Gene Expression Flashcards

Flashcards generated from General Biology II lecture notes on Gene Expression by C. von Roretz.

Euchromatin

Loosely packed DNA, generally expressed.

Heterochromatin

Tightly packed DNA, generally not expressed.

Acetylation of Histones

Adding acetyl groups (COCH3) to lysines on histones, which reduces the attraction between DNA and histones, promoting loose chromatin structure and permitting transcription.

HATs (Histone Acetyl Transferases)

Enzymes that add acetyl groups to histones.

HDACs (Histone Deacetylases)

Enzymes that remove acetyl groups from histones.

Histone Methylation

Promotes association of histones and tighter packing of DNA.

Histone Phosphorylation

Loosens the association of histones with DNA.

DNA Methylation

Reduces transcription and can be used for long-term gene silencing.

Epigenetics

Heritable gene expression that is not encoded in the nucleotide sequence itself, but rather through histone and DNA modifications.

Transcription

The process of copying a specific gene into a short-term version (mRNA).

Promoter Region

A region of DNA where transcription factors associate, containing the TATA box.

Activators

Enhance transcription by binding to distal control elements.

Repressors

Inhibit transcription by binding to proximal control elements.

Control Elements

Regions of DNA that can recruit transcription factors, either close to the promoter (proximal) or far away (distal).

Enhancers

Another name for a distal control element; sequences of DNA that primarily recruit activators of transcription.

Activators

Transcription factors that bind to distal or proximal control elements to help/support transcription.

Repressors

Transcription factors that only bind proximal control elements and inhibit transcription.

Operator Sequence

A sequence located in DNA near the promoter where a repressor can bind to prevent transcription.

Repressible Operon (Trp Operon)

Default is to GO! and Trp allows repression.

Inducible Operon (Lac Operon)

Default is NO! and Lac now allows transcription.

Capping

Protection and export of mRNA

Polyadenylation

Protection and export of mRNA

Splicing

Generating diversity and export

5’ mRNA Cap

Inverted GTP at the 5’ end of the mRNA, protecting it in the cytoplasm and involved in splicing initiation, export, and translation initiation.

PolyA Tail

50 to 250+ adenines at the 3’ end of mRNA, involved in export, protection from degradation, and translation.

Introns

Excess material in premature mRNAs; intragenic regions.

Splicing

The removal of introns from premature mRNAs.

miRNA (microRNA)

Small (~22nt) RNA fragments that bind to mRNA, leading to translational repression or degradation.

Proteasome

A protein with many ubiquitins is taken into the _ for degradation.

Viruses

Obligate intracellular parasites that must produce both protein and genetic material before leaving the host cell.

Lytic

The term for when a cell dies immediately because of a virus.

Lysogenic

The term for when a cell stores a virus and divides.

Silent Mutation

Mutation where the codon gives the same amino acid

Missense Mutation

Mutation where the codon gives a different amino acid

Nonsense Mutation

Mutation where the codon is now a STOP codon

Frameshift Mutations

Mutations that skew the coding of a gene (altered reading frame).

HATs

histone acetyl transferasesthat add acetyl groups to histones, resulting in an open chromatin structure that promotes gene transcription. removes posistive charge reducing attraction between DNA and histone

HDACs

histones deacetylases that remove acetyl groups from histones, leading to a closed chromatin structure that represses gene transcription. positive charge back from lysine heterochromatin

Acetyl CoA

donor of the acetyl group

Hitstone methylation

promotes association of dna to histones

Histone phosphorylation

adds phosphate group greacting a repulsive forve between the histones and dna further loosening up the relationship between them

Methylation of DNA

reduces transcription by inhibiting the binding of transcription factors and RNA polymerase to DNA. can be used for long term silencing of gene expression and may play a role in cellular differentiation. x chromosome in womeninactivation occurs through DNA methylation. this must be copied during replication

DNA methyl transferases

copies dna methylation during replicationThese enzymes are responsible for adding methyl groups to DNA, thereby influencing gene expression and maintaining epigenetic modifications across cell divisions.m

are methylation patterns inhereted?

yes reffered to as genomic imprinting,

can environment afffect methylation

yes, trauma and exposure to toxins can lead to changes in methylation patterns, potentially impacting gene expression and influencing various health outcomes.

