Eukaryotic Gene Expression 1

when the trp is absent what happens

the Trp repressor does not bind to the operator and does not repress the Trp Operon

When the Trp Operon is repressed what will be expressed

structural genes

When Trp is abundant what happens

the Trp repressor binds to the operator and represses the Trp Operon. No Trp structural gene expression should occur

Why does RNA polymerase terminates transcription

So no structural gene for Tryptophan synthesis is transcribed

what is a terminator hairpin?

GC-rich secondary structure formed in a newly synthesized RNA molecule that acts as a signal for Rho-independent (intrinsic) transcription termination in bacteria

how does the terminator hairpin form

it forms in the presence of typtophan. Ribosome proceeds through the sequence

region 4 is called what

the attenuator

when RNA polymerase terminates transcription what happens to the structural genes

the structural genes for tryptophan synthesis is not transcribed

when typtophan levels are low or absent the leader regions contains 2 of what

tryptophan codons

where is the aniterminator hairpin located when the tryptophan levels are low?

between region 2 and 3

the antiterminator hairpin forms in the absence of what? This is results what stall at the codons?

form in absence of tryptophan, ribosomes stalls at codons

when tryptophan level is low what occurs during RNA polymerization

The RNA polymerase continues transcription, structural genes for tryptophan synthesis are transcribed

what region is called the attenuator

region 4 or the hairpin between 3 and 4

a charged tRNA is found in which hairpin

terminator hairpin

where does the ribosome move in the terminator hairpin

the ribosomes moves into the 1-2 regions preventing formation of 2-3 stem loop. Transcription will terminate at the 4 region

when charged tRNA is not available what hairpin is most affected

the antiterminator hairpin

what happens to ribosomes in the antiterminator hairpin

the ribosomes stalls on tryptophan codons, allowing formation of thr 2-3 stem loop.

what happens to transcription in the antiterminator hairpin

transcription proceeds

where is the secondary structure of the 5’ UTR in the terminator hairpin

3+4 hairpin

where is the secondary structure of the 5’ UTR in the antiterminator hairpin

2+3 hairpin

why does attenuation take place in the trp operon

when the repression at the operator is not enough,

why is attenuation needed in the trp operon

some transcription is initiated when the trp is active, the expression of trp structural genes are leaky. The attenuation mechanism prevent futher transcription of trp structural genes

what reduces transcription 70 folds

repressor

what reduced transcription 8-10 folds

attenuation

what will reduce the expression of trp operon more than 600 folds

repressor + attenuation

in attenuation trp structural genes are prededed by what

a leader sequence containing a regulatory site called an attenuator

what terminates transcription before it reaches the structural genes

attenuation mechanism

premature termination of transcription in attenuation affects what

the continuation of transcription not its initiation

attenuation uses what to control transcription, what provides regulation

translation, RNA’s secondary structure provides regulation

what operons uses attenuation

Threonine, histidine, leucine, and phenylalanine

different cell types of a multicellular organism contains the same what

DNA- difference cells type produce different sets of proteins

a cell can change the expression of its genes in response to what

an external signal

gene expression can be regulated at what various steps

DNA to RNA to Protein

eukaryotic gene expression is influenced by what chromatin modifications

histone modification and DNA Methylation

eukaryotic transcription initation is regulated by what

trans acting transcription factors that bind to cis acting sites

what are some examples of trans acting transcription factors that bind to cis acting sites

promoter and enhancer analysis, transcription of the GAL genes of yeast, and human metallothionene II A gene ( h MTIIA)

regulation of alternative splicing determines what

which RNA splice forms of a gene are translated

gene expression is regulated by what

mRNA stability and degradation

noncoding RNAs play diverse roles in where

posttranscriptional regulation

is mRNA localization and translation initiation highly or low regulated

highly

what regulates protein activity

posttranslation modifications

which gene regulation is more complex eukaryotic or prokaryotes and why

eukaryotics because they have a greater amount of DNA asociated with histones and other proteins

in gene regulation the DNA must unwind from where

the histone proteins before transcription

what is monocistronic

Each structural gene has its own promoter and is transcribed separately. Transcription and translation does not occur at the same time.

