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[h] IB DP Biology HL D2.2 Gene expression Flashcards
[q] Gene
[a] A segment of DNA on a chromosome that codes for a specific trait
[q] Gene Expression
[a] conversion of the information encoded in a gene first into messenger RNA and then to a protein
[q] Phenotype
[a] An organism’s physical appearance, or visible traits.
[q] Genotype
[a] An organism’s genetic makeup, or allele combinations for example AA or aa.
[q] Promoters
[a] specific region of a gene where RNA polymerase can bind and begin transcription
[q] Enhancers
[a] A DNA sequence that recognizes certain transcription factors that can stimulate transcription of nearby genes.
[q] Transcription Factors
[a] Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.
[q] RNA polymerase
[a] Enzyme that links together the growing chain of RNA nucleotides during transcription using a DNA strand as a template
[q] Nuclease Enzymes
[a] break down mRNA to RNA nucleotides which can be recycled
[q] Epigenesis
[a] mechanism that turns genes on or off and determines functions of body cells
[q] Epigenetic Tags
[q] Epigenome
[a] The genome-wide distribution of epigenetic marks.
[q] Genome
[a] all of an organism’s genetic material
[q] Transcriptome
[a] all the RNA molecules transcribed from a genome
[q] Proteome
[a] the entire set of proteins expressed by a given cell or group of cells
[q] Methyl Groups
[a] -CH3, act as epigenetic tags by attaching to the promoter region or histones.
[q] Methylation
[a] Additional of a methyl group, this influences behavior by suppressing gene activity and expression
[q] Histone Proteins
[a] A simple protein bound to DNA, involved in the coiling of chromosomes
[q] Nucleosomes
[a] DNA coiled around histones
[q] Reprogramming
[a] A process where most of the epigenetic tags are removed at fertilization of egg and sperm
[q] Genomic Imprinting
[a] 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.
[q] Monozygotic Twins
[a] identical twins formed when one zygote splits into two separate masses of cells, each of which develops into a separate embryo
[q] Lac Operon
[a] group of genes involved in lactose metabolism
[q] Operator
[a] Region of DNA that controls RNA polymerase’s access to a set of genes with related functions.
[q] Repressor Proteins
[a] These bind to DNA and discourage binding of RNA polymerase to start transcription- turns genes OFF
[q] Steroid Hormones
[a] enter the target cells and have a direct effect on the DNA of the nucleus
[q] Hormone-Receptor Complex
[a] Once inside a target cell, steroid and thyroid hormones combine (usually in the nucleus) with specific protein receptors.
[q] Androgen Response Elements
[a] Specific DNA sequences present in the regulatory section of genes.
It is where the hormone-receptor complex binds.
[q] D2.2.1—Gene expression as the mechanism by which information in genes has effects on the phenotype
[a] Students should appreciate that the most common stages in this process are transcription, translation and the function of a protein product, such as an enzyme.
[q] D2.2.2—Regulation of transcription by proteins that bind to specific base sequences in DNA
[a] Include the role of promoters, enhancers and transcription factors.
[q] D2.2.3—Control of the degradation of mRNA as a means of regulating translation
[a] In human cells, mRNA may persist for time periods from minutes up to days, before being broken down by nucleases
[q] D2.2.4—Epigenesis as the development of patterns of differentiation in the cells of a multicellular organism
[a] Emphasize that DNA base sequences are not altered by epigenetic changes, so phenotype but not genotype is altered.
[q] D2.2.5—Differences between the genome, transcriptome and proteome of individual cells
[a] No cell expresses all of its genes.
The pattern of gene expression in a cell determines how it differentiates.
[q] D2.2.6—Methylation of the promoter and histones in nucleosomes as examples of epigenetic tags
[a] Methylation of cytosine in the DNA of a promoter represses transcription and therefore expression of the gene downstream.
Methylation of amino acids in histones can cause transcription to be repressed or activated.
Students are not required to know details of how this is achieved.
[q] D2.2.7—Epigenetic inheritance through heritable changes to gene expression
[a] Limit to the possibility of phenotypic changes in a cell or organism being passed on to daughter cells or offspring without changes in the nucleotide sequence of DNA.