3 stages of transcription

1. initiation

2. elongation

3. termination

mRNA

product of transcription that carries genetic information from DNA to the ribosome for protein synthesis (translation).

after 3 stages of transcription what is the stage of mRNA

it is premature

RNA polymerase

An enzyme that synthesizes RNA from a DNA template during transcription. moves 3’ to 5’ on template strandand synthesizes RNA 5’ to 3’.

promoter region contains

TATAAA BOXa core element that helps initiate transcription in eukaryotic genes. and that is on the non template strandIt also plays a role in recruiting RNA polymerase.

what can influence the TATA box

factors further before the promoter upstreamthat can either enhance or inhibit the binding of RNA polymerase, thus affecting transcription initiation.

elongation

The stage of transcription where RNA polymerase adds nucleotides to the growing RNA in the 3’to 5; on the template and 5’to3’ direction strand after the initiation complex is formed.

can multiple rna polymerase work at the same time

yesmultiple RNA polymerases can transcribe a single gene simultaneously, allowing for increased RNA production.

RNA pol II

is an enzyme responsible for synthesizing mRNA from a DNA template during transcription in eukaryotic cells. ( makes the mRNA)

transcription termination

RNA polymerase continues until it reaches a polyadenylation signal AAUAAAin the mRNA, leading to the cleavage of the transcript and release of the RNA polymerase. after 10-35nt

polyA signal in prokaryothes ?

no, instead there is a terminator sequence, which kicks rna pol off the dna

control elements

are regulatory DNA sequences that control the transcription of nearby genes by binding transcription factors before promoter region in non coding dna

distal control elements

are enhancers located far from the promoter that can significantly increase the transcription of a gene when bound by specific transcription factors. usually enhancers

proximal control elements

are regulatory DNA sequences located close to the promoter that help regulate gene transcription by providing binding sites for transcription factors. usually repressors bind to those control elements and inhibit transcription

enhancers

are short regions of DNA that can be bound with proteins (transcription factors) to increase the likelihood of transcription of a particular gene, often located far from the gene they influence.

activators

are proteins that bind to enhancers or promoter regions to increase the rate of transcription by recruiting the transcription machinery to the gene.

trancriptional operons

are clusters of genes that are transcribed together under the control of a single promoter, allowing for coordinated expression in prokaryotes.

operator

is a segment of DNA that a repressor protein binds to, inhibiting the transcription of nearby genes in operons. near the promoter regionin downstream

low tryptophan

encourages the expression of genes involved in tryptophan synthesis, allowing the organism to produce more of this amino acid.

high tryptophan

prevent tryptophan synthesisby activating the repressor protein that binds to the operator, thus inhibiting the transcription of genes needed for its production.

repressible

refers to a type of operon whose transcription can be inhibited by the presence of a specific molecule, such as a corepressor. in this case tryptophan is allows repression

inducible

describes an operon that can be activated by the presence of an inducer, leading to gene expression. lactose absent, reprossor is active and operon is off

lactose present

the inducer binds to the repressor, inactivating it and allowing the operon to be transcribed, resulting in the expression of genes necessary for lactose metabolism.

how can glucose work as an activator in the lac operon when its low

in absence of glucose transcription of the lac operon is increased as lactose is present. if both are present lac operon not that functional. bacteria prefer glucose.

what happens to mRNA before leaving the nucleus

1. capping

2. polyadeylation

3. splicing

m RNA capping

5’ end cap inverted GTP

1. protects mRNA in cytoplasm

2. added during trancription

3. involved in splicing initiation

4. enables export by binding to cap binfing complex

5. involved in initiation of translation

6. presence of cap is what alloes the two other steps to happen

poly A tail

1.consist of 50+ adedines at the 3’ end of mRNA

2.addition occurs at the end of transcription

3.involved in export

4. protects mRNA from degradation

5. involved in translation

splicing

The process of removing introns and joining exons in pre-mRNA, creating a mature mRNA molecule ready for translation. This occurs in the nucleus before mRNA is exported to the cytoplasm. occurs only if 5’ cap is presentIt typically involves the spliceosome, which is a complex of proteins and RNA ( snRNA) that facilitates the removal of non-coding regions from the pre-mRNA.

