Molecular Biology Test 1

Match each of the following general transcription factors to their functions: a) TFIIA b) TFIIB c) TFIID d) TFIIH 1) assist in establishing the correct direction of transcription 2) Recognition of the TATA box sequence 3) Recruitment of RNA polymerase 4) Unwinding of DNA to expose the template strand

1) TFIIB 2) TFIID 3) TFIIA 4) TFIIH

Match each statement with the correct stage of transcription a) initiation b) elongation c) termination 1) RNA polymerase unwinds the DNA ahead of the transcription bubble 2) The transcription bubble is formed during this stage 3) RNA polymerase encounters a terminator DNA sequence 4) RNA polymerase dissociates from the DNA template 5) RNA polymerase synthesizes a few ribonucleotides of the RNA transcripts while remaining at the promoter

1) elongation 2) initiation 3) termination 4) termination 5) initiation

Describe one similarity and one difference between epigenetic silencing and DNA mutation.

Both are inherited and alter the function of a gene, epigenetic modifications do not alter the DNA sequence.

RNA core polymerase

Cannot bind to DNA or find the promoter. It needs to work with general transcription factors: a. Target the core enzyme to promoters b. TFII proteins with RNA Pol II form pre-initiation complex (PIC)

What is the connection between the histone code and gene regulation?

Chromatin structure affects gene regulation because the presence of nucleosomes at gene promoters can block the binding of regulatory proteins. The histone code is a series of histone modifications that mark the chromatin as closed and inaccessible to transcription factors or open and accessible to transcription factors

What relationship exists between the cell cycle and the chromosome cycle?

Chromosomes are duplicated and segregated to daughter cells during the cell cycle. Both cycles happen at the same time.

What is the purpose of DNA-binding domains, and which DNA conformation do DNA-binding domains usually interact with?

DNA binding domains in proteins direct the protein to bind to specific sequences of DNA. They are often regulatory, stimulating or repressing transcription, but can have other roles such as structural maintenance. DNA-binding domains usually interact with B-form DNA.

Why do most DNA-binding domains interact with the major groove as opposed to the minor groove of DNA?

DNA binding to a specific DNA sequence relies on the exposure of functional groups present on the nitrogen bases of the DNA. More functional groups are exposed in the major groove, allowing for more specific interactions between the DNA binding domain and the specific DNA sequence

What feature of eukaryotic chromosomes presents a barrier to transcription? In general, how do eukaryotic cells overcome this barrier?

DNA in eukaryotic cells is wrapped around nucleosomes that can act as a barrier to the binding of RNA polymerase and other proteins necessary for transcription. Eukaryotic cells overcome this barrier by employing three different classes of enzymes: nucleosome-remodeling complexes, histone chaperones, and enzymes that add and remove histone modifications.

What is the difference in structure and function of the histone core versus the histone tail?

DNA wraps around the core, which has a defined shape.The tails are strands of amino acids without particular structure. Their role in DNA compaction is unclear, but there is evidence that they play a role in the interactions between nucleosomes and the formation of higher order chromatin structure (30nm and 60nm fibers). Additionally, modifications of the tails are known to play a role in the accessibility of DNA to DNA binding proteins.

Describe the molecular events that must occur to enable RNA polymerase to transition from abortive initiation to promoter clearance

During abortive initiation bacterial sigma factor and the beta finger of TFIIB extend into the active site of the bacterial and eukaryotic polymerase respectively. The loop prevents the elongation of the RNA chain beyond a few nucleotides and transcription is aborted. Under appropriate conditions, the loop can become displaced, the RNA nucleotide chain is elongated and RNA polymerase can clear the promoter region

Explain the terms enhancer, co-activator, and co-repressor.

Enhancers are DNA sequences that bind proteins that activate transcription. They differ from promoters in that they are usually further away from the gene (sometimes many kb away) and can be upstream or downstream of the gene. Co-activators and co-repressors are proteins that enhance and inhibit transcription respectively. However, they do not bind DNA directly and must be recruited by DNA-binding proteins.

What is the meaning of the phrase 'eukaryotic regulatory proteins are typically modular in nature'?

Eukaryotic regulatory proteins typically have separate domains that carry out different functions of the regulatory protein. For example, a DNA binding domain, oligomerization domain, and a domain for interaction with other transcriptional regulators.

Eukaryotic DNA is associated with histone proteins and packaged as chromatin. Explain why this is important for transcriptional regulation.