This can happen if epigenetic tags, such as DNA methylation or histone modification, remain in place during mitosis or meiosis.
[q] D2.2.8—Examples of environmental effects on gene expression in cells and organisms
[a] Include alteration of methyl tags on DNA in response to air pollution as an example.
[q] D2.2.9—Consequences of removal of most but not all epigenetic tags from the ovum and sperm
[a] Students can show this by outlining the epigenetic origins of phenotypic differences in tigons and ligers (lion-tiger hybrids).
[q] D2.2.10—Monozygotic twin studies
[a] Limit to investigating the effects of the environment on gene expression.
[q] D2.2.11—External factors impacting the pattern of gene expression
[a] Limit to one example of a hormone and one example of a biochemical such as lactose or tryptophan in bacteria.
In prokaryotes, transcription and translation occur almost simultaneously due to the absence of a nucleus.
Thus, the control of gene expression primarily occurs at the transcriptional level.
1. epigenetic level (how tightly coiled the DNA is)
2. transcriptional level (rate of transcription)
3. post-transcriptional level (pre-mRNA processing)
4. translational level (production of polypeptides from mRNA)
5. post-translational level (alterations to polypeptide after formation)
Gene expression not only involves turning genes ‘on’ or ‘off’ but also modulating levels of expression ‘up’ or ‘down’ (i.e. rate of transcribing a specific gene may be lowered to reduce expression instead of completely stopping it/turning it ‘off’).
The transcriptome is the whole set of mRNA molecules transcribed by a cell.
The proteome is the entire set of all proteins produced by a cell.
The metabolome is the collection of all molecules involved in metabolic reactions within a cell.
No cell expresses all of its genes simply because it is (a) too metabolically expensive (b) would require unfolding all the DNA, which is physically infeasible.
1. Promoter
a) Core promoter: this is the closest region of the promoter to the target gene and ~25-30 base pairs in length.
RNA polymerase to initiate transcription.
b) Proximal promoter elements: located a few hundred base pairs upstream, these regions bind to specific transcription factors and help in regulating transcription.
a) Basal transcription factors: bind exclusively to the core promoter to recruit RNA polymerase and initiate transcription.
b) Specific transcription factors: bind to proximal promoter elements and enhancers to regulate transcription rate (they cannot initiate transcription).
Epigenetics are the inheritable changes in gene expression that control the transcriptional access of DNA without altering its base sequences.
Methylation of amino acids in histones can cause transcription to be repressed or activated.
Students are not required to know details of how this is achieved.
Since DNA is negatively charged and histone proteins are positively charged, methylation of amino acids in histones causes the nucleosomes to pack even more tightly together, causing the gene to be inaccessible to transcription factors hence ‘deactivating’ it.
Methyl is also added to cytosine bases within the promoter region of a gene in a stretch of highly repeated C and G base pairs (5’ – CG – 3’) called CpG sites (CpG = Cytosine Paired with Guanine).
Methylation levels are affected by the environment, such as stress levels, diet, toxins, etc.
Second-hand smoking, traffic-related air pollution, and cigarette smoke have been shown to alter DNA methylation patterns in human cells, leading to a variety of cardiovascular and pulmonary diseases, in addition to multiple types of cancer (lung, breast, etc.).
An example of genome imprinting is a hybrid cross between a tiger and lion.
• Male and female lions have different goals for their offspring: while males want large offspring to outcompete other males for breeding, females want quality and survival, so maternal genes increase offspring survival by inhibiting fetal growth/size (i.e. silencing growth genes through heritable epigenetic tags).
• Tigers are more solitary animals and males do not have to compete for breeding, so inhibiting fetal growth has not evolved in female tigers.
• Thus, if a male lion mates with a female tiger, the offspring (liger) grows to be larger than its parents.
If a male tiger mates with a female lion, the offspring (tigon) grows to be smaller than its parents.
In prokaryotes like bacteria, genes coding for proteins involved in the same biochemical pathway are clustered next to each other to form an operon.
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