introns

Non-coding segments of pre-mRNA that are removed during splicing. XS material

spliceosome

moves from 5’ to 3’ unlike all other enzyme we have seen. folds mRNA to find 3’ ends for splicing. hydrolyzes phosphodiester bonds then ligates free ends

ribozyme

can splice aswell

alternative splicing

a regulated process that enables a single gene to produce multiple protein isoforms by including or excluding specific exons during mRNA processing.

mRNA exportation

transport into cytoplasm is tighly regulated , depends on cap , tails and removal on introns.

mRNA localization

the mechanism by which mRNA molecules are transported to specific locations within the cell, influencing translation and protein synthesis. sometimes localization can prevent trabslation and store the mRNA.

UTR’s

untranslated regions that play a crucial role in the regulation of mRNA degradation, localization, and translation efficiency.

translation

convertion from the language of nucleic acids to the language of amino acids, resulting in protein synthesis. three steps

1. initiation

2. elongation

3. termination

tRNA

a type of RNA that helps decode mRNA into a protein by carrying specific amino acids to the ribosome during translation. Uses RNA Pol III

amino acyl-tRNA syntheses

enzymes that attach specific amino acids to their corresponding tRNA molecules, ensuring accurate protein synthesis.

initiation

the first step in translation where the ribosome assembles around the mRNA and the first tRNA is attached to the start codon met on the p siteThis step initiates protein synthesis.

translation uses energy?

yes in forms of GTP

elongation

next tRNA is added to ribosome at the a site where amino acids on tRNA are sequentially linked to form a polypeptide chain. this step uses energy.then tRNA on the p site loses its bond with polypepetide and exists from the e siteDuring elongation, the ribosome moves along the mRNA, continuously adding amino acids to the growing polypeptide chain. This phase utilizes energy, and tRNA in the P site releases its peptide bond before exiting through the E site.

termination

the final step in translation where the ribosome recognizes a stop codon on the release factor which looks similar to tRNA and the newly synthesized polypeptide is released. This process concludes protein synthesis.

mRNA circularization

process in which mRNA are translated by multiple ribosomes at the same timeto form a circular structure, facilitating efficient translation and protection from degradation.

mRNA degradation

the process by which mRNA molecules are broken down and their components recycled, serving as a regulatory mechanism that controls gene expression and maintains cellular homeostasis. the quicker mRNA is degraded the less proteins it produces.

3’ UTR

are the sequence that recruit proteins to degradation of mRNA or tel them to wait

mRNA decay

1. 5’ end, decapping enzyme can reveal a free 5’ end , which is degraded by a 5’-3’ exonuclease

2. 3’ end where deadenylase removes the poly A tail reveals a free 3’ end , which is then degraded by a 3’-5’ exonuclease

microRNA

small fragments that bind to mRNA, double stranded cannot be translated is degraded they come from non coding rna regions such as introns

after formation of protein

they are controlled through various events

1. localization ( where it functions)

2. folding ( determing function of the protein)

3. post tranlational modifications ( adddition of certain groups )

4. degradation

where is ribosome

1. cytosol

2. rough ER

3. important to keep in mind that it always start in the rough er

SRP

proteins for the ER have signal pepetides with are reconized by signal recognition particlesthat guide the ribosome- chain complex to the endoplasmic reticulum for proper translation and translocation.

proteins for made in ER are destined

1. ER

2. golgi

3. lysosome

4. vesicles

5. membrane

6. exocytosis

prosthetic groups added to proteins for modifications

1. phosphorylation

2. acetylation

3. methylation

4. glycosylation

5. Ubiquitination

6. other

degradation of protein

when it is time for protein to be degraded it is ubiquitinated a protein with alot of ubiquitins is taken into the proteasome, where its bonds are hydrolyzed. if it is deubiquitinated the protein is saved

prokaryote gene expression vs. eukaryotes

In prokaryotes, gene expression occurs in the cytoplasm and involves transcription and translation occurring simultaneously, while in eukaryotes, transcription occurs in the nucleus and translation in the cytoplasm. therefore prokaryotes are less regulated when it comes to gene expression.

what makes prokkaryotes different

1. replication is circular

2. no epigenetics

3. operons

4. no post transcripional regulation