gene expression- chapter 20 Flashcards
(72 cards)
1
Q
what is a mutation
A
Any change to the quantity or the structure of the DNA of an organism
2
Q
what is a gene mutation
A
any change to one or more nucleotide bases, or any rearrangement of the bases, in DNA
3
Q
when may gene mutation arise
A
during the replication of DNA
4
Q
what is the substitution of bases
A
The type of gene mutation in which a nucleotide in a section of DNA molecule is replaced by another nucleotide that has a different base is known as a substitution.
5
Q
what is a deletion
A
The loss of a nucleotide base from a DNA sequence
5
Q
depending on which new base is substituted for the original base, what are the 3 possible consequences
A
- Formation of one of the three stop codons that mark the end of a polypeptide chain. As a result the production of the polypeptide coded for by the section of DNA would be stopped prematurely.
- The formation of a codon for different amino acid, meaning that the structure of the polypeptide produced would differ in a single amino acid. The protein of which this polypeptide is a part may differ in shape and not function properly.
- The formation of a different codon but one that produces a codon for the same amino acid as before. This is because the genetic code is degenerate and so most amino acids have more than one codon. The mutation therefore has no effect on the polypeptide produced and so the mutation will have no effect.
6
Q
what does the one deleted base cause and why
A
a frame shift because the reading frame that contains each three letters of the code has been shifted to the left by one letter
7
Q
what would a deletion cause
A
- The gene is not read in the wrong three-base groups and the coded information is altered.
- The polypeptides will be different and lead to the production of a non-functional protein that could considerably alter the phenotype
8
Q
what are 4 ways in which the base sequence of DNA may be changed
A
- Addition of bases- an extra base becomes inserted in the sequence. Has a similar effect to a base deletion, usually a frame shift and the whole sequence of triplets becomes altered. The frame shift is to the right not to the left.
- Duplication of bases- one or more bases are repeated. This produces a frame shift to the right
- Inversion of bases- a group of bases become separated from the DNA sequence and re-join at the same position but in the inverse order (back to front). The base sequence of this portion is therefore reversed and effects the amino acid sequence that results.
- Translocation of bases- a group of bases become separated from the DNA sequence on one chromosome and become inserted into the DNA sequence of a different chromosome. Often have significant effects on gene expression leading to an abnormal phenotype. These effects include the development of certain forms of cancer and also reduced fertility.
9
Q
when can gene mutations occur
A
spontaneously during DNA replication. These are permanent changes in DNA that occur without any outside influence.
10
Q
what can the basic mutation rate be increased by
A
outside factors know as mutagenic agents or mutagens
11
Q
what do mutagenic agents or mutagens include
A
- High energy ionising radiation- e.g. alpha and beta particles as well as short wavelength radiation such as x-rays and ultraviolet light. These disrupt the structure of DNA.
- Chemicals- such a nitrogen dioxide may directly alter the structure of DNA or interfere with transcription. Benzopyrene is a powerful mutagen that inactivates a tumour-suppressor gene TP53 leading to a cancer.
12
Q
what happens as an embryo matures
A
each cell takes on its own individuals characteristics that adapt it to the function that it will perform when it is mature
13
Q
what are all the cells in an organism derived into
A
- by mitotic divisions of the fertilised egg (zygote). It follows that they all contain exactly the same genes.
- However, only certain genes are expressed (switched on) in any one cell at any one time.
- Some genes are permanently expressed (switched on) in all cells and some permanently not expressed in cells.
14
Q
what are totipotent cells
A
Cells such as fertilised eggs, which can mature into any body cell
15
Q
what does the specialisation for the switching off of genes mean
A
- means that only part of the DNA is translated into proteins so it only makes those proteins it requires to carry out its specialised function.
- Although the cell is capable of making all the other proteins, these are not needed so it would be wasteful to produce them.
- In order to conserve energy and resources, a variety of stimuli (controlling factors) ensure the genes for these other proteins are not expressed.
16
Q
what are 2 ways in which genes are prevented from expressing themselves
A
Preventing transcription and so preventing the production of mRNA.
Preventing translation
17
Q
what are stem cells
A
- In mature mammals, only a few cells retain the ability to differentiate into other cells
- Stem cells are undifferentiated dividing cells that occur in adult animal tissues and need to be constantly replaced. They have the ability to divide to form an identical copy of themselves in a process called self-renewal.
