IB Biology 11: Gene Expression - Topic 10B

what is the genotype of an organism?

the genotype of an organism is all its genetic information

what is the phenotype of an organism?

the phenotype is all aspects of the structures and functions of the organism

- the totality of its characteristics

what is gene expression?

gene expression is the process of turning the genotype into the phenotype

- happens in a series of stages

what are the stages of gene expression?

transcription, translation, and protein function

(gene expression) what is transcription?

genes within the genotype are selected and are used in production of RNA

- the DNA base of a gene determines the base sequence of an RNA molecule, through complementary base pairing

- RNA produced by transcribing protein-coding genes is messenger RNA (mRNA) and it is transported to ribosomes in the cytoplasm

(gene expression) what is translation?

mRNA is used in the production of polypeptides

- the base sequence of an mRNA molecule is translated into the amino acid sequence of a polypeptide

- translation happens on ribosomes

- proteins consist of one polypeptide or more linked together, sometimes with additional non-polypeptide components

(gene expression) what is protein function and how does it work?

the protein may form part of the structure of the organism, but many have other functions, so their effects are not visible in the outward appearance of the organism

- the effects are observable and are therefore part of the phenotype

many proteins act as enzymes and have their effect on phenotype of catalysing reactions

- for example, the ability to digest lactose is due to the protein lactase

how can gene expression be assessed?

it can be assessed by measuring the quantities or proteins

how can organisms respond to their environment?

organisms can respond to their environment by varying their patterns of gene expression and therefore their traits

- this is a form of adaptation, but it is reversible because genes have only been switched on or off, not changed into new alleles

- known as phenotypic plasticity

in what cases is phenotypic plasticity useful?

phenotypic plasticity is particularly useful if the environment a population inhabits is heterogeneous rather than uniform

what is an example of phenotypic plasticity?

a person with pale skin may become darker-skinned if there is an increase in the intensity of sunlight or more time is spent with skin exposed to the sunlight

- a change in gene expression results in increased synthesis of the black pigment melanin in the skin

- if the sunlight stimulus diminishes, gene expression reverts to its former pattern and the skin gradually becomes paler again, as the melanin concentration reduces

what is phenotypic plasticity in some cases?

in some cases, phenotypic plasticity is a switch between two or more alternative forms and/or it cannot be reversed during the lifetime of the individual

what is epigenesis?

epigenesis is the concept that a multicellular organism such as a plant or animal develops from undifferentiated cells

- structures and functions appear during development that were not present at the start of the organism's life

(epigenesis) how is the differentiation of cells achieved?

the differentiation of cells is achieved by the activation of certain genes and the silencing of others

what are epigenetic tags?

chemical modifications to DNA and to the proteins associated with DNA determine which genes are activated or deactivated

does epigenetic modification change the genotype?

epigenetic modification does not influence the genotype of an organism, only the phenotype

- DNA base sequences are not altered during epigenesis

what is a genome?

the whole of the genetic information of a cell

- includes coding and non-coding sequences

what is a trancriptome?

the entire set of mRNAs transcribed in a cell

- because no cell transcribes all its genes at once, its transcriptome is less than an RNA copy of each protein-coding gene

does the transcriptome vary over time?

the transcriptome varies over time within any cell and between cells within an organism

what is a proteome and what is it based on?

a proteome is the entire set of proteins produced by a cell

it is based on the transcriptome because proteins are synthesized from the base sequences of mRNA, but the quantities of each protein in a cell are not directly proportional to the quantity of the corresponding mRNAs

what is regulated as a part of the control of gene expression?

the number of molecules of polypeptide translated from each mRNA molecule is regulated as part of the control of gene expression

what does the pattern of gene expression within a cell determine?

the pattern of gene expression within a cell determines how that cell differentiates

what is methylation of DNA?

methylation of DNA is the substitution of a hydrogen with a methyl group (-CH3) in a base

- methylation of cytosine frequently occurs, converting it to methylcytosine, but adenine can also be methylated

when does the pattern of methylation change?

the pattern of methylation changes during the lifetime of a cell and is affected by environmental factors

does methylation alter the genome of the cell?

it does not alter the genome of the cell, because the methyl group is in a position where it does not affect complementary base pairing

what is the methyl group involved in methylation?

the methyl group is an epigenetic tag and has multiple roles in the regulation of gene expression

what does methylation of cytosine in the promoter of a gene tend to repress?

methylation of cytosine in the promoter of a gene tends to repress transcription of the gene and therefore its expression

what is the promoter of a gene?

a specific region of DNA located upstream (5′ end) of a gene that initiates and regulates its transcription into RNA. It acts as a binding site for RNA polymerase and transcription factors, controlling whether a gene is turned on or off. Promoters are crucial for gene expression and regulation.

how is DNA combined to form a nucleosome?

- DNA is combined with histone proteins to form nucleosomes in eukaryotes and nearly all archaea

- a nucleosome is composed of eight histones with the DNA molecule wound round them twice

what do histones of nucleosomes have?

the histones have long tails extending outward from the compact nucleosome - these tails interact with neighbouring nucleosomes resulting in tight bonding during condensation of chromosomes

histones therefore play a role in the tight packing of DNA

what else do histones play a role in other than the packing of DNA?

they also play a role in the regulation of gene expression, as different types of modifcation can occur to amino acids in the tails of histones including the addition of methyl, acetyl or phosphate groups

- these are all examples of epigenetic tags

how can methylation of amino acids in histone tails influence transcription of a gene?

methylation of amino acids in histone tails can infuence transcription of a gene by either decreasing or increasing the accessibility to transcription factors

what are examples of epigenetic tags?

