D2.2 Gene expression Flashcards
D2.2.1—Gene expression as the mechanism by which information in genes has effects on the phenotype
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
The phenotype is all the functional and structural characteristics of an organism. The genotype is all its
genetic information. Gene expression is the process of turning the genotype into the phenotype. It happens
by transcription to produce mRNA, translation of the mRNA into proteins, and the proteins performing their
functions. Many proteins act as enzymes, so have their effect on phenotype by catalysing a reaction.
Genotype (DNA) transcription - mRNA - t r a n s l a t i o Protein - protein functions Phenotype
D2.2.2—Regulation of transcription by proteins that bind to specific base sequences in DNA
Include the role of promoters, enhancers and transcription factors
Gene expression requires selective transcription of RNA. Promoters, transcription factors and enhancers
have roles in this. Every gene has a promoter, located upstream of it
(in the 5’ direction). Al promoters within the genome of an organism share parts of their base sequence. These
consensus sequences are recognized by RINA polymerase which binds to them, ensuring that the enzyme is correctly placed to start transcribing the gene in a 5’ to 3’ direction.
RNA polymerase cannot by itself start transcription. Other DNA-binding proteins are required, known as
transcription factors. These proteins bind to specific base s e q u e n c e s in the DNA near to the promoter.
There are many different types of transcription factor, corresponding to the different base sequences at
binding sites. This allows a cell to regulate gene transcription and be selective in which genes are transcribed at all times in the life of the cell. In some cases, genes are regulated individually and in other cases shared transcription factors result in groups of
genes being regulated together. Testosterone receptors act as transcription factors. When testosterone has bound to the receptor, the r e c e p t o r- h o r m o ne complex binds to DNA at multiple points, causing transcription by RNA polymerase of a group of genes.
The rate of transcription of genes can be varied by enhancers. These are base sequences located either upstream or downstream of a gene. When transcription factors, known as activators, bind to these enhancers, the rate of transcription of the gene is increased.
D2.2.3—Control of the degradation of mRNA as a means of regulating translation
In human cells, mRNA may persist for time periods from minutes up to days, before being broken down by
nucleases.
A molecule of mRNA is translated repeatedly to produce a protein and is then broken down by nucleases. Some
proteins are p r o d u c e d briefly in a cell, for example those that control the cell cycle. Others such as the milk protein casein are produced continuously for long periods of time. This is achieved by regulation of mRNA
degradation. The poly-A tail has a role in this.
Addition of the poly-A tail to mRNA is described in Section D1.2.15. The tail of an mRNA molecule becomes shorter over time. The shorter the poly-A tail, the less likely mRNA is to be translated and the more likely that it will be degraded by nuclease. The rate of shortening varies by a factor of over a thousand. In some types of mRNA, 30 nucleotides are removed per minute; in others, only one or two per hour are removed. Given an average initial tail length of 200 nucleotides in humans, this implies that mRNA molecules might persist and continue to be translated for between 5 minutes and a week.
D2.2.4—Epigenesis as the development of patterns of differentiation in the cells of a multicellular organism
Emphasize that DNA base sequences are not altered by epigenetic changes, so phenotype but not
genotype is altered.
Epigenesis is the development of a plant or animal from undifferentiated cells. Due to cell differentiation, structures and functions appear that were not present at the start of the organism’s life. Differentiation is achieved by activation of some genes and deactivation (silencing) of others. Activation and silencing are carried out by chemical modifications of DNA and the proteins associated with DNA. These modifications are known as epigenetic tags. They are reversible and do not alter DNA base sequences so the genotype of the organism is unchanged, but they do alter the phenotype.
D2.2.5—Differences between the genome, transcriptome and proteome of individual cells
No cell expresses all of its genes. The pattern of gene expression in a cell determines how it differentiates
Genome: the whole of the genetic information of a cell. It includes coding and non-coding sequences. Transcriptome: the entire set of mRNAs transcribed in a cell. No cell transcribes all its genes at once, so its transcriptome does not include an RNA copy of each protein-coding gene. The transcriptome varies over time within any cell and between cells within an organism.
Proteome: 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.
The number of molecules of polypeptide translated from each mRNA molecule is regulated as part of the control of gene expression. The pattern of gene expression within a cell determines how that cell differentiates.
Which statement correctly describes genome and proteome?
A. Only the genome but not the proteome can be analysed using gel electrophoresis.
B. The genome and the proteome are the same in all tissues in an organism.
C. In cells of different tissues, the genome is the same while the proteome varies.
D. Only mutations in the proteome but not in the genome cause any variability.
[1]
Markscheme
C
A. The genes that code for all the proteins in the ribosome
B. The group of proteins that generate a proton gradient in mitochondria
C. The entire genome of a prokaryote
D. The entire set of proteins expressed by an organism at a certain time
[1]
Markscheme
D
The number of protein-coding genes in the human genome is estimated to be about 20 000, which is much less than the size of the proteome. What is one reason for this?