18
Q
what are 4 type of stem cells from various sources in mammals
A
- Embryonic stem cells- can differentiate into any type of cell in the initial stages of development.
- Umbilical cord blood stem cells- similar to adult stem cells.
- Placental stem cells- develop into specific types of cells.
- Adult stem cells- specific to a particular tissue or organ within which they produce the cells to maintain and repair tissues throughout an organisms life.
19
Q
what are totipotent stem cells
A
found in early embryo and can differentiate into any type of cell. Zygotes are totipotent, as they develop into slightly more specialised cells they become pluripotent stem cells
20
Q
what are pluripotent stem cells
A
are found in embryos and can differentiate into almost any type of cell. Examples: embryonic stem cells and fetal stem cells
21
Q
what are multipotent stem cells
A
found in adults and can differentiate into a limited number of specialised cells. Usually develop into cells of a particular type, e.g. bone marrow stem cells can produce any type of blood cell. e.g. Adult stem cells and umbilical cord blood stem cells
22
Q
what are the unipotent stem cells
A
can only differentiate into a single type of cell. E.g. cardiomyocytes, heart muscle cells which can produce new heart tissue and so repair damage to heart muscle
23
Q
what are induced pluripotent stem cells (iPS cells)
A
- Type of pluripotent cell that is produced from unipotent cell stems
- they may be almost any body cell
24
how are the induced Pluripotent Stem Cells (iPS cells) altered
- These body cells are then genetically altered in a laboratory to make them acquire the characteristics of embryonic stem cells which are a type of pluripotent cell.
- To make them acquire these new characters involves inducing genes and transcriptional factors within the cell to express themselves
25
how are Induced Pluripotent Stem Cells (iPS cells) similar and different to embryonic stem cells
they're very similar to embryonic stem cells in form and function however, although they express some of the same genes expressed in embryonic stem cells, they are not exact duplicates of them
26
what is a feature of induced Pluripotent Stem Cells (iPS cells)
capable of self-renewal so they can potentially divide indefinitely to provide a limitless supply so they can replace embryonic stem cells in medical research and treatment and so overcome many of the ethical issues surrounding the use
27
how can pluripotent cells in treating human disorders
Can be used to regrow tissues that have been damaged in some way by accident or disease
28
what molecules are transcriptional factors
For transcription to begin the gene is switched on by specific molecules that move from the cytoplasm into the nucleus
29
what does each transcriptional factor have
- a site that binds to a specific base sequence of the DNA in the nucleus.
- When it binds, it causes the region of DNA to begin the process of transcription.
- Messenger RNA (mRNA) is produced and the information it carries is then translated into a polypeptide
30
what happens when a gene is not being expressed (transcriptional factors)
- the site on the transcriptional factor that binds to DNA is not active.
- As the site on the transcriptional factor binding to DNA is inactive it cannot cause transcription and polypeptide synthesis
31
what can oestrogen do for a gene
can switch on a gene and start transcription by combining with a receptor site on the transcriptional factor, this activates the DNA binding site by causing it to change shape
32
what is the process of the effect of oestrogen on gene transcription
1. Oestrogen is a lipid-soluble molecule and therefore easily diffuses through the phospholipid portion of cell-surface membranes.
2. Once inside the cytoplasm of a cell, oestrogen binds with a site on a receptor molecule of the transcriptional factor. The shape of this site and the shape of the oestrogen molecule complement one another.
3. By binding with the site, the oestrogen changes the shape of the DNA binding site on the transcriptional factor, which can now bind to DNA.
4. The transcriptional factor can now enter the nucleus through a nuclear pore and bind to specific base sequences on DNA.
5. The combination of the transcriptional factor with DNA stimulates transcription of the gene that makes up the portion of DNA
33
what are epigenetics
- Provides explanations as to how environmental influences such as diet, stress, toxins, etc can subtly alter the genetic inheritance of an organisms offspring.
- It is helping to explain illnesses ranging from autism to cancer.
