BIO 100 Chapter 19 Gene Regulation in Eukaryotes

why is p53 found in over half of all human cancers?

because if p53 is mutated, damaged DNA is replicated, causing further mutations aka CANCER

regulatory sequence

binding sites for proteins that control gene expression

Linking cancer defects in gene regulation

involved uncontrolled cell division mutations lead to cancer when they affect: 1. genes that stop or slow cell cycle 2. genes that trigger cell growth and division by initiating specific phases in the cell cycle genes that are mutated in cancer influence gene regulation

Mediator

large complex of proteins that integrates the input of many regulatory transcription factors

Histone Modification

many enzymes add chemical groups to histones which promotes either condensation or DEcondensation histone code - sets the state of condensation

Chromatin-Remodeling Complexes

molecular machines that reshape chromatin cause nucleosome to slide along the DNA knock histones off DNA open up stretches of chromatin and allow gene expression

Chromatin Modifications can be inherited

patterns of methylation and acetylation can be passed on when cell divides

Enhancer function using ...

positive control

Tumor suppressors

proteins that stop or slow the cell cycle when conditions are unfavorable

repressors

regulatory proteins that bind to silencers, SHUTS DOWN transcription

what do transcriptional activators do?

when they bind to enhancers, transcription begins not composed of DNA sequences

Model for Transcription Initiation

1. Activators bind to DNA and recruit chromatin-remodeling complexes and HATs 2. Chromatin Remodeling opens chromatin exposing the core promoter and regulatory sequences 3. Other activators bind enhancers and promoter-proximal elements; DNA loops so mediator and activators ineract 4. General transcription factors and RNA polymerase assemble on mediator and associate with the core promoter - TRANSCRIPTION BEGINS

Eukaryotes have 3 additional levels of control...

1. Chromatin Remodeling 2. RNA processing to produce a mature mRNA 3. Regulation of mRNA life span or stability

histone protein called H1 causes nucleosomes to interact with each other to form...

30 nm fibers(attached to scaffold proteins to hold entire chromosome in place)

chromatin

DNA is wrapped around proteins to create a structure

What did Weintraub and Groudine use to test why chromatin structure is altered in active genes?

DNase

own distinct region

Each chromosome occupies it's _________ _________ _________ in nucleus

Evidence that Chromatin Structure is altered in Active Genes

Eukaryotic DNA has promoters where RNA polymerase bind Chromatin must be decondensed to expose the promoter for RNA polymerase to bind

Initiating Transcription: Regulatory Sequences and Proteins

Eukaryotic promoters are more complex than bacterial promoters have 2 or 3 regulatory sequences and a core promoter

RNA interference and the expression of Individual RNAs

RNA interference controls the life span of many mRNAs tiny singled-stranded RNA held by a protein complex, binds to a complementary sequence in an mRNA, and either causes destruction of the mRNA or blocks its translation one type of RNA interference works through microRNA(miRNA)

core promoter

RNA polymerase binds to this most common sequence is TATA box TATA-binding protein binds here

Why is Chromatin Remodeling important?

RNA polymerase cannot access the DNA when it is tightly coiled

First step in initiating transcription

TATA-binding protein binds to core promoter(TATA box)

Eukaryotes can control gene expression at levels of...

Transcription, Translation, Post-translation

What is p53?

a tumor suppressor detects DNA damage during cell division by binding to enhancers of genes that: arrest the cell cycle, repair damage or trigger apoptosis(cell death) if all else fails

role of regulatory transcription factors in differential gene expression

activators and repressors are regulatory transcription factors that regulate transcription genes encoding transcription factors are expressed in response to signals from other cells ex: cells signalled to become a muscle cell, it produces transcription factors specific to muscle cells

Histone acetyltransferases(HATs)

adds acetyl groups to histones, DECONDENSING CHROMATIN

epigenetic influence

any inheritance mechanism that is not due to differences in DNA sequences record life events that influence phenotypes of offspring

Acetylation

associated with activation of genes

regulatory protein

binds to a short stretch of DNA located UPSTREAM from the core promoter for each of the 5 genes required by galactose metabolism co-regulated genes have same regulatory sequence