A. Exons are removed from RNA before translation.
B. There are more types of amino acids than nucleotides.
C. mRNA can be spliced after transcription.
D. Base substitutions occur during transcription.
[1]
Markscheme
C
The micrograph of a section through a plant stem shows at least ten different types of cells.
What explains the differences between these cells?
A. Only one gene is expressed in each cell type.
B. Different genes are expressed in each cell type.
C. Only useful genes remain in the DNA of each cell type.
D. Changes in the DNA sequence take place when these cells develop.
[1]
Markscheme
B
What is the proteome of an individual?
A. The amino acids unique to an individual making up the proteins in cells
B. The way in which an individual’s polypeptides are folded into a three-dimensional structure
C. The proteins synthesized as an expression of an individual’s genes
D. All possible combinations of amino acids an individual contains
[1]
Markscheme
C
D2.2.6—Methylation of the promoter and histones in nucleosomes as examples of epigenetic tags
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.
Outline how nucleosomes affect the transcription of DNA.
Methylation is replacement of part of a molecule, usually
hydrogen, with a methyl group (-CH.). Methyl groups are used
as epigenetic tags and have multiple roles in the regulation of
g e n e expression.
2. Methylation of histones in nucleosomes
The structure of nucleosomes is described in Section A1.2.13.
Each of the eight histones has its main globular region in the
nucleosome core, with a long tail consisting of a chain of amino
1. Methylation of the promoter
acids that extends out from the nucleo s ome. The tails are u s e d to
Methylation of bases in the promoter prevents binding of some
bind adjacent nucleosomes tightly together during condensation
of chromosomes, which influences gene expression. Amino
transcription factors, so RNA polymerase does not transcribe
the gene downstream of the promoter and it is not expressed
acids in the histone tails can have methyl or other groups added.
The base that is methylated is usually cytosine (converting it to
methylcytosine), but it can also be adenine.
Methylation can cause gene transcription to be activated or
repressed depending on which amino acid is the target, because
access for transcription factors is increased or decreased.
[1]
Markscheme
(nucleosomes can) promote AND inhibit transcription of genes/expression of genes;
(nucleosomes can) prevent transcription by (tight) condensation/supercoiling/packing of DNA;
(nucleosomes can) allow/prevent binding of RNA polymerase/transcription factors;
tagging/acetylation/methylation of nucleosomes/histones can promote/inhibit transcription;
movement of histones/nucleosomes (along DNA) can affect which genes are transcribed;
The graph shows the effect of methylation on the expression of MT1E, a gene involved in the control of prostate cancer development. Patients with a reduced expression of this gene are more likely to develop prostate cancer.
[Source: © 2017 Demidenko et al. 2017. Decreased expression of MT1E is a potential biomarker of
prostate cancer progression. Oncotarget, 8, pp. 61709–61718. Distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0). Image redrawn and reannotated.]
What are effects of MT1E methylation?
A. It reduces transcription of MT1E, increasing the risk of prostate cancer.
B. It increases translation of MT1E, reducing the risk of prostate cancer.
C. It reduces replication of MT1E, reducing the risk of prostate cancer.
D. It increases the chances of mutation in proto-oncogenes, increasing the risk of prostate cancer.
[1]
Markscheme
A
Outline the difference in methylation pattern between tumorous and normal tissue samples.
[2]
Markscheme
a. «overall» much more methylation in the colon tumour samples than normal ✔
b. tumour and normal samples the markers 258 and 269 similar degree of methylation/fewer differences ✔
c. degree of methylation on certain markers may correlate with the presence of cancer / correct example of a marker only methylated in tumour cells eg marker 32 ✔
Markscheme
a. «DNA» methylation may inhibit transcription of genes that would prevent cancer/tumor formation ✔
b. «DNA» methylation may increase mitosis/cell division leading to tumor formation ✔
DNA methylation profiles in zebrafish (Danio rerio) gametes were determined. The methylated areas were divided into three groups according to the amount of methylation: high, medium and low methylation.
[Source: Potok, M.E., Nix, D.A., Parnell, T.J. and Cairns, B.R., 2013.
Reprogramming the Maternal Zebrafish Genome afterFertilization to
Match the Paternal Methylation Pattern.
Cell, [e-journal] 153(4), pp. 759–772. http://dx.doi.org/10.1016/j.
cell.2013.04.030.]
Methylation of DNA in sperm and egg is removed immediately after fertilization. What is the reason for this?