34
what is an epigenome of a cell
a accumulation of the signals it has received during its lifetime and it therefore acts like a cellular memory
36
where do signals come from within cells
- in early development, it comes from the cells of the foetus and the nutrition provided by the mother is important in shaping the epigenome
- after birth and throughout life, environmental factors affect the epigenome, although signals from within the body also influence it
37
what do environmental signals (epigenome) stimulate
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
38
when the protein attaches to a specific sequence of bases on the DNA what 2 changes can it have
1. Acetylation of histones leading to the activation or inhibition a gene.
2. Methylation of DNA by attracting enzymes that can add or remove methyl groups.
39
what is the DNA-histone complex (chromatin)
- Where the association of histones and DNA is weak, it is loosely packed, this means the DNA is accessible by transcription factors, which can initiate production of mRNA, that can switch a gene on.
- Where the association is stronger, the DNA-histone complex is more condensed (tightly packed). The DNA is not accessible by transcription factors, which cannot start the production of mRNA, the gene is switched off.
- Condensation of the DNA-histone complex inhibits transcription, it can be brought about by decreased acetylation of the histones or by methylation of DNA.
40
what is acetylation
the process where an acetyl group is transferred to a molecule
41
explain the decreased acetylation of associated histones
- In this case acetylcoenzyme A donates the acetyl group.
- 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 so the gene is switched off.
42
what is methylation
the addition of a methyl group (CH3) to a molecule
43
explain the increased methylation of DNA
- In this case the methyl group is added to the cytosine bases of DNA.
- This inhibits the transcription of genes in two ways:
1. Preventing the binding of transcriptional factors to the DNA.
2. Attracting proteins that condense the DNA-histone complex (by inducing deacetylation of the histones) making the DNA inaccessible to transcription factors.
44
what have experiments on rats shown for female offspring who had good care when young compared to not good care
what does good maternal behaviour transmit
respond better to stress later in life and themselves nurture their offspring better.
Female offspring receiving low-quality care, nurture their offspring less well
Good maternal behaviour in rats transmits epigenetic information onto their offspring’s DNA without passing through an egg or sperm.
45
what happens in humans, when a mother has gestational diabetes and the foetus is exposed to high concentrations of glucose
- causes epigenetic changes in the daughter’s DNA increasing the likelihood that she will develop gestational diabetes herself
- It is thought that in sperm and eggs during the 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’
46
why can epigenetic changes also be responsible for certain diseases
- Altering any of the epigenetic processes can cause abnormal activation or silencing of genes.
- Such alternations have been associated with a number of diseases including cancer.
- In some cases the activation of a normally inactive gene can cause cancer, in other cases, it is the inactivation of a normally active gene that gives rise to the disease.
- There are specific sections of DNA (ones near regions called promoter regions) that have no methylation in normal cells. However, in cancer cells these regions become highly methylated causing genes that should be active to switch off.
- 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. This means damaged base sequences in DNA are not repaired and so can lead to cancer.
47
what can epigenetic changes increase the incidence of
mutations
48
how can epigenetic therapy treat diseases
- Treatments use drugs to inhibit certain enzymes involved in either histone acetylation or DNA methylation
- Epigenetic therapy must be specifically targeted on cancer cells. If the drugs were to affect normal cells they could cause cancer.
49
how can epigenetic be used to develop diagnostic tests
- help to detect the early stages of diseases such as cancer, brain disorders and arthritis.
- These tests can identify the level of DNA methylation and histone acetylation at an early stage of disease. Seek early treatment and better chance of a cure.
50
what is the mechanism involved in small double stranded section of siRNA
1. An enzyme cuts large double-stranded molecules of RNA into smaller sections called small interfering RNA (siRNA)
2. One of the two siRNA strands combines with an enzyme.
3. 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.
4. Once in position, the enzyme cuts the mRNA into smaller sections.
5. The mRNA is no longer capable of being translated into a polypeptide.
6. This means that the gene has not been expressed, that is, is has been blocked.
51
when can the mRNA produced by a gene be inhibited 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 that may be involved is small interfering RNA (siRNA).
52
what is cancer
- is a group of diseases caused by damage to the genes that regulate mitosis and the cells cycle
- leading to unrestrained growth of cells
- as a consequence, a group of abnormal cells, tumour, develops and constantly expands in size
53
what are the types of tumours
- Not all tumours are cancerous.
- Cancerous- malignant
- Non-cancerous- Benign
54
how are cancer cells 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.
