction domains.
leucine zip
important sequence motif facilitating protein–protein interactions
sequence-specific DNA-binding proteins that regulate transcription
monocistronic
one promotor
one gene
eukaryotes
polycistronic
one promotor
many proteins
prokaryotes
epigenetic
Heritable gene regulation that does not involve
changes in the DNA code
structural gene
gene that codes for the amino acid sequence of a protein (such as an enzyme) or for a ribosomal RNA or transfer RNA
ubiquitin
histone modification
small regulatory protein that regulates turnover of proteins
acylation
post-translational modification of proteins via the attachment of functional groups through acyl linkages
sumoylation
covalent attachment of SUMO family f proteins to lysine of a specific target via enzymatic cascade
microRNA
controls gene expression mainly by binding with messenger RNA (mRNA) in the cell cytoplasm
half-life
time at which the amount of message produced has been reduced to one half the starting value
Hoagland & Zmaecnick
proposed that The code was transcribed from DNA onto RNA
Gamow
proposed that In order to make 20 different amino acids from 4 different nucleotides would require that a minimum of 3 nucleotides must be present since 42 = 16 and 43 = 64
redundant
a different sequence may specify the same amino acid, e.g. serine is coded by 6 different
codons
wobble base
the first 2 nucleotides of the codon and anticodon interact tightly, the 3rd is looser