gene expression year 2 Flashcards
The structure of a gene
- ‘upstream’ refers to the DNA before the start of the coding region
- the promoter is a section of DNA upstream of the coding region that is the binding site for proteins that control the expression of the gene including RNA polymerase and transcription factors
- while DNA is translated in the 3’ to 5’ direction it is transcribed in the 5’ to 3’ to produce messenger RNA (mRNA)
how transcription factors work
- proteins that enter the nucleus from the cytoplasm through nuclear pores
- transcription factors are activated through a signalling pathway that usually starts from outside the cell
-some transcription factors bind to the promoter region of a gene. This binding can either allow or prevent the transcription of the gene from taking place. Transcription factors interact with RNA polymerase either by assisting it binding to the gene or preventing it from binding
-therefore the presence of a transcription factor will either increase or decrease the rate of transcription of a gene
oestrogen
- steroid hormone- small, hydrophobic and lipid soluble so can diffuse through cell membrane and can pass to nucleus through nuclear pores
pathway:
1. oestrogen diffuses through the cell surface membrane into the cytoplasm
2. diffuses through nuclear pore into nucleus
3. attaches to an ERa oestrogen receptor that is held within a protein complex, causing this receptor to undergo a conformational change
4. new shape of the receptor allows it to detach from the protein complex and diffuse towards the gene to be expressed
5. the ERa oestrogen receptor binds to a cofactor which enables it to bind to the promoter region of the gene, this stimulates RNA polymerase binding and gene transcriptipn
epigenetics
- evidence how environmental influences eg diet, stress, toxins can subtly alter genetic inheritance of an organism’s offspring.
epigenome
- DNA and histones are covered in chemicals, sometimes called tags. These chemical tags form a second layer known as the epigenome. The epigenome determines the shape of the DNA-histone complex. eg keeps genes inactive as tightly packed arrangment means some genes cannot be read (epigenetic silencing) and can unwrap active genes so DNA is exposed and can be easily transcribed
- flexible. Chemical tags respond to environmental changes. Factors like diet and stress can cause chemical tags to adjust the
- wrapping and unwrapping of DNA and so switches genes on and off
- epigenome of a cell is the accumulation of signals it has recieved during its lifetime and therefore acts like cellular memory
- in early development the signals come from within the cells of the fetus and the nurtition provided by the mother, after birth environmental factors affect the epigenome although signals from within the body eg hormones also influence it. These factors cause the epigenome to activate or inhibit specific sets of genes
environmental affect on proteins
- environmental signal stimulates proteins to carry its message inside the cell from where it is passed by a series of other proteins into the nucleus. Here the message passes to a specific protein which can be attached to a specific sequence of bases on the DNA. Once attached protein has two possible effects. It can change:
- acylation of histones leading to the activation or inhibition of a gene
- methylation of DNA by attracting enzymes that can add or remove methyl groups
The DNA- histones complex (chromatin)
where the association of histones with DNA is weak, the DNA-histone complex is less condensed. In this condition the DNA is accessible by transcription factors which can initiate the production of mRNA, that can switch the gene on.
Where this association is stronger, DNA- histone complex is more condensed (tightly packed). In this condition the DNA is not accessible by transcription factors, which therefore cannot initiate production of mRNA, that is, the gene is switched off
- condensation of the DNA- histone complex therfore inhibits transcription. It can be brought about by decreased acetylation of the histones or by methylation of DNA
decreased acetylation of associated histones
- acetylation is the process where an acetyl group is transfered to a molcule. In this case the group donating the acetyl group is acetylcoenzyme A. Deacetylation is the reverse reaction where an acetyl group is removed from a molecule.
- Decreased acetylation increases the positive charges on histones and therefore increases their attraction to the phosphate groups of DNA. The association between DNA and histones is stronger and the DNA is not accessible to transcription factors. These transcription factors cannot initiate mRNA production from DNA, so gene is switches off (in other words)
increased methylation of DNA
methylation is the addition of a methyl group (CH3) to a molecule. In this case the methyl group is added to the cytosine bases of dna. Methylation normally inhibits the transcription of genes in two ways:
* preventing the binding of transcriptional factors to the DNA
* attracting proteins that condense the DNA- histone complex (by inducing deacetylation of the histones) making the DNA inaccessible to transcription factors
epigenetics and inheritence- experimental evidence
experiments on rats have shown that female offspring who recieved good care when young, respond better to stress later in life and themselves nurture their offspring better. Female offspring revieving lower quality care nurture their offspring less well. Good maternal behaviour in rats transmits epigenetic information onto their offsprings DNA without passing through an egg or sperm.