Define RISC

blocks miRNA from translating by preventing mRNA translation or cuts complementary miRNA

miRNA

can be targeted by one mRNA at multiple amounts regulates gene expression

DNA Methylation

causes chromatin to condense by the use of DNA methyl transferases which adds methyl groups(-CH3) to cytosines in DNA mammals - recognize a C next ot a G (CpG) Actively transcribed genes have LOW levels of methylated CpG near promoters(which is another proof that chromatin is altered in ACTIVE genes because they want decondense chromatin)

Is decondensed chromatin or degraded DNA easier to be transcribed?

decondensed chromatin

Post-Transcriptional Control

each event can regulate gene expression 4 post-transcriptional control points: 1. different ways of splicing the same primary transcript 2. Inhibiting translation of most mRNAs in the cell 3. Destroying or altering the ability to translate mRNAs 4. Altering protein activity after translation

How do transcription factors recognize specific DNA sequences?

each transcription factor must be able to recognize and bind to a specific DNA sequence DNA bases are partially exposed in the major and minor grooves of the DNA double helix edges of an AT base pair and a GC base pair have different surface shapes differences in composition and shape can be recognized by transcription factors

What is DNase?

enzyme that cuts DNA at random locations cannot cut tightly condensed DNA(hence why DNA must be DEcondensed) preferentially cuts genes that are ACTIVELY being transcribed

How are proteins targeted for destruction?

enzymes mark proteins by adding many copies of a small polypeptide called ubiquitin PROTEASOME recognizes and destroys tagged proteins

proto-oncogenes

genes that stimulate cell division active when conditions FAVOR GROWTH in cancer cells, they stimulate growth at all times because mutations converted them to ONCOGENES for cancer to develop, MANY mutations must occur in a SINGLE cell

What is chromatin's basic structure?

has several layers of organization wrapped around histones and other proteins 200 bases of negatively charged DNA wrap around a core of 8 positively charged histone proteins - nucleosome repeating, beadlike structures spaced with linker DNA

transcription factors

must interact with regulatory sequencer to initiate transcription are not restricted , do NOT regulate gene expression, interact with core promoter, and are required for transcription

How is translation controlled?

once mRNA is in cytoplasm, other levels of gene expression come into play global regulation of translation occurs when most translation is shut down: caused by stressful conditions such as low O2 or nutrients mT or protein kinase is inactivated stops phosphorylating translation initiation factors

Alternative Splicing of Primary Transcripts

regulated by proteins that interact with spliceosomes over 90% of human sequences undergo this 20,000 genes produce 60K - 100K proteins gene is now defined as a nucleotide sequence number of different proteins and mature RNAs is far larger than number of genes

promoter-proximal elements

regulatory sequences close to the promoter that are unique to the sets of genes UPSTREAM of the promoter

Enhancers

regulatory sequences far from the core promoter needed for enhanced transcription in the intron of a gene DOWNSTREAM of the promoter all EUKARYOTES have this can be more than 100,000 bases away can bind to more than one type of regulatory protein can work even if their orientation is flipped or moved to a new location

Histone deacetylases(HDACs)

remove acetyl groups from histones, leading to chromatin condensation

what other types of small RNAs can RNA interference use?

short interfering RNAs(siRNA) PIWI-interacting RNAs (piRNAs) used to decrease expression of particular genes to study effects

silencers

similar to enhancers, except they REPRESS gene expression "silence" gene expression

Why is it good when chromosomes condense before cell division?

they become more tightly packed which allows the DNA to fit in the nucleus and plays a key role in gene expression

Post-Translational Control

this is similar in both eukaryotes and bacteria enzymes add carbohydrate groups or cleave off amino acids proteins may be phosphorylated by protein kinases proteins may be targeted for destruction

Chromatin Remodeling

unpacks DNA at particular genes so they can be transcribed

hypothesis about 5 genes

when galactose is present, yeast greatly increases transcription of five galactose-utilization genes five genes are regulated together even if they are on different chromosomes normal cells have an activator protein mutant cells have a mutation that DISABLES mutation