Chapter 13

Question 1

What are the 5 major types of gene expression regulation in eukaryotes?

Answer 1

1) Transcriptional regulation - producing pre-mRNA
2) mRNA processing - modifying pre-mRNA (5’ cap, etc.)
3) Regulation of mature mRNA
4) Translation
5) Post-translation

Question 2

Eukaryotic regulatory proteins are either ____________ or ____________ and are usually large complexes that regulate __________________ of target genes.

Answer 2

activators, repressors, tens to hundreds

Question 3

T or F: trans-acting activator proteins bind cis-regulatory sequences to stimulate transcription but repressor proteins bind other regulatory sequences to hinder transcription

Answer 3

True

Question 4

Enhancer Sequences

Answer 4

bind to activator proteins to activate transcription, forming enhanceosomes, bending DNA into loops allowing for enhanced transcription

Question 5

Silencer Sequences

Answer 5

bind to repressor proteins to suppress transcription

Question 6

T or F: cis-acting regulatory sequences regulate transcription of genes located on any chromosome that the regulatory sequence is on while trans-acting regulatory proteins bind to regulatory sequences on the same chromosome

Answer 6

False, cis-acting regulatory sequences regulate genes located on the same chromosme

Question 7

Pioneer Factors

Answer 7

initiate binding and recruit activators and repressors to enhancer and silencer sequences respectively

Question 8

Explain how SHH expression is different between limb cells and brain cells.

Answer 8

On the SHH gene, the limb and brain have different enhancer sites and thus, different activator proteins.

Question 9

Describe Hemoglobin in humans and what the Locus Control Region is.

Answer 9

A hemoglobin molecule is composed of two beta-globin polypeptide and alpha-globin polypeptide subunits.
The beta-globin gene is one of six globin genes that forms the beta-globin complex.
The LCR is beside the beta-globin complex and regulates the transcription of multiple genes packaged in complexes of related genes - contains 4 cis-acting regulatory sequences (HS1 to HS4)

Question 10

T or F: the order of expression of beta-globin complex genes during development matches the order in which they occur on the chromosome - HS1 to HS4 components of the LCR bind regulatory proteins that form small DNA loops (bridge to promoter)

Answer 10

True

Question 11

T or F: enhancer sequences are retained by natural selection to keep the capacity to bind specific regulatory proteins - evidenced by animals who share the same enhancer sequences

Answer 11

True

Question 12

Insulator Sequences

Answer 12

cis-acting sequences located between enhancers and the promoters of genes that direct enhancers to interact with the intended promoter, blocking communication between enhancers and other promoters

Question 13

What are the 5 Important Features of Epigenetic Modification?

Answer 13

1) Chromatin structure change
2) Transmissible during cell division
3) Reversible
4) Impact transcription
5) Do not alter DNA sequence

Question 14

What are the 3 basic mechanisms used by trans-acting proteins to access target DNA sequences packaged in chromatin?

Answer 14

1) intrinsically loose association between histones and regulatory sequences
2) chromatin remodelers change the distribution or composition of histones
3) chromatin modifiers enzymatically modify histones - adding or removing acetyl/methyl groups

Question 15

Open Promoters

Answer 15

are associated with constitutively active genes such as housekeeping genes, have a nucleosome-depleted region (NDR), no TATA box, and a poly A/T tract

Question 16

Covered Promoters

Answer 16

are associated with genes whose transcription is regulated in some way - transcription of these genes is blocked until nucleosomes are displaced or removed from the promoter to allow activators to bind to regulatory sequence, and they have TATA boxes.

Question 17

T or F: there is no active competition between nucleosomes and transcription factors for binding, they share.

Answer 17

False, there is competition

Question 18

Describe writer, eraser, and reader proteins.

Answer 18

Writer - proteins that add chemical groups to histones
Eraser - proteins that remove chemical groups from histones
Readers - proteins that bind to these chemical groups

Question 19

What is the affect of histone acetyltransferase, histone deacetylase, histone methyltransferase, histone demethylase, and DNA methyltransferase

Answer 19

H Acetyltransferase: adds acetyl groups, makes histone less positively charged and less attracted to DNA (negative)
H Deacetylase: removes acetyl groups
H Methyltransferase: adds methyl groups, either opens or closes chromatin
H Demethylase: removes methyl groups
DNA Methyltransferase: adds methyl groups to DNA nucleotides, represses expression

Question 20

T or F: recall that chromatin structure is broken down during DNA replication, during mitosis, some histones are re-packaged after replication influencing the epigenetic state of newly translated histones - during meiosis, most epigenetic marks are lost, although some are passed to the next generation

Answer 20

True

Question 21

Genomic Imprinting

Answer 21

an example of epigenetic regulation where both copies of a gene are functional but only one is expressed

Question 22

Genomic imprinting affect a _______ number of genes, with the silenced copy being dependent on the gene, this is achieved by _____________ on cytosines located in ______________

Answer 22

small, methylation, CpG dinucleotides

Question 23

Explain the two human genes on chromosome 11 that demonstrate genomic imprinting.

Answer 23

The IGF2 paternal copy is expressed while the maternal is silenced. The opposite is true for H19 - on chromosome 11, there is IGF2, the ICR (imprinting control region), H19, and an enhancer sequence. On the maternal chromosome, the ICR is occupied by an insulator protein allowing the activator protein to direct transcription of H19. However, on the paternal chromosome, the ICR and H19 is heavily methylated, allowing the expression of IGF2

Question 24

Hunger Winter children

Answer 24

children conceived during the 1944-1945 famine in the Netherlands that had a higher risk for metabolic disease due to alterations of CpG methylation

Question 25

T or F: in females, one X is almost completely inactivated randomly via XIST expression (long noncoding RNAs)

Answer 25

True

Question 26

Explain Gene Silencing by Double-stranded RNA

Answer 26

RNAi silences gene expression transcriptionally or post-transcriptionally, Dicer (enzyme) cuts the dsRNA and RISC (includes Argonaute) denatures the dsRNAs into single strands (guide strand)

Question 27

T or F: the significance of RNAi is that it can protect their genomes against mutational effects of transposable genetic elements (TGEs) and protect against viral infection - RNA commonly used to “knock down” expression of selected genes to determine effect of phenotype

Answer 27

True