Gene Expression I

Question 1

What determines amount of protein?

Answer 1

The protein’s mRNA, the frequency mRNA is translated, and stability of protein

Question 2

DNA control elements

Answer 2

DNA elements that act locally. Binding of trx factors to these elements controls expression of gene that the element is associated with.

Question 3

TATA box/initiator sequence

Answer 3

This element is 25-35 bp’s upstream of trx start site. Determines site of trx initiation and directs binding of RNA polymerase II.
Site where general trx factors bind!

Question 4

RNA polymerase mnemonic

Answer 4

Pol One Run: rRNA
Pol Two Moo: mRNA
Pol Three Tree: tRNA

Question 5

Promoter Proximal elements

Answer 5

within 200 bps upstream of trx start site. are 20 bps long.

Help to regulate trx, can be bound by factors in a CELL TYPE SPECIFIC manner.

Question 6

Enhancers

Answer 6

Contain multiple control elements, each 8-20bps in length.

An entire enhancer can be 100-200bps long. Enhancer can be way downstream or upstream from promoter, in exons or introns.
Can help regulate trx in a CELL SPECIFIC MANNER

Question 7

Diseases from mutations in DNA control elements

Answer 7

Thalassemias: beta (inherited anemia, deficient B globin protein. Can occur due to diff mutations, one can be in beta-glob promoter. Usually mild.)
Gamma-delta-beta: deletion of LCR of beta globin cluster

Hemophilia B leyden: x-linked. Have 1% normal factor IX until puberty because of inherited mutations in a DNA control element in promoter of factor IX gene. Alt trx activators can bind overlapping sites in the promoter, at puberty, when AR becomes active, it can bind promoter site and increase trx so males produce 60% of factor IX.

Fragile X: CGG repeats in 5’ UTR region of FMR1 gene facilitates methylation of cytosine residues in CpG islands trx inactivation of FMR1 (expanded repeat copies). get trx. silencing.

Question 8

Trx activators and repressors

Answer 8

Proteins encoded by one gene that act on other genes to regulate their trx. Can diffuse around nucleus and affect trx of numerous genes.
Can activate or repress.

Question 9

2 classes of activators and repressors

Answer 9

1. ) Sequence-specific DNA binding proteins

2. ) Co-factors

Question 10

Sequence-specific DNA binding proteins

Answer 10

bind to promoter or enhancer elements (DNA control elements) in their target genes to regulate trx.
Elements they bind are usually small.

Bind DNA by inserting alpha-helices into MAJOR GROOVE of DNA, making contacts between amino acid side chains of the protein and bases in the DNA.

Question 11

Co-factors

Answer 11

Do not bind directly to the DNA elements, but bind to sequence-specific DNA binding proteins and affect trx through this contact!

Question 12

Modularity

Answer 12

Sequence-specific DNA binding proteins are modular, contains 2 major domains

Question 13

Domains of sequence-specific DNA binding proteins

Answer 13

1. ) DNA binding domain: highly structured and conserved. Folded so they can “read” the DNA seq and bind their specific target DNA
2. ) Activation (or repression) domain. NOT highly conserved, very unstructured (until they bind co-factors or general trx factors).

Question 14

Families of SSDBP?

Answer 14

4 families. Distinguished by a conserved DNA binding domain! Domains have certian AA seq and are similar in tertiary structure.

1. ) Homeodomain proteins (helix-turn-helix) (hox, pit1)
2. ) Zinc-Finger Proteins (estrogen, androgen…_
3. ) Basic leucine zipper proteins (bZIP, cfos cjun)
4. ) Basic helix-loop-helix (bHLH) (myoD etc)

Question 15

Craniosynotosis

Answer 15

premature closure of skull sutures.
Boston type variant: MSX2 homeodomain protein mutation. It is nec for genes important in proper craniofacial development.
AA substitution in the homeodomain, so protein binds DNA more strongly- giving a “gain of fx” allele. Mutated hyperactive protein then affects other genes nec. for suture closure.

Question 16

Androgen Insensitivity Syndrome

Answer 16

Feminization of external genitalia at birth. Abnormal secondary sex development in puberty, infertility.
46XY.
Mutations in DNA binding domain of androgen receptor (zinc finger DNA BP), makes pt less responsive to androgens. Can have varying levels of AIS.

Question 17

Waardenburg Syndrome type II

Answer 17

Deafness, pigmentation anomalies in eyes, pigmentation defects (hair, skin).
Mutations in trx factor gene (encodes a bHLH DNA binding protein). This gene encodes a trx. factor that plays a major role in the development of melanocytes.

Question 18

Dimerization

Answer 18

Many sequence specific DNA binding factors bind DNA as homo or heterodimers.
Zing finger, bZIP, and bHLH can all form heterodimers.
If each monomer of heterodimer has a diff DNA binding specificity, formation of heterodimers will increase the number of potential sequences to which that family of seq specific trx factors can bind

Combinatorial control.

Many trx factors can come together in diff ways to regulate genes differentially.

Question 19

How do activators or repressors stimulate trx?

Answer 19

1. ) Regulate assembly of initiation complexes and rate of initiation of trx
2. ) Regulate changes in chromatin structure influencing ability of general trx factors to bind promoters