Histone proteins form a physical barrier that reduces access to promoter regions for RNA polymerase and DNA-binding proteins. Chromatin rearrangements that allow or impede access are important additional ways for eukaryotic cells to regulate their transcription.

Once the pre-initiation complex is formed on DNA, initiation will proceed in vitro but not in vivo. Why is this the case, and what must be added to overcome the in vivo problem?

In vivo, DNA is packaged into chromatin and must be cleared of nucleosomes in order for initiation to proceed. Histone modification enzymes and nucleosome remodeling complexes are recruited to the initiation complex by regulatory proteins

RT-PCR (reverse transcriptase PCR)

It is primarily used to measure the amount of a specific RNA. This is achieved by monitoring the amplification reaction using fluorescence, a technique called real-time PCR or quantitative PCR (qPCR). mRNA is really susceptible to getting wrecked mRNA is therefore isolated and replicated into cDNA or a more stable copy to work with

In eukaryotes, how might the level of transcription change if the Mediator were deleted?

Mediator is responsible for the regulation of transcription. Without Mediator, if all other components were present, transcription would likely occur at a basal level.

Briefly describe the two main mechanisms by which genes can become silenced.

Modifications to histones (mainly deacetylation) and methylation of DNA.

What is the significance of the fact that histone modifications are reversible?

Modifications to these proteins affect different processes in the cell such as the activation/inactivation of transcription, chromosome packaging, DNA damage and DNA repair. The modification of histones is an important post-translational process that plays a key role in gene expression

Bromodomain

Protein structural domain that recognizes and binds to certain acetylated Lys residues in proteins

Chromodomain

Protein structural motif that recognizes and binds certain methylated Lys residues in proteins.

Why regulate protein production at every step in the process rather than just at the level of transcription?

Regulation at different steps in the process affects the speed of response. The further down the path to a functional protein, the faster the response. However, if you did everything this way, a lot of energy would be wasted making proteins and waiting for their activation.

Compare the mechanisms by which the cell can respond to an extra-cellular signal that can diffuse through the cellular membrane versus a signal that cannot.

Signals that can diffuse through the membrane bind to receptors that are inside the cell. The combination of receptor and signal leads to changes in the conformation of the receptor, which leads to changes in DNA binding and changes in gene expression. Signals that cannot diffuse through the membrane rely on a signaling cascade. The signal binds to membrane receptors, activating them. The activation of the membrane receptor leads to changes in the phosphorylation of proteins within the cell. The cascade ultimately phosphorylates a transcription factor that is capable of entering the nucleus and altering gene transcription. In what way is transcriptional silencing distinguished from transcriptional repression?

In addition to RNA polymerase, what protein is required for transcription initiation by all eukaryotic polymerase?

TATA binding protein

In eukaryotes, how does RNA polymerase get oriented on a gene for transcription?

TFIIB binding tells RNA polymerase the orientation for binding

What two factors facilitate the formation of the 30 nm fiber?

The H1 histone that binds to the linker DNA between nucleosomes helps nucleosomes interact to form the higher order structure and the interactions between the tails of histones in different nucleosomes stabilize the fiber.

Compare and contrast the allosteric and torpedo models for eukaryotic transcription termination.

The allosteric model, like other forms of enzyme inhibition, means that something else binds to the enzyme and changes its conformation, leading to enzyme inactivity. In this case, once the Poly A sequence is read, the termination proteins bind to the CTD tail of RNA polymerase. That binding changes the shape and causes RNA polymerase to fall off the DNA. The torpedo model represents more of an active process - more like Rho termination in bacteria. After the termination, proteins on the CTD tail cleave the mRNA at the appropriate position, the remaining RNA that is still in the polymerase is actively degraded by an exonuclease. This degradation destabilizes the complementary base pairing that keeps RNA polymerase on the DNA and then it falls off.

What relationship exists between the phosphorylation of the CTD tail of RNA polymerase and transcriptional pausing?

