D2.2

D2.2 : Gene Expression 

D2.2.1: Gene expression as teh mechanism by which information in genes has effects on the phenotype

Gene expression

• Mechnaism by which genetic information in a gene is expressed in a function protein-mechanism by which information in genes has an effect on the phenotype

• Involves transcription of a gene to produce mRNA and the translation of mRNA by ribosomes to produce functional proteins which had an effect on an organis’s phenotype

  • Functional proteins: proteins that possess a biological activity adn are involved in the biological function of a living organism (have a job)

  • Transcription: DNA → mRNA

  • Translation mRNA →Amino acid sequence/protein 

• Genotype: Combination of alleles inherited by an organism 

• Phenotype : physcial represtnation of the genotype
  
  

D2.2.2: Regulation of transcription by proteins that bind to specific base sequences in DNA 

Regulating of Transcription

• Is regulated by promoter regions, enhancer adn transcription factors

Promoter region 

• Promoter region : Located near the beginning of agene, serve as a binding site for RNA polymerase

• RNA polymerase: enzyme that transcibes gene to mRNA 

Enhancers

• Enhancers: regulatory sequences of DNA which are located away from a gene 

• Transcription factors: bind to teh enhancer region which interacts and activates the promoter region 

Transcription factors 

• Are proteins which bind to enhancer and promoter regions and regulate transcription 

• Differnt transcrpition factors can activate or repress transcription by interacting with each other, other proteins adn RNA polymerase

• Promoters, enhancers, and regulatory proteins allow a cell to respond to internal and external factors and control teh genes that are transcribed

D2.2.3: Controls of degradation of mRNA as a means of regulating translation

Controlling translation 

• The regulation of transcription regulates the qaunity of mRNA that is produced, which regulates teh rate of translation in a cell

• Translation can be further regulated by teh degradation of mRNA by nuclease enzymes

  • Nuclease enzyme: enzymes that are specially designed to break apart the nucleotides that make up the nucleic acids DNA and RNA 

• Nuclease breaks down mRNA to RNA nucleotides which can be recycled by teh cell to produce new mRNA molecules 

• In human cells, mRNA may be present from minutes up to days before it is broken down by nucleases

D2.2.4: Epigenesis as the development of patterns of differentiation in a cells of a multicellular organism 

Epigenesis 

• Epigenesis : the process by which a multicellular organism develops from a zygote through a sequence of steps in which cells differentiate and organs form 

  • Results from an interactio between genes and their environment during development

• Epigenetics: the study of changes in organisms causesd by modification of geen expression, by epigenetic tags, rather than changes in teh genetic code 

• Epigenetic tags : chemical markers that attach to DNA or histone proteins and infleucne the transcription of genes 

D2.2.5: Differences between the genome, transcriptome and proteome of individual cells 

Genome 

• Genome: all of teh genetic infromation of an organism 

• The genome includes all of chromosomes and mitrochondrial and chloroplast DNA found in a cell 

• No cell expresses all of the gene in its genome. The pattern of gene expression determines how a cell differentiate 

Transcriptome 

• Transcriptome: all of the aRNA molecules transcribed at a specific time within a cell or organism 

• Respresnts the active genes and their expression within a cell or organism 

Proteome

• Larger than genome due to a range of factors including 

  • Alternative splicing of mRNA exons produces multiple proteins

  • Modifications of proteins after translation increases the proteome 

D2.2.6: Methylation of the promoter and histones in nucleosomes as examples of epigenetic tags 

Methlyation of promoter regions and histones 

• Methyl groups (-CH3) can act as epigenetic tags by attaching to the promote region or histones 

• Methyl groups, attahed to cysteine nucleotides in a promoter region, repress the activity of the promoter, preventing the gene from being transcribed 

• Can also attach to amino acids of histone proteins found in nucleosomes

• Methylation of histone proteins can cause transcription to be repressed (by the DNA binding tighter to the nucleosome), or activated (by unwinding DNA from the nucleosome

  • Methylation–chemical reaction where a methyl molecule is added to DNA, proteins, or other molecule

D2.2.7: Epigenetic inheritance through heritable changes to gene expression 

Epigenetic Inheritance

• Epigenetic inheritance: a parent’s experiences, in the from of epigenetic tags, can be passed to future generations

  • Ex-trauma, PTSD, and interactions with genes 

• The tags often remain in place during mitosis and meiosis 

• The faughter cells inherit phenotypic changes, epigenetic tags of teh parent cell, without changes to the DNA sequence

