Gene Expression Shred Fest I LO

Question 1

what determines the amount of protein within each cell? (4)

Answer 1

1. amount of mRNA
2. frequency of mRNA translation
3. stability of the protein
4. Rate of degradation of protein

Question 2

what is the most important mechanism for determining gene expression and amount of protein synthesized?

Answer 2

transcription initiation

Question 3

what are the 2 basic components important to eukaryotic gene expression?

Answer 3

1. DNA control elements-part of DNA that acts locally (cis)

2. transcriptional activators/repressors that act on other genes to regulate their transcription (trans)

Question 4

where do DNA control elements act?

Answer 4

locally, transcription factors bind to elements that control expression of that gene

Question 5

what are the 3 DNA control elements?

Answer 5

1. TATA box/initiator (promoter)
2. promoter proximal element
3. enhancer

Question 6

what is the TATA box?

Answer 6

located 25-35 bp upstream of transcription start, determines site of transcription initiation and directs binding of RNA pol II

Question 7

what is the promoter proximal element?

Answer 7

200 bps upstream of start site and about 20 bps long, helps regulate transcription

Question 8

what is the enhancer?

Answer 8

200-tens of thousands bps upstream or downstream from promoter or within an intron

Question 9

what binds at the TATA box?

Answer 9

general transcription factors like TATA binding protein

Question 10

what are the 3 diseases associated with mutations in the DNA control elements?

Answer 10

1. Thalassemias
2. Hemophilia B-Leyden
3. Fragile X-Syndrome

Question 11

what does an enhancer do?

Answer 11

binding of proteins enhances transcription levels

Question 12

what is a silencer?

Answer 12

Section of DNA that binds transcription regulating factors called repressors

Question 13

how does a silencer work?

Answer 13

when repressors bind, RNA polymerase is prevented from initiating transcription, thus lowers or eliminates transcription

Question 14

how is thalassemias inherited?

Answer 14

autosomal recessive

Question 15

what is thalassemias?

Answer 15

blood disease that occurs due to different genetic mutations such as mutation or deletion

Question 16

what mutation causes B-Thalessemias?

Answer 16

B-globin promoter mutation causing decreased transcription of this protein but not complete loss of this protein

Question 17

what mutation causes yDB thalessemias?

Answer 17

deletion of locus control region (LCR) of B-globin gene cluster, very severe form because LCR directly regulate expression of all genes in that cluster

Question 18

what chromosome is hemophilia B leyden linked to?

Answer 18

X

Question 19

what does hemophilia B leyden affect?

Answer 19

blood clotting

Question 20

how does hemophilia B leyden affect males?

Answer 20

have 1% of normal factor IX active until puberty, once androgen receptor becomes active, produce about 60% of normal factor IX

Question 21

what is the presentation of fragile X syndrome?

Answer 21

mental retardation, dysmorphic facial features, postpubertal macroorchidism (abnormally large testes)

Question 22

why does fragile-X syndrome develop?

Answer 22

expansion of CGG trinucleotide repeats in the 5’ region of FMR1 gene on X chromosome. normal humans have about 6-55 repeats but fragile X syndrome patient have between 230-4000 repeats

Question 23

why does increasing the amount of CGG repeats cause fragile X syndrome?

Answer 23

there is an increase in the methylation of cytosine residues in CpG islands of FMR1 promoter, methylation then causes silencing of FMR1 gene

Question 24

what is the severity of fragile X syndrome directly related to?

Answer 24

the number of CGG repeats

Question 25

what does the mutation in hemophelia B leyden disease prevent?

Answer 25

binding of appropriate transcriptional activators to Factor IX gene

Question 26

what are transcriptional factors?

Answer 26

proteins encoded by one gene that act on other genes to regulate their transcription (activators and repressors)

Question 27

what are the 2 classes of activators and repressors?

Answer 27

1. sequence-specific DNA binding proteins | 2. Co-factors

Question 28

what is a sequence-specific DNA binding protein?

Answer 28

protein that binds to the promoter or enhancer elements in their target genes to regulate transcription

Question 29

how do sequence-specific DNA binding protein binds to the DNA?

Answer 29

insert alpha helices into the major groove of DNA

Question 30

what are co-factors?

Answer 30

proteins that bind to sequence-specific DNA binding proteins rather than directly to DNA

Question 31

what are the 4 families of sequence-specific DNA binding proteins?

Answer 31

1. homeodomain proteins (helix-turn-helix) 2. Zinc-finger proteins 3. basic leucine zipper proteins (bZIP) 4. Basic helix-loop-helix motif (bHLH)

Question 32

What is the difference between a DNA binding domain and an activation domain?

Answer 32

DNA binding domain protein binds directly to the DNA molecule. Activation domain has a protein to protein interaction that modifies transcription

Question 33

what are the characteristics of a DNA binding domain?

Answer 33

- highly structured - evolutionarily conserved - structure allows them to bind directly to the DNA molecule

Question 34

what are the characteristics of an activation/repressor domain?

Answer 34

- not highly conserved - not very structured until they bind cofactors or general transcription factors - recruits additional factors to upregulate or downregulate transcription

Question 35

what are some examples of homeodomain proteins (helix-turn-helix)?

Answer 35

Hox family (embryologic development), Pit1 (pituitary development and hormone expression), msx (limb pattern formation)

Question 36

what are some examples of zinc-finger proteins?

Answer 36

nuclear receptors such as estrogen, androgen receptors

Question 37

what does a basic leucine zipper proteins and basic helix-loop-helix proteins require to bind to DNA?

Answer 37

homodimerization

Question 38

what are some examples of basic leucine zipper proteins?

Answer 38

c-fos and c-jun (proto-oncogene)

Question 39

what are some examples of helix-loop-helix (bHLH) proteins?

Answer 39

MyoD (muscle differentiation), myogenin (skeletal muscles development and repair), and MyF5 (muscle differentiation)

Question 40

what is craniosynotosis and what mutation causes it?

Answer 40

- premature closing of one or more sutures in the skull. - mutation in homeodomain of protein MSX2 (required in proper cranio-facial development) - proline to histidine amino acid substitution - one amino acid change in binding domain makes bind more strongly causing "gain of function" or "hypermorphic allele" leading to suture closure

Question 41

what is the presentation of androgen insensitivity syndrome (AIS)?

Answer 41

feminization, undermasculinization of external genetalia at birth, abnormal secondary sexual development in puberty, and infertility

Question 42

where is the mutation in androgen insensitivity syndrome?

Answer 42

DNA binding domain or ligand binding domain of androgen receptor (zinc finger binding domain), causes decreased sensitivity to androgen

Question 43

what is Waardenburg syndrome type II?

Answer 43

mutation in MITF gene, renders gene nonfunctional, affects transcription of genes important in pigmentation and in hearing

Question 44

what is combinatorial control?

Answer 44

when thousands of transcription factors can regulate tens of thousands of genes

Question 45

what do activators and repressors regulate?

Answer 45

- assembly of initiation complexes - rate of initiation of transcription - changes in chromatin structure influencing binding to promoters

Question 46

what is dimerization?

Answer 46

where multiple DNA binding factors (zinc finger etc) come together at binding sites and illicit different gene responses based on which factors are present in a cell at a certain time

Question 47

what does heterodimerization allow for (2)?

Answer 47

- recognize different DNA sequences allows recognition of new DNA sites - new combinations of activation domains to be brought together