The relationship couples transcription elongation to RNA processing. The example given in the text relates to the addition of the 5' cap. The initial phosphorylation at serine 5 recruits negative elongation factors to RNA polymerase and pauses transcription. Once the 5' cap is added to the transcript, p-TEFb is recruited and adds phosphates to serine 2. This phosphorylation releases the negative elongation factors and RNA polymerase resumes transcription

What is the difference between heterochromatin and euchromatin in terms of: a) gene expression b) dye staining c) nuclease sensitivity d) level of acetylation e) chromosome territory location

The tightly packed form of DNA in the chromosome is called as heterochromatin, while the loosely packed form of DNA in the chromosome is called as euchromatin. In heterochromatin, the density of DNA is high and are stained dark, whereas in euchromatin the density of DNA is little and are lightly stained. euchromatin is found in the inner body of the nucleus, is transcriptionally active, acetylation is higher, and nuclease sensitivity is greater since the DNA isn't as compact. heterochromatin examples are repetitive telomere sequences or barr bodies (inactive X chromosome)

Describe features of the following DNA-binding domain and how it interacts with DNA: Homeodomain

This is a specialized helix-turn-helix found in eukaryotes, and has a longer recognition helix than prokaryotic equivalents, as well as an additional N-terminal arm that slots into the DNA minor groove.

If every cell in an individual human contains the same DNA, how is it that cells of different tissues have unique characteristics?

This is one of the basic principles of gene regulation. Cells of different tissues have the same genome, but they regulate the expression of genes in such a way that only the subset of genes in the genome necessary for their particular function are expressed.

Propose a reason for the maintaining attachment of sister chromatids in the transmission of genes to the next generation?

To ensure that the genes that are copied are copied properly. They are proofread using base pairing to see if any corrections need to be made before they are separated.

The protein eleven-nineteen lysine rich leukemia (ELL) is a known elongation factor that facilitates transcription elongation and reduced transcriptional pausing. Misregulation of ELL is also known to be associated with several forms of cancer. Propose a mechanism by which this association might occur.

Transcriptional pausing can be a normal method for regulation of gene expression, preventing transcription until the appropriate time or until appropriate conditions exist. Overexpression of ELL may reduce transcriptional pausing and lead to the overexpression of proteins that stimulate the cell cycle, thereby leading to cancer.

In what way is transcriptional silencing distinguished from transcriptional repression?

Transcriptional repression is transient and not inherited. Transcriptional silencing is a relatively more permanent form of repression that can be inherited in an epigenetic manner.

Describe features of the following DNA-binding domain and how it interacts with DNA: Helix-turn-helix

Two alpha helices at a fixed angle to one another, with a tight bend in between. One helix (the recognition helix) fits into the major groove of the DNA. HTH can be dimers, with the recognition helices 34 Å apart so as to fit in adjacent grooves.

What evidence was presented to suggest that chromosome puffs correspond to regions of transcription?

Was looking at Drosophilla busker polytene chromosomes and found puffing of Drosophilla busker salivary gland polytene chromosomes when the temperature was raised (when heated saw puffing in different areas of the chromosome) puffing corresponds to genes that are actively being transcribed (puffing is the unwinding of strands because transcription)

Describe features of the following DNA-binding domain and how it interacts with DNA: Zinc finger

Zinc fingers contain one alpha helix and two antiparallel beta strands, and have a zinc ion to stabilize the protein structure. The zinc interacts with two cysteines and two histidines. The alpha helix inserts end-on into the major groo

What is the function of an organism's chromosomes?

a chromosome is a compacted form of DNA that acts as the vehicle that ensures stable maintenance of the genetic info and facilitates its transmission to the next generation.

Define gene

a heritable factor that controls a specific characteristic

Comparative Genomic Hybridization (CGH)

a hybridization technique to determine if cells (e.g., cancer cells) have changes in chromosome structure, such as deletions or duplications.

deletion mutation

a mutation in which one or more pairs of nucleotides are removed from a gene

Define chromosome

a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.

Angiotensin converting enzyme (ACE1) is a key regulatory enzyme in the pathway that regulates blood pressure. ACE1 activation leads to the constriction of blood vessels and the retention of salt and water. In comparing normal to hypertensive rats, it was determined that there was a difference in the histone modifications H3Ac a) what is hypertension more commonly known as? b) would you expect ACE1 to be more expressed in the normal or the hypertensive rats? Why? c) For the H3Ac modification, is it associated with increased or decreased expression? Which rat type would you expect to be enriched for the modification?

a) high blood pressure b) is would be higher in rats since it causes hypertension and ace inhibitors are common high blood pressure drugs c) H3Ac (histone 3 acetylation) is associated with increased expression.

