Genetics Exam 4
what is the NFT region flanked by?
-1 and +1 nucleosomes
how long is the NFR region typically?
150 bp
what percent of the human genome encode transcription factors
2-3%
approx what percent of DNA is methylated in mammals?
2-7%
PcG recognizes histone H3 and trimethylates a lysine at (?) thus causing repression
27
what percentage of human RNA are alternatively spliced?
70%
atp hydrolysis is used to drive a change in the positions and or compositions of nucleosomes, thereby making theDNA more or less amenable to transcription
ATP-dependent chromatin remodeling
becomes activated in response to cell signaling molecules that cause an increase in the cytoplasmic concentration of the molecule cAMP
CREB protein
How do chromatin remodelers change chromatin structure? (3)
Change in nucleosome position (change in the relative positions, or change in the spacing over a long distance) Histone Eviction Replacement with histone variants
catalyzes covalent bond formation in the sugar phosphate backbones of both DNA strands after the stick ends have h bonded with each other
DNA Ligase
acetylation of core histone proteins results in
DNA being less tightly bound
attaches a methyl group to the number 5 position of the cytosine base
DNA methyltransferase
Standard linker histone
H1
Which histone genes have histone variants been identified for in eukaryotes?
H1, H2A, H2B, H3
linker histone associated with chromatin connection and gene repression
H1V
important role in repair of damaged DNA
H2A.X
What does the +1 nucleosome typically contain?
H2A.Z and H3.3
what do PcG complexes regulate?
Hox genes
Core histone that is abundant on the inactivated X chromosme
MacroH2A
Inhibits transcription in three different ways: chromatin compaction covalent modification of histones direct interaction with a transcription factor
PRC1
catalyzes the attachment of 3 methyl group onto lysine 27 of histone H3
PRC2
bings to the PRE and recruits PRC2
PRE-binding protein
binding of this protein enhances RNA stability
PolyA-binding protein
double stranded RNA that comes from pre-miRNA or pre-siena associates with proteins to form a complex called
RISC
recognizes specific cellular mRNAs due to complementary sequences
RISC
a type of splicing factor that contains a domain at their carboxyl-terminal end that is rich in series and arginines and is involved in protein protein recognition
SR proteins
a general transcription factor that binds to the TATA box and is needed to recruit RNA pol 2 to the core promoter
TFIID
key regulators of epigenetic changes that are programmed during development that are involved with gene activation
TrxG
two different transcription factors come together to form
a heterodimer
Tsix active leads to
active x chromosome
exons that vary from one cell type to another in the mature mRNA
alternative exons
the phenomenon that a pre-mRNA can be spliced in more than one way
alternative splicing
Xist active (tsix inactive) leads to
barr body
where are the sequences that act as destabilizing elements in mRNAs with short half lives located?
beyond the stop codon in a region called the 3'-UTR
the regulatory element functions in the forward or reverse direction
bidirectional
characteristic of all remodeling complexes (what it is and its name)
catalytic ATPase subunit DNA translocases
found at the centromeres of each chromosome and functions in the binding of kinetochore protiens
cenH3
dynamic changes in the structure of chromatin that occur during the life of a cell
chromatin remodeling
proteins that increase the rate of transcription but do not directly bind to the DNA itself
coactivators
always found in mature mRNA from all cell types
constitutive exons
the methylation of DNA that was previously unmethylated
de novo methylation
an enzyme that cuts pre-mi/siRNA into a double stranded RNA about 20-25 bp long
dicer
regions of transcription factor proteins that have specific functions
domains
a well positions nucleosome that is followed by an NFR is characteristic of/important for
ends of eukaryotic genes/ transcriptional termination
the study of mechanisms that lead to changes in gene expression that can be passed from cell to cell and are reversible but do not involve a change in the sequence of DNA
epigenetics
stores excess Fe3+
ferritin
what causes Igf2 to be turned on in females but not in males?