- The two main types of genes that play a role in cancer are tumour suppressor genes and oncogenes
55
what are oncogenes
Are mutations of proto-oncogenes
56
what do pronto-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
57
what are two reasons a proto-oncogene that mutates into an oncogene can become permanently activated
1. The receptor protein on the cell-surface membrane can be permanently activated, so that cell division is switched on even in the absence of growth factors.
2. The oncogene may code for a growth factor that is then produced in excessive amounts, again stimulating excessive cell division.
This results in cells dividing too rapidly and out of control, and a tumour or cancer, develops.
58
what are tumours suppressor genes and explain them
- Slow down cell division, repair mistakes in DNA and ‘tell’ cells when to die (apoptosis).
- They have to opposite role from proto-oncogenes.
- If a tumour suppressor gene becomes mutated it is inactivated. As a result, it stops inhibiting cell division and cells can grow out of control.
- The cells that are formed are usually structurally and functionally different from normal cells.
- Most of these will die, but those that survive can make clones of themselves and form tumours.
- TP53, BRCA 1 and BRCA 2 are examples of tumour suppressor genes.
59
what is abnormal DNA methylation
- common in the development of a variety of tumours
- The most common abnormality is hypermethylation (increased methylation)
60
explain the process of hypermethylation
where in the abnormal methylation of this type thought to occour
1. Hypermethylation occurs in a specific region (promoter region) of tumour suppressor genes.
2. This leads to the tumour suppressor gene being inactivated.
3. As a result, transcription of the promoter regions of tumour suppressor genes is inhibited.
4. The tumour suppressor gene is therefore silenced (switched off)
5. As the tumour suppressor gene normally slows the rate of cell division, its inactivation leads to increased cell division and the formation of a tumour.
in a tumours suppressor knows as BRAC1
61
62
what is another type of abnormal methylation that’s not hypermethylation and where is this found
- hypomethylation (reduced methylation)
- This has been found to occur in oncogenes where it leads to their activation and hence the formation of tumour.
63
how does oestrogen concentration and breast cancer link
- After menopause, a woman’s risk of developing breast cancer increases.
- The production of oestrogen from the ovaries diminishes after the menopause, however, the fat cells of the breasts tend to produce more oestrogen after the menopause.
- These locally produced oestrogens appear to trigger breast cancer, once a tumour has developed it further increases oestrogen concentration which therefore leads to increased development of the tumour.
- It also appears that white blood cells that are drawn to the tumour increase oestrogen production, leading to an even greater development of the tumour.
- Oestrogen activates a gene by binding to a receptor which promotes transcription, if that gene 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 develop into oncogenes.
64
what does the human genome exist of
over 3 billion base pairs organised into 20,000 genes. It took 13 years to complete
65
what is bioinformatics
- the science of collecting and analysing complex biological data such as genetic codes.
- It uses computer to read, store and organise biological data at a much faster rate then previously.
- It utilises algorithms to analyse and interpret this data
66
what technique determines the complete DNA base sequence
explain this technique
- whole-genome shotgun (WGS) sequencing
- This involves researchers cutting the DNA into many small, easily sequenced sections and then using computer algorithms to align overlapping segments to assemble the whole genome.
- Sequencing methods such as these are continuously updated which, along with the increased automation of the processes involved, have led to extremely rapid sequencing of whole genomes.
- This has helped with medical advances as we able to see single base variations (SNPs) that are associated with disease and other disorders.
- This allows from quick identification of potential medical problems and early intervention to treat them.
67
what is a proteome
All the proteins that genes code for that are produced
68
what is a cellular proteome
Proteins produced by an given type of cell
69
what is a complete proteome
proteins produced by an organism at any given time under specified conditions
70
why is it easy to determine the proteome of prokaryotic organisms like bacteria
1. The vast majority of prokaryotes have just one, circular piece of DNA that is not associated with histones.
2. There are none of the non-coding portions of DNA which are typical of eukaryotic cells.
71
what is the problem in determining the genome and proteome of complex organisms
translating knowledge of the genome into the proteome because the genome of complex organisms contains many non-coding genes as well as other that have a role in regulating other genes
72
what project is currently underway for humans
human microbiome project
human proteome project to identify all the proteins produced by humans