Answer the following pertaining to bacteria: a) number of chromosomes b) the shape of chromosomes c) type of extra-chromosomal DNA d) Is the main life stage haploid or diploid?

a. 1 b. circular c. plasmid d. haploid

Answer the following pertaining to eukaryotes: a) number of chromosomes b) the shape of chromosomes c) type of extra-chromosomal DNA d) Is the main life stage haploid or diploid?

a. 2n b. linear c. mitochondrial DNA (DNA in other organelles) d. diploid

In the domestic dog, Canis familiaris, there are 39 different chromosome types. a) How many chromosomes are in a diploid cell of this organism? b) How many chromosomes are in a haploid cell of this organism? c) How many chromosomes are in a single gamete of this organism? d) How many chromosomes are in a skin cell of this organism?

a. 78 b. 39 c. 39 d. 78

template strand

a. Antisense strand b. DNA strand that is transcribed c. RNA transcript is complementary d. 3' to 5'

GAL4 is a transcription repressor for the galactose-digesting enzyme gene. Describe how transcription would be affected in the presence of the following mutations: a. a mutation that resulted in an inability of GAL80 to enter the nucleus. b. a mutation that resulted in a lack of ability of GAL3 to bind galactose. c. a mutation that resulted in GAL4 being unable to bind the UASg.

a. Gal4-regulated genes would be transcribed even in the absence of galactose, because Gal80 would not be in the nucleus to prevent the Gal4 activation domain from recruiting transcriptional activators. b. Gal4-regulated genes would not be transcribed even in the presence of galactose. Normally, galactose-bound Gal3 binds to Gal80 and sequesters it in the cytoplasm, preventing it from inhibiting Gal4 interactions with SAGA and Mediator and thus activating transcription. If Gal3 were unable to bind galactose, not binding to Gal80 and hence no cytoplasmic sequestration would occur. c. Gal4-regulated genes would not be transcribed, irrespective of the presence of galactose, because Gal4 would not be present at UASg, and hence would not be able to recruit SAGA and Mediator to the right place to activate transcription

Transcription of heat-shock protein genes can be regulated by protein proximal pausing. a. What is promoter proximal pausing? b. Explain why regulation by promoter proximal pausing of heat-shock genes is beneficial to the cell. c. Give a brief overview of how promoter proximal pausing occurs and is regulated at the Drosophila hsp70 gene.

a. In proximal pausing, RNA polymerase binds to the promoter and begins transcription but pauses after a few dozen nucleotides while remaining associated with DNA. b. Heat shock is a rapid increase in temperature. This affects protein folding and can cause proteins to misfold, unfold and aggregate. Heat-shock proteins chaperone damaged proteins to minimize deleterious cellular effects. In order to be able to respond rapidly to a sudden change in temperature, it is important that heat-shock genes be transcribed very quickly. Proximal-pausing allows RNA polymerase to be present at a gene and ready to transcribe, minimizing any delay in production of transcripts from assembly of transcription machinery. c. RNA polymerase binds and begins to transcribe, but fails to elongate due to the activity of negative elongation factors and lack of phosphorylation of the CTD of Rpb1. When the temperature rises, heat-shock factor protein (Hsf) converts from a monomeric to a trimeric form. The trimer binds to heat shock elements (HSEs) in the hsp70 promoter, recruiting Mediator and a kinase. The kinase phosphorylates the CTD of Rpb1 and also phosphorylates the negative elongation factors. The combination of Mediator and phosphorylation allows RNA polymerase to resume and continue elongation

Transcriptional pausing: a. What is transcriptional pausing? b. Why does it happen? c. How is it overcome?

a. when RNA polymerase stalls during transcription b. DNA damage cannot be passed over, shortage of nucleotides due to nutrition, mismatch error correction c. RNA polymerase backtracks and allows some of the completed transcript to extend out the front of the polymerase. Specialized enzymes (endonucleases) cut the transcript and then RNA polymerase continues and remakes the cleaved section.

