DNA Regulation

what did Francois Jacob and Jacques Monad discover about protein production?

through their discovery of the Lac Operon, protein production is regulated by transcription

explain the structure of an operon

regulatory section - DNA sequences with regulatory control sites (promoter and operator)
coding section - genes that code for the protein(s) used by the cell (structural genes)
regulatory gene - next to operon, codes for activators and/or repressors

please explain the formation of a chromosome (starting with DNA double helix)

the DNA double helix is wrapped around histone proteins; 8 DNA wrapped histones come together to form a nucleosome; these nuelcosomes wrap around in a helical fashion to form a coil called a solenoid; the coils wrap even further forming supercoils; the supercoils form DNA-protein fibre called chromatin; chromatin condenses even further to form a chromosome

what makes up the basic transcription appparatus in prokaryotes?

general transcription factors, RNA polymerase, mediator multiple protein complex

how do activators enhance the interaction between RNA polymerase and promoters?

they increase the attraction of the RNA polymerase for the promoter through interactions with subunits of the polymerase or indirectly changing the structure of DNA

differences in prokaryotes and eukaryotes when it comes to transcription regulation

prokaryotes → needed for the cell to be able to quickly adapt to its ever changing environment. a combo fo activators, repressors and rarely enhancers determine whether gene is transcribed
eukaryotes → involves a combination of interactions b/w several TFs allowing for more sophisticated response to multiple conditions in the envi

what makes up a eukaryotic promoter and their function?

core promoter → TATA box, remains consistent in all euk genes, about 40 bases upstream of the transcription start site. core proteins bind to form complex for gene expression
upstream promoters → found upstream of core promoter; can bind activators/repressors; number of types vary from gene to gene

what are 2 core proteins that make up the complex for gene expression?

TF IID → a complex of proteins consisting of TATA binding proteins
TF IIB → helps TBP interact with RNA polymerase II

5 cancer types

carcinoma → form in epithelial cells (skin/tissues) lining internal organs
sarcoma → develop in soft tissue (bones, cartilage, fat, muscle, connective tissue)
leukemia → begins in lymphoblastic or myeloid cells of blood-forming tissue
lymphomas → start in lymphocytes (T/B cells) in the immune system
brain and spinal cord tumors → develop in brain/spinal cord named based on cell of origin

how pRb functions as a tumour suppressor proteins?

pRb prevents cell from replicating when DNA is damaged by preventing it from leaving G1; attracts histone deacetylase to the chromatin reducing transcription of S phase promoting factors

how p53 functions as a tumour suppressor protein?

activates DNA repair proteins (p21) when DNA is damaged and can stop the cell growth by holidng the cell cycle hostage b/w G1 and S to repair the DNA; can also initiate apoptosis if DNA cannot be repaired

a) II and III only
b) I, II, and III
c) II only
d) I and II only

d) I and II only

Thyroxine (T4) is a peptide hormone released primarily by thyroid follicular cells. Thyroxine release is limited to thyroid follicular cells because these cells contain:
a) the gene that codes for thyroxine
b) the promoter of the set of genes that codes for thyroxine
c) the operator of the set of genes that codes for thyroxine
d) TF for thyroxine expression

d) TF for thyroxine expression

explain how operons with inducible systems work

a repressor is bonded tightly to the operator, acting as a roadblock for RNA polymerase; acts as a negative control mechanism

how are inducible systems aliken to competitive inhibitors?

as the concentration of the inducer increases, it will bind to more repressors causing them to fall off the operator, freeing the gene for transcription

why don’t bacteria just digest both lactose and glucose?

it is more energetically expensive than digesting glucose, so they only want to use this option when glucose is low and lactose is high

negative vs positive control mechanisms

binding of a protein reduces transcriptional activity (repressor binding to operator) vs binding of molecule increases transcription of gene (CAP)

explain how operons with repressible systems work

repressors made by the regulator gene is inactive until it binds to a corepressor, which will then bind to operator to prevent further transcription

how are repressible systems aliken to negative feedback?

the corepressor is often the final structural product, thus as its levels increase, it can bind to repressor to bind to operator preventing further transcription

explain the trp operon

Tryptophan can be acquired from local environment. when trp is high in the local envi, it acts as corepressor, turning off its machinery to synthesize its own trp

what are transcription factors?

transcription-activating proteins that search the DNA for specific DNA-binding motifs

purpose of the DNA-binding and activation domains on TFs?

DNA-binding domain → binds to specific sequence in promoter or to a DNA sequence that binds only to specific TFs (response element) to help recruit transcriptional machinery
activation domain → can bind several TFs and other important regulatory proteins to help remodel the chromatin structure

purpose of basal transcription

to maintain moderate, but adequate levels of the protein encoded by this gene

what helps with gene amplification

enhancers and gene duplication

enhancers

several response elements grouped together outside the normal promoter which can be recognized by specific TFs to enhance transcription levels

receptors for signal molecules:
cAMP
cortisol
estrogen

cyclic AMP response element-binding protein (CREB)
glucocorticoid receptor
estrogen receptor

location of enhancers

can be up to 1K bps away from the gene they regulate and even located within an intron (noncoding region)

gene duplication in series vs parallel

series → on same chromosome, yielding many copies in a row of the same genetic info
parallel → open gene with helicase and permitting DNA replication only of that gene, can continue until hundreds of copies exist in parallel on same chromosome

what does acetylation do to histones that loosen DNA?

decrease the positive charge on lysine residues and weakens the interaction of the histone with DNA

function of DNA methylases

add methyl groups to cytosine and adenine nucleotides