Gene expression I

Question 1

how many base pairs does a human cell contain?

Answer 1

6X10^9

Question 2

3 things that determine amount of protein in a particular cell

Answer 2

1. protein’s corresponding mRNA
2. frequency of mRNA translation into protein
3. stability of protein

Question 3

What is most important mechanism for determining if genes are expressed?

Answer 3

transcription initiation

Question 4

location of tata box/ initiator sequence

Answer 4

25-35 bps upstream of transcription start sight

Question 5

3 roles of tata box

Answer 5

1. determines site of transcription initiation
2. directs binding of RNA polymerase II
3. Site of binding of transcription factors

Question 6

location of promoter or proximal elements

Answer 6

200bps upstream of transcription start site

20bps long

Question 7

role of promoter proximal elements

Answer 7

1. help regulate transcription

2. bound by factors in cell specific manner

Question 8

location of enhancers

Answer 8

200- tens of kilobases upstream or downstream from promoter, or last exon of gene, or within an intron

Question 9

length of enhancers

Answer 9

control element 8-20bps in length, with multiple control elements contained in each enhancer

Question 10

function of enhancers

Answer 10

regulate transcription in cell type specific manner

Question 11

beta thalassema pathology

Answer 11

deficient production of beta globin by erythroid cells

Question 12

beta thalassemia cause

Answer 12

mutation in beta globin promoter- reducing amount of beta globin mRNA and thereby protein produced

Question 13

hemophilia b Leyden cause

Answer 13

x- linked disorder
mutations in DNA control element of promoter of factor IX gene (thereby inhibiting binding of transcriptional activators)

Question 14

hemophilia b leyden and puberty

Answer 14

prior to puberty: males have 1% of normal factor 9 that is active

after puberty: androgen receptor becomes active and can bind at promoter site and increase transcription to 60% normal around factor 9

Question 15

gamma alpha beta thalassemia

Answer 15

deletion of locus control region of beta globin gene cluster

-lcr is essential for transcription of all genes within the cluster

Question 16

fragile x syndrome rate and symptoms

Answer 16

1/1500 males

Symptoms: mental regardation, dysmorphic facial features, postpubertal macroorchidism

Question 17

What are CGG repeats?

Answer 17

CGG repeats in 5’ region of FMR1 gene

facilitates methylation of cytosine residues in CpG islands and transcriptional inactivation of FMR1 Gene

Question 18

Fragile x syndrome pathology

Answer 18

expansion of repeat sequence CGG in 5’ region of FMR1 gene to >200 vs normal 6-50 repeats in the region

leads to increased methylation of FMR1 gene and thereby increase transcriptional silencing of FMR1 gene

Question 19

what are transcriptional activators and repressors?

Answer 19

proteins encoded by one gene that act on another gene to regulate their transcription

can diffuse around nucleus and activate or repress transcription

Question 20

what are two classes of activators and repressors?

Answer 20

1. sequence specific dna binding proteins

2. co- factors

Question 21

where do sequence specific DNA binding proteins bind?

Answer 21

promoter or enhancer elements (dna control elements) in target genes to regulate transcription

usually bind to elements 6-8 base pairs long

Question 22

how do sequence specific DNA binding proteins bind?

Answer 22

inserting alpha helices into major groove of DNA

contacts between amino acid side chains of protein and the bases of the dna

Question 23

where do co-factors bind?

Answer 23

bind to sequence specific DNA binding proteins to modify transcription before this contact

Question 24

Two components of modular sequence specific dna binding proteins

Answer 24

1. dna binding domain: highly structured and evolutionary conservation, folded so they can read DNA sequence and bind to specific target dna
2. Activation or repression domain: not highly conserved and are unstructured until they bind to co-factors

Question 25

What are families of sequence specific DNA binding proteins?

Answer 25

characterized by conserved DNA binding domain; domains of a particular family contain certain consensus amino acid sequences and are similar in tertiary structure more than 80% fall into one of four categories

Question 26

homeodomain proteins (helix turn helix)

Answer 26

Hox Pit1 Msx

Question 27

zinc finger proteins

Answer 27

nuclear receptors: estrogen androgen retinoic acid

Question 28

basic leucine zipper proteins (bZIP)

Answer 28

c-fos | c-jun

Question 29

basic helix loop helix motif (bHLH)

Answer 29

MyoD myogenin Myf5

Question 30

craniosynostosis rate

Answer 30

1/3000 infants

Question 31

craniosynostosis mutation

Answer 31

mutation in homeodomain of MSX2 (helix turn helix) | required for proper craniofacial development

Question 32

what is the quality of mutation that occurs in craniosynostosis?

Answer 32

gain of function/ hypermorphic allele: one amino acid substitution that allows protein to bind more strongly affects transcription of other genes critical for suture closure leading to premature closure of one or more sutures in the skull

Question 33

androgen insensitivity syndrome phenotype

Answer 33

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

Question 34

androgen insensitivity syndrome karyotype and mutation

Answer 34

males with normal karyotype 46 X,Y mutations in either DNA binding domain or ligand binding domain of androgen receptor (zinc finger)

Question 35

what is the quality of mutation that occurs in androgen sensitivity syndrome?

Answer 35

mutation makes individual less responsive to androgens to varying levels (complete, partial, or mild)

Question 36

phenotype of waarden burg syndrome type II

Answer 36

deafness, pigmentation anomalies of eyes, hair and skin

Question 37

mutation in waardenburg syndrome type II

Answer 37

15-20% of patients: mutations in microphthalmia associated transcription factor (bHLH) gene encodes transcription factor that plays important role in development of melanocytes

Question 38

What is combinatorial control?

Answer 38

dna binding factors can bind as heterodimers thus increasing the number of potential sequences to which that family of specific transcription factors can bind though combination of different monomers zinc finger, bZIP, and bHLH all form heterodimers

Question 39

After transcriptional activators are bound to DNA control elements, how do they stimulate transcription?

Answer 39

1. regulate assemby of initiation complexes and rate of initiation of transcription 2. regulate changes in chromatin structure influencing the ability of general transcription factors to bind promoters