A. Methylation allows RNA polymerase to join the promoter.
B. It is needed to form homologous pairs of chromosomes.
C. It allows expression of genes linked to early development.
D. Transcription of promoters only occurs in methylated genes.
[1]
Markscheme
C
D2.2.7—Epigenetic inheritance through heritable changes to gene expression
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.
Epigenetic tags affect gene expression, so influence phenotypes. Each cell in a multicellular organism has a specific pattern of tags, helping it to produce the proteins needed to perform its functions. The pattern of tags changes during the life of a cell, partly in response to environmental factors. When cells in a tissue divide by mitosis, the pattern of epigenetic tags can be passed on to daughter cells. As a result, the new cells are differentiated for the same functions and changes made to respond to the environment can be conserved.
It had been assumed that all methyl groups and other epigenetic tags would be removed during meiosis and gamete development, so zygotes start life with the “blank canvas” of an undifferentiated cell. There is now evidence that a few epigenetic tags are not removed, so they are passed from parent to offspring and remain in the zygote. This is transgenerational epigenetic inheritance. It might allow the environment encountered by one generation to have impacts on gene expression in the next generation. However, epigenetic tags can easily be changed, unlike base sequences which are only altered by random mutations.
What is the difference between the DNA of adult identical (monozygotic) twins?
A. Order of genes
B. Sequence of nucleotides
C. Methylation pattern
D. Ratio of complementary base pairs
[1]
Markscheme
C
D2.2.8—Examples of environmental effects on gene expression in cells and organisms
Include alteration of methyl tags on DNA in response to air pollution as an example.
Air pollution can alter the pattern of epigenetic tags in cells and organisms. Particulates, nitrous oxides, ozone and polyaromatic hydrocarbons in air can decrease DNA methylation across the genome. Expression of genes for proteins that regulate the immune system increases, which may account for increased rates of heart disease, inflammation and asthma.
D2.2.9—Consequences of removal of most but not all epigenetic tags from the ovum and sperm
Students can show this by outlining the epigenetic origins of phenotypic differences in tigons and ligers
(lion–tiger hybrids).
During the production of sperm and eggs in humans, about 99% of epigenetic tags are removed, but some persist into the next generation. This is an example of transgenerational epigenetic inheritance.
Offspring inherit one allele of each autosomal gene from their mother and one from their father. If an individual is heterozygous, with one dominant and one recessive allele, it is the dominant allele which is usually expressed. However, if the dominant allele is silenced by epigenetic tags, the recessive allele will be expressed. As patterns of epigenetic tags can be passed on to daughter cells in mitosis, all cells could then express the recessive allele, despite also having a dominant allele.
Some of the epigenetic tags passed on to the zygote are added during gamete development and there are differences between sperm and eggs in the pattern of these tags. This helps to explain the differences between tigons (o tiger X f lion) and ligers (o lion X & tiger).
D2.2.10—Monozygotic twin studies
Limit to investigating the effects of the environment on gene expression.
Dizygotic (fraternal) twins are formed by release of two eggs during ovulation, with each fertilized by a different sperm.
Dizygotic twins share 50% of their genome on average.
Monozygotic (identical) twins are formed by splitting of an early-stage embryo to form two parts, each of which develops into a separate individual. Apart from any mutations that may occur, monozygotic twins share all their genes. Any differences in their phenotypes are due to environment, not genotype. They are therefore very useful in research into impacts of the environment on phenotype.
D2.2.11—External factors impacting the pattern of gene expression
Limit to one example of a hormone and one example of a biochemical such as lactose or tryptophan in
bacteria.
There are many examples of gene expression being affected by factors external to the cell.
- Lactase production in the bacterium E. coli
A group of genes in E. coli codes for proteins needed to absorb and digest lactose, including the gene for lactase.
In the absence of lactose, a repressor protein binds to the promoter for this group of genes so they are not expressed.
If lactose is present, it enters the cell where it binds to the repressor protein, preventing the repressor from binding to the promoter. This allows RNA polymerase to transcribe the genes, so the cell can utilize lactose in its environment. - Testosterone-a hormone affecting gene expression
Testosterone secretion and sperm production are described in Topic D3.1. Leydig cells in the testes secrete testosterone from puberty onwards. The high testosterone concentrations generated in the testes affect gene expression in cells responsible for sperm production, especially Sertoli (nurse) cells.
Testosterone is a steroid, so it can diffuse into these cells and bind to androgen receptor proteins in the cytoplasm.
The testosterone-receptor complexes formed move to the nucleus where they bind to specific DNA base sequences (androgen response elements). This allows other transcription factors to bind to some promoters, resulting in expression of downstream genes. At many other promoters, binding of transcription factors is prevented, so presence of testosterone inhibits expression of genes.