formation of a loop by CTCF (binds to unmethylated sequences) that inhibits the H19 enhancer from stimulating the Igf2 gene
the process of making many copies of a gene
gene cloning
The phenomenon that the level of gene expression can be controlled so that genes can be expressed at high or low levels
gene regulation
required for the binding of RNA polymerase to the core promoter and its progression to the elongation stage
general transcription factors
genes experience different patterns of DNA methylation that affect wether the maternal or paternal allele is expressed
genomic imprinting
methylation of only one strand of DNA
hemimethylation
acetylate positively charged lysine within core histone proteins
histone acetyltransferases
proteins that bind histones and aid in the assembly of histone octamers
histone chaperones
the pattern of histone modification acts much like a language or code in specifying alterations in chromatin structure
histone code hypothesis
what must occur so that RNA pol 2 can transcribe DNA
histone octamers are evicted or destabilized
Histone genes that have accumulated mutations that change the amino acid sequence of the histone proteins
histone variants
when two identical transcription factors come together
homodimer
genes that encode proteins required in most cells of a multicellular organism
housekeeping genes
involved in specifying the structures that form along the anteroposterior axis in animals
hox genes
where are regulatory elements often located?
in a region within 200 bp upstream of the promoter
preserves the methylated condition of parent strand DNA in subsequent cells (how methylation is transferred from mother cell to daughter cell)
maintenance methylation
what does the recognition helix often contain that allows it to favorably interact with DNA?
many positively charged amino acids that interact with the negatively charged DNA backbone
bind methylated sequences and recruits other proteins to the region that inhibit transcription
methyl-CpG-binding proteins
Two ways in which methylation can affect transcription
methylation of CpG islands may prevent binding of activators or enhance binding of repressors methyl-CpG-binding proteins
mRNA sent to a p-body where it may be store and later reused or eventually degraded
miRNA
RNAs that are transrived form eukaryotic genes that are normally found in the genome
miRNA's
advantages of alternative splicing
more than one functional polypeptide product from one strand of RNA
When a domain or portion of a domain has a very similar structure in many different proteins
motif
Where and why does DNA methylation usually occur?
near the promoter CpG Islands
are the CpG islands of housekeeping genes often methylated?
no
does methylation slow down the movement of RNA Pol along a gene?
no
where is the transcriptional start site at the core promoter found for active genes or those genes that can be activated?
nucleosome free region
what type of sequences do restriction enzymes typically recognize
palindromic (same when read forwards or backwards)
stimulate the expression of Tsix
pluripotency factors
short strand of DNA that acts as a primer containing thymine nucleotides
poly-dt primer
key regulators of epigenetic changes that are programmed during development that are involved with gene repression
polycomb group (PcG)
what is one of the main functions of siRNAs
preventing certain viral infections
how to repressors exert their effects? (2)
preventing the binding of TFIID to the TATA box or by inhibiting the ability of TFIID to recruit RNA Pol 2 to the core promoter
the use of in vitro molecular techniques that manipulate fragments of DNA to produce new arrangements
recombinant DNA technology
serve to regulate the rate of transcription of target genes
regulatory transcription factors
bind to a specific base sequence and then cleave the DNA backbone at two defined locations, one in each strand
restriction endonucleases
uses RNA as a template to make a complementary strand of DNA
reverse transcriptase
what structure of protein is typically found in transcription factor proteins?
secondary - alpha helix (proper width to bind into the major groove of the DNA double helix)
mRNA is degraded
siRNA
originate from sources that are exogenous (not normally made in cells)
siRNAs
does the RISC complex have the double stranded RNA or single stranded?
single
found in remorse in sperm cells
spH2B
single stranded regions of DNA that can hydrogen bond to a complementary sequence of DNA from a different source
sticky ends
miRNA and an mRNA h bond to each other because
they have sequences that are PARTIALLY complementary
promotes the activation of RNA polymerase, often by interacting with general transcription factors
transactivation domain
used to describe proteins that influence the ability of RNA polymerase to transcribe a given gene
transcription factors
aids in the uptake of iron into a cell
transferrin/transferrin receptor
TrxG recognizes histone H3 and attaches three methyl groups to a lysine at position 4 thus activating the gene
trimethylation
True or false, in most cases sirens are exact maths to a single type of mRNA
true
what is the effect of DNA methylation
usually inhibits transcription
a small DNA molecule that can replicate independently of host cell chromosomal DNA
vector
how does mediator control the the ability of RNA polymerase II to progress to the elongation stage of transcription?
via phosphorylation of the carboxyl-terminal domain
When can polyA-binding protein no longer bind?
when the number of adenosine becomes less that 10-30 in length
what even initiates the XCI (x inactivation)
x chromosome pairing
