Regulation of Gene Expression

Question 1

Regulation of transcription in prokaryotes

Answer 1

If protein encoded by a gene is needed, the gene will be transcribed. If protein encoded by a gene is not needed, the gene will not be transcribed

Question 2

Prokaryotic gene expression

Answer 2

DNA is not segregated in a nucleus, ribosomes can begin protein synthesis before mRNA is transcribed fully, control lies in determining which mRNAs are made

Question 3

Operons

Answer 3

Polycistronic genes, related control sequences, one promotor regulates production of one mRNA, single RNA codes for several proteins in a pathway

Question 4

Positive control of transcription

Answer 4

Requires a protein for transcription to occur

Question 5

Negative control of transcription

Answer 5

Protein required to block transcription

Question 6

Regulation of Lac operon

Answer 6

Negative control, repressor binds to operator- no transcription, inducer binds to repressor- transcription, decrease in inducer concentration- no transcription

Question 7

Negative control of Lac operon

Answer 7

Repressor protein (lac I gene product), binds to operator region of Lac operon, prevents transcription from occuring

Question 8

Function of inducer of Lac operon

Answer 8

Binds to repressor, prevents repressor from binding to operator, allows transcription, decrease in inducer concentration leaves repressor free to bind operator, no transcription

Question 9

Repressors

Answer 9

Proteins produced by regulatory genes, normally bind to operator region of specific promoters, prevent mRNA transcription and protein production

Question 10

Inducers

Answer 10

Small molecules that bind to repressors, repressor becomes inactive, leaves promoter, transcription and translation proceeds, repressor is bound in the absence of an inducer

Question 11

Co-repressors

Answer 11

Some repressors are inactive on their own, require another molecule to bind before they bind to promoters and prevent transcription (co-repressors)

Question 12

Catabolite repression of lac operon activity

Answer 12

Lac operon activity affected by glucose level, low glucose- high cAMP, activates cyclic AMP receptor protein (CRP), CRP at operator stimulates RNA polymerase binding

Question 13

Regulation of RNA polymerase binding by sigma factors

Answer 13

Sigma factors bind RNA polymerase, sitmulate binding to certain sets of promoters, simultaneously activates transcription of several operons

Question 14

Attenuation of transcription

Answer 14

Sequence and structure of mRNA can regulate gene expression, codons for Trp early in sequence, rate of translation influences RNA folding, low trp- genes expressed, high trp- no translation

Question 15

Eukaryotic gene regulation

Answer 15

Much more complex, chromatin can be organized to allow or prevent transcription, different cell types have different regulatory patterns

Question 16

Eukaryotic vs. prokaryotic gene expression

Answer 16

DNA in eukaryotes is organized into nucleosomes, operons are not present in eukaryotes, genes that encode proteins that function together are usually located on different chromosomes, transcription and translation are separated by intracellular compartmentation

Question 17

Levels of regulation of eukaryotic gene expression

Answer 17

DNA and the chromosome, transcription, processing of transcripts, RNA transport and localization, initiation of translation, stability of mRNA, stability of protein

Question 18

Regulation through histones and chromatin

Answer 18

Regulation by chromatin remodeling- displacement of nucleosomes from specific DNA sequences, histones tightly associated with chromatin may be modified to alter binding, acetylation changes charge and can regulate gene expression

Question 19

Methylation of DNA

Answer 19

Cytosine residues in DNA can be methylated to produce 5-methylcytosine (5mC), methyl-cytosines are located in GC-rich sequences (CpG islands)- near promoter, can activate or repress transcription

Question 20

Methylation and genetic disorders

Answer 20

Prader-Willi syndrome and Angelman syndrome, very different symptoms, from deletions of the same region of chromosome 15

Question 21

Genome modifications

Answer 21

Some cells change their genomes- gene rearrangement, changes in gene copy number, chromosomal translocations, triplet repeats

Question 22

Gene rearrangement

Answer 22

Segments of DNA can move from one location to another in genome

Question 23

Example of gene rearrangement

Answer 23

Occurs in cells that produce antibodies, ordered rearrangement of B-lymphocyte variable gene regions coding for immunoglobulin chains, contributes to antibody diversity

Question 24

VDJ recombination/somatic recombination

Answer 24

Mechanism of genetic recombination in immunoglobulin (B cells) and T cell receptor genes, takes place in primary lymphoid tissue, recombine variable regions to create large number of combinations, DNA spliced like mRNA

Question 25

Gene amplification

Answer 25

Not the normal physiologic means of regulating gene expression in normal cells, regions of a chromosome undergo repeating cycles of DNA replication, new DNA forms double minutes, double minutes integrate into other chromosomes, amplify the gene

