15

Question 1

structural motif

Answer 1

DNA-binding regulatory proteins (in eukaryotes) are categorized on the basis of their structure, called the structural motif of the protein.

Many different structural motifs exist.

most common elements are alpha helices and other protein secondary structures that form the functional domains of regulatory proteins.

Question 2

functional domain

Answer 2

allow regulatory proteins to identify and bind specific regulatory DNA sequences in the major groove, or minor groove, of DNA.

These DNA binding domains generally consist of a few dozen amino acids, which are able to recognize specific DNA sequences by means of interactions with unique arrays of nitrogen, oxygen, and hydrogen atoms extending from each base pair.

Question 3

enhancer sequences (enhancers)

Answer 3

DNA sequences that bind regulatory proteins and interact with proteins bound to other promoter segments. They can be upstream, downstream, or within genes. They can also be up to tens of thousands of base pairs away from the genes they regulate.

as opposed to core promoter and proximal promoter elements, which are always upstream of and close to the genes they regulate.

enhancer activity controls the timing and location of eukaryotic gene transcription to help ensure proper function and development.

often control genes required for particular metabolic or developmental processes.

They also control the expression of genes in specific tissues or cell types, producing tissue-specific patterns of polypeptide production

Question 4

Cis-acting regulatory sequences

Answer 4

DNA regulatory sequences that can ONLY regulate transcription on the same chromosome as the sequences.

Question 5

trans-acting regulatory proteins

Answer 5

regulatory proteins that are able to identify and bind target regulatory sequences on ANY chromosome. As long as the appropriate sequences or transcription factors or what not are present, the protein gives no fucks about what chromosome it is on.

Question 6

enhanceosome

Answer 6

a large proein complex formed by the aggregation of multiple proteins, a few binding enhancer sequences and others binding other proteins.

They direct DNA bending into loops that bring the enhanceosome into contact with RNA polymerase and transcription factors bound at the core promoter or with protein complexes bound to proximal promoter elements.

The DNA loops can be small or large, in keeping with the observatiion that enhancers many be close to or quite distant from the genes they regulate.

Question 7

upstream activator sequence (UAS)

Answer 7

in the case of yeast utilization of galactose, the Gal4 transcription activator protein binds to the upstream activator sequence which is an enhancer-like element and in this case is referred to as UASvG

v=subscript

cis-acting regulatory elements, and Gal4 is a trans-acting regulatory protein.

Question 8

GAL4 complex formation for gene regulation mechanism

Answer 8

update later

Question 9

Mediator

Answer 9

an enhanceosome that forms after (in the case of yeast galactose utilization) GAL4 binds UASvG

when enducing the formation of a DNA loop, Mediator makes contact with the general transcription apparatus-including TFIID (transcription factor II D) and RNA polymerase II (Pol II)- at a GAL gene promoter. Thus, the transcription of GAL genes by RNA polymerase II is dependent on transcription activation by Gal4 binding to UASvG elements and causing the formation of the mediator.

DISTANT enhancers and silencers use the same mechanism of DNA loop formation to regulate transcription of targeted genes because the mediator is also DISTANT.

Question 10

locus control region (LCR)

Answer 10

highly specialized enhancer elements that regulate the transcription of multiple genes packaged in complexes of closely related genes.

MULTIPLE ENHANCERS

remember human B-globulin example

Question 11

silencer sequences

Answer 11

cis-acting regulatory sequences that block transcription by directly preventing enhancer mediated transcription.

Question 12

insulator sequencs

Answer 12

cis-acting sequences located between enhancers and promoters of genes that are to be insulated from the effects of the enhancer. Insulators are protein-binding sequences that direct enhancers to interact with the intended promoter and that block communication between enhancers and other promoters.

Mechanism MAY consist of allowing the formation of DNA loops containing enhancers and their intended promoter targets while preventing the formation of DNA loops containing an enhancer AND a promoter that is not its intended target.

some have the function of stopping the spread of heterochromatin. an example is position effect variegation (PEV)

Question 13

Position effect variegation (PEV)

Answer 13

position effect variegation (PEV) in fruit flies is seen in the X-chromosome inversions that bring the white gene close to the centromere. the spread of centromeric heterochromatin that blocks gene transcription is controlled by insulators. In this case, their function is to prevent the uncontrolled spread of heterochromatin following replication, thus keeping the expression of critical genes from being blocked.