- in humans when a mother has a condition known as gestational diabetes, the feotus is exposed to high conc of glucose. These high glucoses conces cause epigenetic changes to the daughters DNA, increasing the likelihood that she will develop gestational diabetes herself.
- earliest stages of development a specialised cellular mechanism searches the genome and erases its epigenetic tags in order to return the cells to a genetic ‘clean state’, however a few epigenetic tags escape this process and pass unchanged from parent to offspring
epigenetics and disease
- altering any of the epigenetic processes can cause abnormal activation or silencing of genes. Such alterations have ben associated with a number of diseases including cancer. In some cases the activation of a normally inactive gene can cause cancer, in other cases the inactivation of a normally active gene gives rise to the disease
- in cancer cells regions that normally have no methylation (promotor regions) now become highly methylated causing genes that should be active to switch off.
- some active genes normally help repair DNA and so prevent cancers. In people with various types of inherited cancer, it is found that increased methylation of these genes has led to these protective genes being switched off. As a result, damaged base sequences in DNA arent repaired so can lead to cancer
treating genes with epigenetic therapy
- use drugs to inhibit certain enzymes involved in either histone acetylation or DNA methylation
- must be targeted specifically on cancer cells. If drugs were to affect normal cells could activate gene transcription and make them cancerous
- also used in diagnostic tests to help detect early stages of diseases such as cancer, arthritis and brane disorders. These tests can identify the level of DNA methylation and histone acetylation at an early stage of disease. This allows those with these diseases to seek early treatment and so have a better chance of cure
effect of RNA interference on gene expression
-in eukaryotes and some prokaryotes the translation of mRNA produced by a gene can be inhibited by breaking mRNA down before its coded information can be translated into a polypeptide. One type of small RNA molecule involved is small interfering RNA (siRNA)- double stranded.
* an enzyme cuts large double-stranded molecules of RNA into smaller sections called siRNA
* one of the two siRNA strands combines with an enzyme
* the siRNA molecule guides the enzyme to a messenger RNA molecule by pairing up its bases with the complementary ones on a section of the mRNA molecule
* once in position, the enzyme cuts the mRNA into smaller sections
* the mRNA is no longer capable of being translated into a polypeptide
* this means gene hasnt been expressed so has been blocked
cancer
group of diseases caused by damage to the genes that regulate mitosis and the cell cycle. This leads to unrestrained growth of cells. As a consequence, a group of abnormal cells, called a tumour develops and constantly expands in size
benign tumours
- can grow to a large size
- grow very slowly
- cell nucleus has relatively normal appearance
- cells are often well differentiated/ specialised
- cells produce adhesion molecules that make them stick together and so they remain within the tissue from which they arise= primary tumours
- much less likely to be life threatning but can disrupt functioning of a vital organ
- tend to have localised effect on the body
- can usually be removed by surgery alone
- rarley reoccur after treatment
malignant tumours
- can grow to a large size
- rapid growth
- cell nucleus is often larger and appears darker due to abundance of DNA
- cells become de- defferentiated/ unspecialised
- cells dont produce adhesion moecules so tend to spread to other regions of the body , metastasis- forming secondary tumours
- tumours not surrounded by a capsule so can grow finger like projections into the surrounding tissue
- more likely to be life- threatning as abnormal tumour tissue replaces normal tissue
- often have systemic (whole body) effects eg weight loss and fatigue
- removal usually unvolves radiotherapy and chemotherapy
- more frequently reoccur after treatment
secondary tumours form when the tumour cells squeeze into blood and lymphatic vessels. The tumour cells then circulate and adhere to blood vesse, walls and squeeze through to form distant metastases. Metastasis then continue to grow
control of genetic division and cancer
DNA analysis of tumours has shown that in general, cancer cells are derived from a single mutant cell. The initial mutation causes uncontrolled mitosis in this cell. Later, a further mutation in one of the descendant cells leads to other changes that cause subsequent cells to be different from normal in growth and appearance. Two main types of genes that play a role in cancer are tumour suppressor genes and oncogenes
oncogenes
- most oncogenes are mutations of proto-oncogenes. Proto-oncogenes stimulate a cell to divide when growth factors attach to a protein receptor on its cell surface membrane. This then activates genes that cause DNA to replicate and the cell to divide. If a proto-oncogene mutates into an oncogene it can become permanently activated/ switched on for two reasons:
- receptor protein on the cell-surface membrane can be permanently activated so that cell divison is switched on even in the absence of growth factors
- the oncogene may code for a growth factor that is then produced in excessive ammounts, again stimulating excessive cell divison.
