17.3 Messenger RNA to Phenotype in Eukaryotes

  • mRNA must exit the nucleus before translation occurs

  • In the cytoplasm there are opportunities for gene regulation (translation, protein activity, mRNA stability)

    Small Regulatory Molecules assist in Gene Regulation:

    Small Regulatory RNAs: Regulatory RNA molecules that assist in gene regulation; there are two types

    • siRNA (small interfering RNA)

    • miRNA (micro RNA)

  • Small regulatory RNAs are synthesize through DNA transcription in which they form either hairpin or stem-and-loop structures within the nucleus and are stabilized through the formation of base pairing in the stem. Enzymes will cleave the structure and result in the formation of small fragments of base pairs around 20-25 BP in length

  • They will assist in regulation as one of the strands will incorporate itself to RISC (RNA-induced silencing complex) in which it will target specific mRNA molecules, leading to their degradation of transcript, an inhibition of translation, or chromatin repression

Translation Regulation Effects:

  • RNA-Binding proteins help with mRNA translation and degradation

    • They will adhere to the untranslated regions at both the 5’ and 3’ areas (enhancer sequences)

    • They can help with transporting RNA to certain regions of the cell, they can be present in some locations in which they repress their translation as they bind to RNA in the area.

    • In general these protein will help mRNA to be translated in certain places in the cell

    RNA Structure helping with Translation

    • The cap structure of the mRNA is used for translation initiation in which many proteins (25) are needed to facilitate the binding of ribosomes, ensuring that the mRNA is efficiently translated into proteins.

    • The untranslated regions and poly a tail are important to translation initiation. When a RNA binding protein binds to the poly a tail and 5 cap of the mRNA it will create a loop in which the 3’ end is brought to the start site for translation

Protein Structure and Chemical Modification effects on Phenotype

  • A synthesized protein can alter phenotype of a cell/organism by affecting metabolism, signaling, gene expression, and cell structure

    Post-translation Modification: The process in which proteins are modified after translation occurs to regulate structure/function

    • Important process since proteins can be expressed at certain moments (TIMEANDPLACEPROTEINS>:() some of these protein are altered into their active forms after modification to function when necessary (

      • Tryspin (an enzyme) breaks down in its active form, its translated into its inactive form in the cell since it might harm the cell when active. once out of the cell it will be modified to become active and function as necessary

      • Help with regulation as the addition of sugars during some modifications can alter the protein folding and stability

        • An addition of a negatively charged phosphate group can alter the confirmation of a protein and make it negative of positive

  • The folding of a protein is necessary for controlling the function of a protein (a type of ptm)

    • Protein can fold properly on their own and others may require chaperone protein to help with their folding since they can’t do it on their own (a type of ptm)

    • If a protein is unable to fold properly it will aggregate the cell (destroy it and cause harmful effects eg. disease)

  • Some protein can be marked to be broken down by an enzyme through the addition of chemical groups to control their activity

17.4 Chromatin Remodeling and Epigenetics

Chromatin: A complex of DNA,RNA, and nucleosome proteins which give chromosomes their structure(DNA is packaged in the form of a chromatin in the nucleus)

  • DNA is not always always available for transcription and will be found in the form instead

  • in order for transcription to occur CHROMATIN REMODELING must occur

Chromatin Remodeling: The repositioning of nucleosomes that expose different stretches of DNA to the environment in the nucleus, the chromatin must be loosened in order for transcription to occur

Gene Expression influenced by Chemical Mod. or Histones

Histone Modification:

Histones: A group of proteins found in the chromatin

  • Chromatin can be remodeled by the post-translational modification of the histones around DNA which will occur on histone tails

    • They can be modified through addition of chemical groups (methyl, acetyl groups. etc)

    • Addition of chemical groups can activate or repress transcription

Histone Code: A pattern of modifications to the histone tail that will affect chromatin structure and gene transcription

  • Histone modification will ensure that specific genes will be expressed or repressed when necessary as well in response to environmental cues

Chemical Modification:

  • DNA methylation: the addition of a methyl group to bases in the DNA (cytosine)

    • Affects chromatin structure, histone modification, nucleosome position (restrict transcription)

    • Occurs in CpG Islands: clusters of CG nucleotides near the promoter

    • Heavy methylation is associated with gene expression repression; this could be seen as a defense mechanism

    • Methylation state can change over time depending on which genes should be on or off

Epigenetic Modifications: Change to the DNA packaging and not the actual DNA

  • Can affect gene expression and be inherited

  • they’re reversible and occur according to their environment

  • Methylation to Cytosine, Histone modification, and chromatin structures alterations are examples of this type of modification

  • Imprinting: Preprogrammed epigenetic modifications, in which gene expression is sex specifics (silenced)

    • Mothers allele of a gene is silenced while the allele of a gene from the father is allowed to be expressed

Gene Expression Regulation on the entire chromosome

  • The number of gene copies is related to gene expression

    • Higher Gene dosage=more levels of gene expression

Dosage Compensation: the process by which organisms equalize the expression of X chromosome genes between members of different biological sexes

  • Occurs through the XIC ( X- Chromosome Inactivation Center)which is noncoding RNA that when abundant will signal epigenetic modifications and stop X Chromosome Expression)

  • The XIC gene is necessary for inactivation, if the gene is inserted in another chromosome it will also inactivate it (interesting)

    • Ex: Since females have one more X chromosome they will express 1/less of the chromosome to express the same amount as men (X-Inactivation: the expression will not be entirely repressed but will be expressed less)

    • Ex. In fruit flies Male fruit flies double their expression of their X Chromosome

  • Gene expression can be regulated in Eukaryotes at many levels between the processing of DNA to protein in chromatin remodeling, transcription, RNA processing, mRNA stability, translation, most translation

  • Genetic environment and lifestyles choices will also affect gene expression

    • Intake of food/other lifestyles choices such as exercise will signal the expression or repression of genes and will affect the steps that occur after transcription (regulation of mRNA stability, translational regulation, post-translational modification)

    • A change in environment creates feedback loops that determine gene expression

17.2 Transcription and RNA processing in Eukaryotes

  • Features of eukaryotic cell (DNA packaging, mRNA processing, the space in which translation occurs, space in which translation occurs) provide different levels of gene regulation

Transcription

  • Regulatory Transcription Factors: Diverse proteins that regulate transcriptional regulation in eukaryotic cells by binding to an enhancer will attract general transcription factors to TATA box

    • Some will bind to enhancers to promote transcription, others will bind to silencers to repress transcription

  • General Transcriptional Factors: Proteins that bind to TATA box that will attract the RNA polymerase complex

    • Transcription will not occurs without these factors attracting and binding the RNA polymerase complex

  • Combinatorial Control: Transcription occurring with the correct combination of regulatory transcriptional factors on the silencer or enhancer

RNA processing:

  • Addition of 5’ Cap, addition of 3’ Poly (a) tail, the splicing of introns out of the primary transcript are examples of RNA processing important to gene regulation

  • Alternative Splicing

    • Splicing is important to gene regulation because of Alternative Splicing in which primary transcript can be spliced to create different proteins

  • RNA Editing

    • Modifications to the bases of RNA such as the removal of amino groups, changes to amino groups, etc.

    • Editing does not occur on the same level and results in some genes producing different types of proteins in a single cell