Question 14

open promoters

Answer 14

• they cause genes to be constitutively transcribed. –they have an NDR, defined in another card.
• instead of a TATA box, they have a region rich in adenine and thymine located in the NDR

the downstream nucleosome, identified as the +1 nucleosome, is placed at the transcription start site. This +1 nucleosome contains variant histone 2A protein known as H2AZ that is easily modified for removal from the transcription start site at transcription initiation, allowing RNA polymerase II to bind and access the transcription start sequence.

extreme end of the spectrum

Question 15

Nucleosome-depleted region (NDR)

Answer 15

a 150 to 100 base pair long region containing few nucleosomes that lies immediately upstream of the start of transcription.

They contain a Poly A/T tract near the transcription start site

the poly A/T tract contains binding sequences (BS) that attract transcription activators (ACT). This is usually flanked by sequences that help position two nucleosomes, one upstream and one downstream of the NDR.

The downstream nucleosome is the +1 nucleosome described in the open promoters flash card

Question 16

Covered promoters

Answer 16

genes whose transcription is regulated

transcription is blockd until nucleosomes are displaced or removed from the promoter to allow transcription activators to bind to the necessary sequences, an event that leads to RNA Pol II binding and transcription initiation

they have TATA boxes and other transcription-factor binding sequences

there is an active competition between nucleosomes and transcription-activation factors which leads to regulatory mechanisms that remodel chromatin in order to give activator protein access to binding sequences in order to initiate transcription

Question 17

Chromatin remodeling

Answer 17

refers to chromatin modifications that reposition nucleosomes in such a way as to open or close promoters and other regulatory sequences.

Question 18

open chromatin

Answer 18

is chromatin in which the association of DNA with nucleosomes is relaxed in regions containing regulatory sequences, allowing access by regulatory proteins.

Question 19

closed chromatin

Answer 19

regulatory sequences cannot be efficiently accessed by regulatory proteins, and genes are transcriptionally silent.

Question 20

DNase I hypersensitive sites

Answer 20

regions of open chromatin which are sensitive to DNase I digestion.

they are observed when biologists introduce DNase I to a region of DNA . DNase I randomly cuts DNA in open chromatin regions but is not able to do so where chromatin is closed.

these regions surround promotors, enhancers, and other transcription regulating sequences. The sites are for binding by transcription activating proteins and for transcription.

Question 21

Chromatin remodelers

Answer 21

the protein complexes that carry out chromatin remodeling by removing nucleosomes in two ways:

1) can cause nucleosomes to slide along DNA. DNA spools around the nucleosome until promoter or enhancer sequences are freefrom their connection to the nucleosome.
2) can cause nucleosomes to be relocated from one DNA molecule to another

examples are:
SWI/SNF complex
ISWI complex
SWR1 complex

Question 22

SWI/SNF complex

switch sniff

Answer 22

both slides and and relocates nucleosomes

composed of 8 to 12 proteins

functions to open chromatin by displacing or ejecting nucleosomes.

Question 23

ISWI complex
(imitation switch)

Answer 23

helps direct the placement of nucleosomes

functions primarily to control the placement of nucleosomes into an arrangement that causes the region to be transcriptionally silent.

have the ability to “measure” the length of linker DNA beween bound nucleosomes in order to place the nucleosomes at regular intervals where they will cover promoters, thus preventing regulatory proteins from having access to the TATA box and other regulatory sequences

Question 24

SWR1 complex

Answer 24

substitutes the variant histone protein H2AZ in nucleosomes in place of the more common H2A protein

the H2AZ protein is most often at the +1 nucleosome. They tend to contain NDRs and are constitutively transcribed.

Question 25

Chromatin modifiers

Answer 25

chemically modify histone proteins in nucleosomes by adding or removing specific chemical groups altering the strength of association between nucleosomes and DNA.

can either cause chromatin structure to relax or close either activating or inhibiting transcription

main chemical modifications are through addition and removal of acetyl and methyl groups at specific amino acids in the N-terminal region of histones.

occasionally addition and removal of phosphate groups also

Question 26

histone acetyltransferases (HATs)

Answer 26

chromatin-modifying enzymes that add acetyl groups to specific positively charged amino acids (usually Lysine) in the N-terminal tails of histones.

unacetylated, positively charged histones adhere to negatively charged DNA, so when acetylation neutralizes the positive charge, the tight hold of nucleosome on DNA is relaxed.