genes on numerous chromosomes are enclosed in what

a double membrane nucleus

what must occur for mRNAs to be transported from the nucleus

it must be sliced, capped, and polyadenylated

what are the processes that control post translation control

protein processing, modification, and degradation

what are the steps for gene regulation in eukaryotes

DNA, RNA transcript, mRNA in the nucleus, mRNA in the cytosol, protein and degradation of protein

what does transcriptional control in the eukaryotic gene regulation

DNA

what does RNA processing control in Eukaryotic gene regulation

RNA transcript

what doe mRNA transport and localization control in the eukaryotic gene regulation

mRNA in the nucleus

where does degradation of mRNA takes place in the cell

the cytosol

what does translational control during Gene regulation in Eukaroytes

mRNA

what does the protein activity control consist of

active and inactive proteins

what does protein degration control in gene regulation in eukaryotes

proteins

eukaryotic regulation of gene expression occurs at the level of what

transcriptional

where does posttranscriptional regulation take place in eukaryotic cells

in the nucleus and cytosol

In posttranscriptional regulation in eukaryotes, regulation of alternative splicing determines what

which RNA splice forms of a gene are translated

In posttranscriptional regulation in eukaryotes, gene expression is regulated by what

mRNA stability and degradation

In posttranscriptional regulation in eukaryotes, noncoding RNAs play diverse roles in what

posttranscriptional regulation

In posttranscriptional regulation in eukaryotes, mRNA localization and translation initiation are highly or low regulated?

highly

In posttranscriptional regulation in eukaryotes, posttranslation modification regulated what

protein activity

what are the two structural features of eukaryotes distinguish them from prokaryotes

eukaryotic genes are situated on chromosomes that occupy a distinct location and eukaryotic DNA is combined with histones and nonhistone protein to form chromatin

a compact chromatin (heterochromatin) structure inhibits what

transcription, replication, and DNA repair

can gene expression be influenced by chromatin modifications

yes

How much DNA is in eukaryotic chromosomes and how is it stored?

about 2 meters of DNA is tightly packed into a nucleus that is only 5–10 µm in diameter.

what is the basic structural unit of chromatin

nucleosome

why is nucleosome important in DNA organization

it is the major structure associated with the organization of chromatin in the nucleus

what structural components resembles the beads on a string model with each bead being a nucleosome

a 10 nm chromatin fiber and the unfolded chromatin,

what is the beadlike structural units of a eukaryotic chromatin composed of

histones and DNA

What is a nucleosome in eukaryotic cells?

a structure where DNA wraps around a core made of eight histone proteins (four pairs), forming about two turns around the histones.

what is histones/ octameric

eight protein complex found at the center of a nucleosome core particle

what does histones contain

two copies of each of the four core histone proteins H2, H2B, H3, and H4

what is the role of histones

it prevents DNA from become tangled and protect it from DNA damage, it plays an important role in gene regulation and DNA replication

positively charge/ highly basic proteins are associated with what

chromosomal DNA in eukaryotes

Why do DNA strands wrap around histones?

Histones are positively charged, which attracts negatively charged DNA, causing it to wrap around them and form a compact supercoiled structure.

what contain large amounts of lysine and arginine

positively charged proteins/ histones

what does the H1 histone do

it pulls nuceleosomes together into a regular repeating array

what does not form part of the octameric core

H1 histone

to allow gene expression, chromatin must

relax compact structure, expose region of DNA to regulatory proteins, and have a reversal mechanism for inactivity

chromatin remodeling b chromatin remodeling complexes bind directly to where and reposition what

it binds directly to DNA and reposition nucleosomes

How does nucleosome repositioning affect gene expression?

Repositioning nucleosomes makes certain regions of DNA more accessible to proteins, including those needed to start transcription, by exposing areas like the TATA box.

How do chemical modifications of chromatin affect gene expression?

Chemical changes to histone proteins in nucleosomes can alter chromatin structure, which in turn influences gene expression.

what are not packed into folded histone domains within nucleosome

unstructured histone tails

What are histone tails and how are they structured?

Histone tails lack a defined secondary structure and extend outward from the nucleosome core, passing through the minor groove of the DNA

What is the significance of different histone tail modifications?

Different combinations of histone tail modifications can create specific signals that determine how a region of chromatin is interpreted and regulated.

what enzyme is found in acetylation

histone acetyltransferase

addition of acetyl group to postivitely charged amino group on side chain/ lysine changes what

net charge of protein by neutralizing positive charge

A positive correlation with gene activity does what to expression

increases expression

what is histone deacetylation

it is a process that removes acetyl groups from histones

histone deacetylase is carried out by what

histone deacetylase enzymes (HDAC)

what does HDAC inhibitors do

it prevents the deacetylation of histones leading to increased histones acetylation and changes in gene expression

imagine that a fly mutant was isolated that contained histones resistant to acetylation. What phenotype would you predict for this mutant

the mutant will show decrease levels of gene expression

what is neutralized upon acetylation creating euchromatin which increases transcription and expression of the target gene

histone

what encodes a transcription factor/ regulator that represses flowering

flowering locus (FLC) gene

what encodes a protein/ histones deacetylase activity that promotes FLC repression

Flowering locus D (FLD) gene

high FLC=

late flowering

low FLC=

early flowering

active FLC reduced what for what flowering

reduced FLC for earlier flowering

inactive FLD creates what for what flowering

high FLC for late flowering