- chemical modifcations of chromatin such as methylation of bases in DNA and acetylation

- methylation of amino acids in the tails of histones

epigenetics have an impact on gene expression and so affect the visible characteristics of an individual

what is the epigenome of a cell? how does it affect protein production?

the sum of all epigenetic tags in a cell or organism is the epigenome

each type of cell in a multicellular organism has its own distinctive patterns of epigenetic tags, so that it produces the proteins needed to perform its functions

how can the epigenetic pattern be passed on to daughter cells and what happens as a result?

when cells in a tissue divide by mitosis, the epigenetic pattern can be passed on to daughter cells

- as a result, the new cells are differentiated for the same functions

- also, any effects of the environment on the epigenome can be conserved

haploid gametes are formed by meiosis from diploid cells that have what?

haploid gametes are formed by meiosis from diploid cells that have a characteristic pattern of epigenetic tags, including those due to environmental influences encountered during the organism's lifetime

- some of the pattern is passed on to the haploid cells but it has been assumed that this epigenome will be entirely erased before gametes fuse to produce a zygote

what this erasure of the epigenome called?

the process of wiping the epigenome is called "reprogramming"

what is transgenerational epigenetic inheritance?

there is now evidence that a few epigenetic tags may not be removed, so they remain in the zygote and are thus passed from parent to offspring

what does transgenerational epigenetic inheritance opens the possibility for?

it opens the possibility that the environment encountered by one generation could have an impact on gene expression in the next generation

- this does not amount to the environment directing specific and heritable changes in genes

- even if an epigenetic tag is passed from parent to offspring, it can easily be reversed, unlike mutations in DNA, which are changes to the base sequence and are likely to be permanent

what is an example of environmental effect on gene expression?

air pollution directly damages tissue, but there is also strong evidence that it can alter the epigenome

- exposure to air pollution such as particulate matter, nitrous oxides, ozone and polyaromatic hydrocarbons has been found to decrease DNA methylation across the genome in people of all ages

(environmental effects) what can the decreased DNA methylation across the genome cause?

impacts greater expression of proteins that regulate the immune system

these changes might be the cause of increased risk of heart disease and incidence of inflammation and diseases such as asthma

why is air pollution more damaging during pregnancy?

air pollution is particularly damaging during pregnancy because it causes changes to methylation in specific genes that have impacts during both gestation and the early years of life

what percentage of epigenetic tags are removed during the production of sperm and eggs in humans?

during the production of sperm and eggs in humans, approximately ninety-nine percent of epigenetic tags are removed

what is genomic imprinting?

some tags persist into the next generation - this type of non-Mendelian inheritance can have an impact on the phenotype of the organism

how does genomic imprinting work?

the epigenetic tags are imprinted in the gametes of the parents and can be maintained through mitotic cell divisions in the somatic cells of the offspring

how does genomic imprinting change Mendelian inheritance?

in Mendelian inheritance, if the allele inherited from one parent is recessive and does not produce a gene product, the allele from the other parent may be dominant and thus result in a functional gene product

however, in the case of genomic imprinting, the allele of a gene inherited from one parent is silenced and the allele from the other parent is expressed

- even though two copies of the gene are present, it is as if the individual were haploid

- alleles and mutations that might normally be recessive are expressed if the dominant allele is silenced by imprinting

how is Angelman syndrome caused? examples?

consider the example of a mother who is homozygous recessive for a condition and the father is homozygous dominant

genotypically, the offspring would be heterozygous and we would expect it to show the phenotype associated with the dominant allele

however, if the allele inherited from the father is silenced, the recessive condition will appear in the offspring

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Lions and tigers are closely related so that they have been known to interbreed in zoos. The outcome of the cross differs depending on whether the mother or the father is a lion. Female lions carry litters from multiple fathers. There is an advantage to the father to sire the largest sized cub of the litter. There is an advantage to the mother to sire the largest number of cubs. Paternal imprinting favours the production of larger offspring, and maternal imprinting favours smaller offspring. Normally, these competing priorities balance out when both parents are lions. Tiger litters are sired by a single father, so there is no competition that favours imprinting.

how do dizygotic or fraternal twins arise?

twins can arise when two eggs are released during ovulation and both are fertilized

- such twins typically have about fifty percent of their genetic information in common

how are monozygotic twins formed?

*one in two hundred and fifty pregnancies results in the formation of monozygotic or identical twins

- this occurs when the cells of a very early embryo become separated and each develops into a separate individual

do variations in environmental factors have an impact in gene expression? what is an example?

variations in environmental factors can have an impact in gene expression

for example, the genes responsible for the absorption and metabolism of lactose in the bacterium Escherichia coli are expressed when lactose is present and not expressed when lactose is absent

in this case, the breakdown of lactose results in regulation of gene expression by negative feedback

a repressor protein is deactivated when lactose is present - once the lactose has been broken down, the repressor protein is no longer deactivated and blocks genes that cause lactose metabolism when they are expressed

how many genes does a cell in a multicellular eukaryotic organisms express?

each cell in a multicellular eukaryotic organism expresses only a fraction of its genes

the regulation of eukaryotic gene expression is a critical part of cellular differentiation and development - this is seen in the passage of an insect through its life cycle stages or in development of a human embryo

what can affect gene expression?

hormones can affect gene expression

- for example, oestrogen passes through the phospholipid bilayer of cells in the endometrium of the uterus and binds to an oestrogen receptor within the nucleus

with oestrogen bound to it, the receptor can bind to the promoters of target genes causing their expression

the gene that codes for production of the progesterone receptor is an example of a target gene for the oestrogen receptor

thus, oestrogen makes the endometrium more responsive to progesterone during the luteal phase of the uterine cycle