The subunits that make up the core RNA polymerases are capable of synthesizing RNA molecules using a DNA template. Why do they need accessory proteins to function properly?

accessory proteins target the RNA polymerase to promoter sequences

Histone acetyltransferases (HATs)

add acetyl groups to the positively charged lysine residues in histones

TFIIE

attracts and regulates TFIIH

Which of the following statements most accurately describes chromatin state and transcription? a. Open chromatin is associated with hypoacetylation and has high levels of transcription. b. Histone deacetylases promote closed chromatin and result in repressed transcription. c. Hyperacetylation is associated with closed chromatin and low levels of transcription. d. Histone acetyltransferases result in hypoacetylation and high levels of transcription.

b

Which of the following statements regarding RNA is NOT true? a) RNA contains the nitrogen base uracil b) RNA is predominantly double stranded c) RNA contains the sugar ribose d) RNA nucleotides are connected by phosphodiester bonds

b

Which of the following definitions best describes the term chromatin? a) The basic repeating unit of DNA packaging in eukaryotes b) The circular DNA of bacteria c) The highly condensed DNA structure formed during cell division d) The complex of DNA and proteins that forms the eukaryote chromosome e) The two copies of DNA that are held together at the centromere

c

TFIIH

contains a DNA helicase to unwind DNA and activates RNA polymerase by phosphorylation (kinase)

Define DNA

deoxyribonucleic acid, a self-replicating material present in nearly all living organisms as the main constituent of chromosomes. It is the carrier of genetic information.

Put these terms in order from least to most inclusive: chromosome, DNA, gene, genome

gene, DNA, chromosomes, genome

In case studies with mice and queen bees, those that are fed a diet high in vitamins can counteract methylation

helps keep genes active that lead to skinnier, healthy offspring or queen bees.

Why is it significant that bacteria, archaea, and eukaryotic RNA polymerases have the highest similarity in the amino acid sequence that contains the active site?

it means that all the RNA polymerases have an identical mechanism for synthesizing RNA. it has been conserved throughout life

What is H1?

linker histone binds to linker DNA between nucleosomes

TFIIB recognition element (BRE)

located slightly upstream of the TATA box

M cell cycle stage

main events: prophase- chromosomes condense since prior to this they looks like noodles. nuclear envelope dissolves. sister chromatids present? Yes. sister chromatids attached? Yes. prometaphase- centrosomes begin to migrate to opposite ends of the cell. spindle fibers begin to form out from centrosomes. sister chromatids present? Yes. sister chromatids attached? Yes. metaphase- sister chromatids migrate to the center of the cell and spindle fibers attach at the centromere. sister chromatids present? Yes. sister chromatids attached? Yes. anaphase- sister chromatids are pulled apart to opposite ends of the cell. sister chromatids present? Yes. sister chromatids attached? No. telophase- nuclear envelope begins to reform around the seperate chromsomes. chromosomes begin to uncondense and the cells begin to pull apart. sister chromatids present? No. sister chromatids attached? NA

G2 cell cycle stage

main events: centrosomes are amplified. chromatids begin to condense a little. last stage of interphase. sister chromatids present? Yes sister chromatids attached? Yes

G1 cell cycle stage

main events: gap phase. cell growth occurs until cells reach a certain size. it is part of interphase. cells produce the most proteins in this stage, and create enzymes that will be needed for the rest of the cell cycle. Cellular contents that aren't chromosomes are duplicated. sister chromatids present? no sister chromatids attached? NA

S cell cycle stage

main events: synthesis. chromosomes are duplicated into sister chromatids. cell is still in interphase. sister chromatids present? Yes sister chromatids attached? Yes

Histone methyltransferase (HMT)

methylates lys and arg in the histone tails

frameshift mutation

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide

What is the overall charge of DNA?

negative due to the phosphate group

Do general transcription factors (GTFs) contribute to differential gene expression?

no

Draw a picture of a DNA molecule featuring a transcription bubble.

pay attention to the bubble, the upstream/downstream (5' and 3' directions), the RNA polymerase, RNA transcript, +1 label, non-coding (template) strand

What is the relationship between chromosome puffs and heat shock?

pon elevated temperature, the heat shock locus is turned on to make heat shock proteins that act as chaperones (like bandages) to protect proteins that are temperature sensitive and prone to denaturation and destruction. The activation of transcription from the heat shock locus is coupled with unraveling of the chromosome strands to permit access to RNA polymerase and appear expanded under the microscope. These are called "Puffs".

