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