The result is that cells divide too rapidly and out of control and a tumour or cancer develops. A few cancers are caused by inherited mutations of proto-oncogenes that cause the oncogene to be activated but most cancer- causing mutations involving oncogenes are acquired, not inherited
tumour suppressor genes
- slow down cell division, repair mistakes in DNA, and tell cells when to die- apoptosis
- if tumour supressor gene becomes mutated it is inactivated/ switched off. Stops inhibiting cell division and cells can grow out of control, The mutated cells formed usually structurally and functionally different from normal cells. While most of these die, those that survive can make clones of themselves and form tumours. Number of forms of tumour suppressor genes including TP53, BRCAI and BRCA2
- some cancers are caused by inherited mutations of tumour suppressor genes but most are acquired, not inherited
abnormal methylation of tumour suppressor genes
-abnormal methylation is common in development of variety of tumours. Hypermethylation (increased methylation):
1. hypermethylation occurs in a specific region (promoter region) of tumour suppressor genes
2. leads to tumour supressor genes being inactivated
3. transcription at promoter regions of tumour suppressor genes is inhibited
4. tumour suppressor gene is therfore silenced/ switched off
5. as tumour suppressor gene normally slows the rate of cell division, its inactivation leads to increased cell division and the formation of a tumour
another form of abnormal methylation is hypomethylation (reduced methylation). This has been found to occur in oncogenes where it leads to their activation and hence the formation of tumours
oestrogen concentrations and breast cancer
- oestrogens play a central role in regulating menstrual cycle in woman. After the menopause a womans risk of developing breast cancer increases. Due to increased oestrogen concentrations. Fat cells of the breasts tend to produce more oestrogens after the menopause. These locally produced oestrogens appear to trigger breast cancer in postmenopausal woman. Once a tumour has developed it futher increases oestrogen concentration which therfore leads to increased development of the tumour. W.B.C are drawn to the tumour increase oestrogen production, leads to even greater development
- oestrogen can lead to a tumour as if the gene oestrogen acts on is one that controls cell division and growth, then it will be activated and its continued division could produce a tumour. Oestrogen causes proto-oncogenes of cells in breast tissue to form oncogenes
genome
complete map of all genetic material within an organism
sequencing genomes
- bioinformatics is the science of collecting and analysing complex biologic data such as genetic codes. Uses computers ro read, store and organise this data at a much faster rate than usual
- DNA sequencing- WGS (whole-genome shotgun). Researchers cutting the DNA into many small, easily sequenced sections and then using computer algorithms to align overlapping segments to assemble the entire genome. These methods are continuously updated which along with increased automation of the processes involved have led to extremly rapid sequencing of whole genomes
- over 1.4 million single nucleotide polymorpisms (SNPs) have been found in the human genome. SNPs are single-base variations associated with disease and other disorders.
- medical screening of individuals has allowed quick identification of potential medical problems and for early intervention to treat them
proteome
all the proteins produced in a given type of cell or organism at a given time under specified conditions
determining the genome and proteome of simpler organisms
- genomes of thousands of prokaryotic and single- celled eukaryotic organisms are currently being sequenced and this knowledge is hoped to help cure disease and provide knowledge of genes
- determining the proteome of prokaryotic organisms is relatively easy because:
1. most prokaryotes have just one , circular piece of DNA not associated with histones
2. none of the non-coding portions of DNA which are typical of eukaryotic cells - one particular interest is identification of proteins that act as antigens on surface of pathogens. These can be used as vaccines against diseases caused by these pathogens.
determining the genome and proteome of complex organisms
the problem in complex organisms is translating knowledge of the genome into the proteome. This is because the genome of complex organisms contains many non-coding genes as well as others that have a role in regulating genes.
all individuals except identical twins have different base sequences on their DNA so DNA mapped will differ
epigenetics definition
heritable changes in gene function without changes to base sequence of DNA