Question 27

histone deacetylases

HDACs

Answer 27

remove acetyl groups from lysine and other N-terminal amino acids on Histones

Question 28

histone methyltransferases (HMTs)

Answer 28

methylate amino acids in N-terminal tails of histone proteins (usually Lysine or Arginine).

methylation converts OPEN TO CLOSED
demethylation converts CLOSED TO OPENED
(this is the opposite of acetylation)

Question 29

histone demethylases (HDMTs)

Answer 29

demethylate histones

Question 30

genomic imprinting

Answer 30

a specialized example of the mechanism behind the resetting of epigenetically controlled patterns of gene expression that occurs in mammalian meiosis

for the small number of mammalian genes subject to genomic imprinting, both copies of the gene are functional but just one is expressed

for most autosomal genes, both copies of the gene are expressed and if one gets messed up there are abnormalities

imprinted genes, if the silent gene gets messed up, who cares? (the kids. there fucked)

Question 31

imprinting control region (ICR)

Answer 31

an insulator sequence that is one of the regulatory sequences responsible for certain instances of genomic imprinting

Question 32

CpG dinucleotides

Answer 32

Nucleotide methylation for Genomic imprinting is performed by specialized DNA methyltransferases that add methyl-groups primarily to cytosines located in these nucleotides.

they are side-by-side cytosine and guanine nucleotides in the same DNA strand. the p in CpG represents the single phosphoryl group in the phosphodiester bond connecting the nucleotides. complementary strands of DNA containing CpG dinucleotides each have 5’ - CG - 3’

Question 33

CpG islands

Answer 33

sequences rich in CpG that are targeted for methylation.

in mammalian genomes, they are clustered at promoters. When they are unmethylated, chromatin in the promoter region is open, allowing access by transcription factors and RNA polymerase.

thus active transcription is linked to low levels of methylation of CpG islands. when they are methylated, promoter regions are closed and transcription is repressed

Question 34

cosuppression

Answer 34

expression of both an introduced and a natural gene are suppressed

Question 35

RNA interference (RNAi)

Answer 35

double stranded RNA (dsRNA) molecules take part in this post-transcriptional regulatory mechanism

silences gene expression either by blocking transcription of targeted genes or by blocking gene expresion posttranscriptionally.

Question 36

Dicer

Answer 36

an enzyme that cuts double stranded RNAs in RNAi into 21 to 25 base pair fragments.

these are then bound by the RNA induced silencing complex (RISC)

Question 37

RNA induced silencing complex

Answer 37

Denatures double stranded RNAs into single strands of 21 to 25 nucleotides.

Question 38

guide strand

Answer 38

an RNA single strand produced by RISC
stays attached to RISC

RISC then directs one of 3 gene silencing processes

1) it uses complementary base pairing to attach the guide strand to mRNA, and the mRNA is destroyed
2) the RISC-guide RNA binds to complementary mRNAs and blocks their translation
3) the complex directs chromatin modifying enzymes to the nucleus, where they silence transcription of selected genes

Question 39

miRNA

Answer 39

often a precursor to dsRNA which is a precursor to single stranded RNA in RNAi

Question 40

small interfering RNAs (siRNAs)

Answer 40

not usually derived from genes, but rather are complementary RNAs that come from exogenous sources or from other endogenous transcription.

Question 41

primary microRNA (pri-miRNA)

Answer 41

the transcript that after the drosha enzyme cuts it in two pieces one of which is precursor microRNA.

it folds to form a double stranded stem typically containing 65 to 70 nucleotides and having free ends on one side and a single stranded loop on the other side.

Question 42

Drosha enzyme complex

Answer 42

in animals, it cuts up pri-miRNA near the middl of the stem and produces two segments, one of which is precursor microRNA (pre-miRNA)

Question 43

precursor microRNA (pre-miRNA)

Answer 43

contains the remainder of the upper stem, which is approximately 21 to 25 base pairs, and the terminal loop. It is then transported to the cytoplasm, where Dicer removes the terminal loop, leaving dsRNA of approximately 21 to 25 bp.

RISC then binds the dsRNA and seperates the strands to create miRNAs.

Question 44

argonaute

Answer 44

a gene family which produces a protein part of the RISC complex.

the protein plays a central role in how the RISC-guide strand silences gene expression.

Question 45

RNA-induced transcription silencing (RITS) complex

Answer 45

some kind of single stranded DNA binds with Argonaute , which then joins a protein known as Chpl and other proteins to form this RISC-like complex

the siRNA-RITS complex is attracted to the centromere, where the siRNA appears to use complementary base pairing to form a duplex with transcripts of the centromeric repeat sequences. this pairing attracts other proteins that promote the deacetylation of histones and the methylation of H3K9 to close the chromatin structure and spread heterochromatin outward from the centromere.