Question 26

Double minutes

Answer 26

Small unstable chromosomes formed from newly synthesized DNA created during gene amplification

Question 27

Gene deletions

Answer 27

Can occur through errors in DNA replication and cell division and are usually noticed only if a disease results, ex- loss of tumor suppressor gene results in cancer

Question 28

Gene translocations

Answer 28

Ex- chronic myelogenous leukemia- Philadelphia chromosome, Burkitt’s lymphoma

Question 29

Fragile X syndrome

Answer 29

Triplet repeat expansion, CGG triplet is amplified, 5’ of FMR-1 gene, 5-54 normal, 60-230 carrier, 230-4000 affected

Question 30

Huntington disease

Answer 30

Triplet repeat expansion, CAG repeat in coding region, normal is 10-35 copies, disease is >35 repeats

Question 31

Regulation at level of transcription

Answer 31

Promoters have core elements and regulatory elements (enhancers, silencers, hormone response elements), some proteins bind to elements, some to other proteins, external elements can influence binding

Question 32

Regulation at transcription- steroid response

Answer 32

Hormone receptors have multiple domains, in cytosol bound to HSP, steroid binds, receptor dimerizes, nuclear localization signal (NLS) activated, migrate to nucleus, interact with transcription complex

Question 33

Androgen insensitivity

Answer 33

Patients produce androgens, target cells fail to respond, lack the appropriate intracellular transcription factor receptors, leads to ambiguous genitalia or testicular feminization

Question 34

Regulation at transcription- thyroxin and gene regulation

Answer 34

Thyroid hormone receptor in dimer with RXR on DNA, binds co-repressor with histone deacetylase, thyroxine changes conformation, coactivator with histone acetylase can bind

Question 35

Thyroid hormone receptor disorders

Answer 35

Important in brain development in neonates, hypothyroidism increases T3 or TSH

Question 36

DNA binding domains- zinc fingers

Answer 36

Estrogen receptor, one zinc ion is coordinated with four cysteine residues, alpha-helix with nucleotide recognition signal (NRS), NRS binds to a specific base sequence in the major groove of DNA

Question 37

DNA binding domains- leucine-zipper

Answer 37

Alpha-helix of 30-40 amino acids, contains a leucine every seven amino acids, homo or hetero dimers, fos and jun genes

Question 38

DNA binding domains- helix-turn-helix

Answer 38

One helix fits into the major groove of DNA, stable in binding the DNA without dimerization, homeodomain proteins

Question 39

DNA binding domains- helix-loop-helix

Answer 39

Transcription factors, function as dimer (homo or hetero-dimers), myogenin in skeletal muscle

Question 40

Regulation at transcription- regulatory cascades

Answer 40

One transcription factor can regulate many genes, may include another transcription factor, can regulate other sets of genes, one stimulus, many responses

Question 41

Regulation at transcription- multiple sites in promoters

Answer 41

Promoters may have several transcription factor binding sites, different sites may direct activity in different circumstances

Question 42

Regulation at mRNA processing- alternative splicing

Answer 42

Splicing can generate multiple mRNAs, may be tissue specific, can change function of the product, more than one poly A addition site in gene, use of site prevents splicing, alters carboxy terminus of protein

Question 43

Regulation at mRNA processing- mRNA editing

Answer 43

mRNA sequence altered after transcription- rare, ex- ApoB100 gene, C deaminated to U, produces stop codon, shorter protein product

Question 44

Regulation at translation- regulation of protein synthesis initiation by eIFs

Answer 44

Globin protein made only in presence of heme, heme inactivates kinase that inactivates eIF-2, globin mRNA translation can proceed, heme levels are high, eIF2 is not phosphorylated and is active

Question 45

Regulation at translation- blocking translation

Answer 45

Ferritin synthesized when iron levels increase, ferritin mRNA has IRE, IRE-BP binds in absence of iron- no translation, increase in iron- translation occurs, ferritin binds excess iron

Question 46

Regulation at translation- miRNAs

Answer 46

Small RNA molecules that regulate protein expression at translational level- induce degradation, repress translation

Question 47

Actions of miRNAs

Answer 47

May be located within introns of target genes or organized in miRNA families, multiple target mRNAs, mRNAs bind multiple miRNAs, good potential drug targets

Question 48

Regulation of stability of mRNA

Answer 48

Degradation rate of mRNA is important, transferrin receptor mRNA has 3’ IREs, low iron, bound IRE-BP protects 3’ ends, more protein made, more iron can enter the cell, high iron, no binding, mRNA degraded faster

Question 49

Thalassemias

Answer 49

Defect in production of either alpha- or beta-globulin, tetramers form due to excess of other subunits, damage to RBCs, shorten lifespan of RBCs, cause anemia, splenomegaly common