• Beneficial as an organism grows, as daughter cells will have teh same epigenetic tags as teh parent cell 

• This means that the daughter cells will express the same genes as the parent cell, and carry out the same functions

• Most epigenetic tags, though not all, are erased after fertilization. Most epigenetic tags are not passed onto future generations

D2.2.8: Examples of environmental effects on gene expression in cells and organisms 

Environmental effecs on gene expression 

• Epigenome consists of all the epigenetic tags on the DNA and histone proteins. Interaction between environmental and DNA can impact the epigenome of cells and organisms

• Examples 

  • Diet: a person’s diet or the diet of their mother while she was pregnant with tehm alters the epigenome 

  • Cigarette smoke: epigentic changes from expossure to cigarette smoke may lead to lung cancer 

  • Air pollution: poor air quality can lead to epigenetic changes
    
    

Air pollution and gene expression 

• Air pollution, like diesel fumes, can add or remove methyl epigenetic tags from a person’s epigenome 

• Teh addition adn removal of epigenetic tags changes which genes are expressed 

Transcriptome 

• Transcriptome: all of the RNA molecules transcribed at a specific time within a cell or organism 

• Represents the active genes and their expression within a cell or organism 

Proteome

• Proteome: the complete set of proteins present in a cell or organisms at a given tim e

• The proteome of different cell types in same organism will be different because gene expression varies depending on the cell type 

• The proteome is larger than the genome due to a range of factors including:

  • The alternative splicing of mRNA exons produces multiple proteins 

  • Modifications of proteins after translation increases the  proteome 

D2.2.9: Consequences of removal of most but not all epigenetic tags from the ovum and sperm 

Removal of epigenetic tags during fertilization 

• Most of the epigenetic tags are removed at fertilization of egg anf sperm in a process known as reprogramming 

• The epigenome of sperm and eggs allows tehm to be specialized cells 

• Reprogrammingthe epigenome of a zygote produces stem cells 

  • However, a small number of epigenetic tags are not erased

• tigons are the offspring of a male lion and a female tiger 

• Ligers are teh offspring of a male tiger and a female lion 

Tigons and Ligers 

• The difference in phenotype, including size and appearances, of tigons and ligers, is partly due to difference in imprinted genes

• Genomic Imprinting–the process by which only one of the two inherited genes for a trait is expressed. One copy of the gene is silenced by epigenetic tags during egg and sperm formation

D2.2.10: Monozygotic twin studies

Monozygotic Studies 

• Monozygotic Twins are identical twins resulting from the fertilization of one egg. Monozygotic twins are clones and have the same genome

• Monozygotic twins have the same genome and very similar epigenomes. 

• The epigenomes are very similar because the twins developed within the same uterus 

• Throughout life, the epigenomes of identical twins become increasingly different

D2.2.11 : External factors impacting the pattern of gene expression 

External factors and Gene expression 

• Gene expression can be impacted by factors outside the cell such as: 

  • The presence of biochemical molecules which a cell metabolizes. Gene expression in E. coli bacteria is impacted by the presence or absence of sugar lactose

  • Many hormones form hormone-receptor complexes within the cytoplasm of the cell. The hormone-receptor complex then moves into the nucleus where it binds to genes regulating transcription of DNA

The Lac Operon 

• The lac operon regulates the transcription of the enzymes required for lactose metabolism 

• The lac operon consists of a promoter, an operator and a sequence of three genes

• RNA polymerase binds to the promoter

• A repressor protein may bind to the operator. The presence or absence of the repressor protein regulates the transcription of the genes

• The presence or absence of lactose regulates the attachment of the repressor protein to the operators

• When lactose is not present, a repressor protein binds to the operator and blocks RNA polymerase from transcribing the genes

• When lactose is present, it binds to the repressor protein. The repressor protein changes shape and is released from the operator.

• RNA polymerase is no longer blocked, and the three genes are transcribed to mRNA

• The mRNA is translated to proteins involved in lactose metabolism

Testosterone regulates gene expression 

• Testosterone is a steroid hormone which regulates gene expression

• Testosterone diffuses through the plasma membrane of the cell, where it binds to a testosterone receptor, forming a hormone-receptor complex

• The hormone-receptor complex moves to the nucleus where it interacts with specific DNA sequences known as androgen response elements, which are present in the regulatory sections of the target genes

• The testosterone hormone-receptor complex may enhance or repress the transcription of the target genes