Histone deacetylases (HDACs)

proteins that function to remove the acetyl groups from histones make the chromatin in a more closed conformation overall decreases the gene expression levels of the cell

histone demethylases (HDMTs)

remove methyl groups

coding strand

sense strand the strand of DNA that is not used for transcription and is identical in sequence to mRNA, except it contains uracil instead of thymine Goes 5' to 3' Upstream to downstream Transcription always moves 5' to 3' for both RNA and DNA, meaning nucleotides are added to the 3' end i. It is based on the transcription start sight (+1)

Not all RNAs produced in the cell encode proteins. Explain.

some RNAs function as RNAs- rRNA, tRNA, and regulatory RNAs

TFIIF

stabilizes RNA polymerase interaction with TBP and TFIIB; helps attract TFIIE and TFIIH

TFIIA

stabilizes binding of TFIIB and TBP to the promoter

Define genome

the complete set of genes or genetic material present in a cell or organism

TFIID

the first general transcription factor to bind the promoter, binds to the TATA box through the TATA binding protein (TBP)

Immunostaining

used to detect REELIN. We would have reelin primary antibodies that bind to reelin, then secondary antibodies that bind to the primary antibody that has some kind of signaling molecule on it (like fluorescence or color) in order to indicate that the protein is there.

sodium bisulfite

used to sequence DNA. Any unmethylated Cs turn into Us, so it becomes a T in PCR copying. If it is methylated, the Cs stay Cs since they are protected and the sequences can be compared.

Propose a theory that explains why the histone protein sequences are among the most highly conserved sequences across species

virtually all amino acid changes are harmful in histone H4. We assume that individuals who carried such harmful mutations have been eliminated from the population by natural selection. If it isn't broken, don't fix it.

missense mutation

A base-pair substitution that results in a codon that codes for a different amino acid.

TATA-binding protein (TBP)

A general transcription factor that binds to the TATA box and assists in attracting other general transcription factors and RNA polymerase II to eukaryotic promoters.

silent mutation

A mutation that changes a single nucleotide, but does not change the amino acid created.

nonsense mutation

A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.

What main physical barrier must be overcome for DNA to be successfully methylated?

Access must be gained to the bases inside the DNA double helix. DNA methyltranferases are capable of flipping a base out of the helix and into the enzyme active site for methylation.

the flowering locus (FLC) gene in Arabidopsis is a regulator of plant flowering. When FLC is expressed, it produces a protein that reduces the expression of genes that promote flowering. Therefore, when FLC is active, the plant is in the vegetative growth pause and when FLC is silenced, the plant flowers. The expression of FLC is regulated in part by chromatin structure. Give three examples of mechanisms by which the plant might modify nucleosomes to promote the expression of FLC and explain how each of these modifications can be altered, or new modifications made to silence the expression of FLC.

Acetylation of histone tails.-Acetylation neutralizes the positive charges on the histones and loosens the negatively charged DNA that is wrapped around the nucleosome, making it more accessible to transcription factors. Deacetylases can remove the modification and retighten the DNA / histone interaction making the DNA less accessible and silenced. Incorporation of histone variants into nucleosomes.-Variant histones like H2A.Z are often incorporated upstream of genes and seem to be associated with transcriptional activation. Nucleosome remodeling.-Remodeling complexes can use ATP to shift the position of nucleosomes so that transcription factor binding sites can become exposed or covered.

AIMS

Amplification of inter-methylated sites Cut genomic DNA with restriction enzymes gDNA (genomic DNA) is within the nucleus and contains introns and exons. cDNA is copied from mRNA so no introns. Only exons and is a copy of mRNA

Compare and contrast the use of DNA methylation in bacteria versus eukaryotes?

Bacteria use DNA methylation as a mark to distinguish the old strand of DNA (methylated) from the new strand of DNA (unmethylated) in DNA replication. They can also distinguish their own DNA (eventually all methylated) from invading virus DNA (unmethylated). The viral DNA is recognized by restriction enzymes and digested. In eukaryotes, DNA methylation is used as a mark for silencing DNA transcription.

Describe features of the following DNA-binding domain and how it interacts with DNA: Basic region-helix-loop-helix

Basic region-helix-loop-helices contain both coiled coil domains and an alpha helix. The alpha helix interacts with the major groove of DNA.

Describe features of the following DNA-binding domain and how it interacts with DNA: Basic region-leucine zipper

Basic region-leucine zippers have long alpha helices of around 60 residues that coil round one another from their C-termini to form a coiled coil. Leucine residues are hydrophobic and are found at the interacting surfaces of the two helices, mediating the formation of the coiled-coil. The Ntermini of the helices do not interact, and insert into the major grooves of DNA on either side of the DNA-helix, rather like chopsticks