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Biology A2 > Gene expression > Flashcards

Gene expression Flashcards

1
Q

What is a mutation?

A

Any change to the quantity or the structure of DNA of an organism.
A gene mutation is a change or rearrangement of nucleotide bases.

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2
Q

What is substition of bases?

A

A nucleotide in a section of DNA molecule is replaced by another nucleotide with a different base.

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3
Q

What is substitution of bases - stop codons?

A

The formation of one of the three stop codons that mark the end of a polypeptide chain.
The production of the polypeptide chain would stop prematurely.
The final protein would be significantly different and the protein not perform its normal function.

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4
Q

What is substitution of bases - different?

A

The formation of a codon for a different amino acid, so the polypeptide would differ by a single amino acid.
The protein may differ in shape and not function properly.
For an enzyme, the active site may no longer fit the substrate and so not catalyse the reaction.
Example is the mutation that causes sickle cell anaemia.

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5
Q

What is substitution of bases - same?

A

The formation of a different codon but one that produces the same amino acid as before.
This is due to the degenerate nature of the genetic code.
The mutation has no effect on the protein.

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6
Q

What is deletion of bases?

A

The loss of a nucleotide base from a DNA sequence.
This creates a frame shift, and so the gene is read in the wrong three-base groups.
Most triplets and hence amino acids will be different.
It will lead to a non-functional protein that could considerably alter the phenotype.
A deleted base at the end of the chain will have a smaller effect but still have consequences.

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7
Q

What is addition of bases?

A

An extra base is inserted in the sequence.
This causes a frame shift, unless 3 bases are added, or any multiple of 3.
The resulting polypeptide will be different, but not to the same extent as if there was a frame shift.

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8
Q

What is duplication of bases?

A

One or more bases are repeated.
This produces a frame shift.

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9
Q

What is inversion of bases?

A

A group of bases become separated from the DNA sequence and rejoin at the same position but in the inverse order.
This effects the amino acid sequence that results.

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10
Q

What is translocation of bases?

A

A group of bases becomes separate from the DNA sequence on one chromosome and become inserted into the DNA sequence on another chromosome.
They often have significant effects and lead to an abnormal phenotype.
This includes developing some cancers and reduced fertility.

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11
Q

What are the causes of mutations?

A

Mutations occur with predictable frequency, around 1 or 2 mutations per 100,000 genes per generation.
This rate can be increased by mutagenic agents - radiation and chemicals.

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12
Q

How does radiation increase mutations?

A

High energy ionising radiation for example alpha and beta particles, and short wavelength radiation like X-rays and UV light.
These disrupt the structure of DNA.

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13
Q

How do chemicals increase mutations?

A

E.g. Nitrogen dioxide may alter the structure of DNA or interfere with transcription.
Benzopyrene, a constituent of tobacco smoke, is a powerful mutagen that inactivates a tumour-suppressor gene TP53, leading to cancer.

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14
Q

What are the costs and benefits of mutations?

A

They produce the genetic diversity necessary for natural selection and speciation.
But they are almost always harmful and produce an organism less well suited to its environment.
They occur in body cells rather than gametes, leading to the disruption of normal cellular activites - cell division -> cancer.

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15
Q

Why are cells differentiated?

A

Cells cannot be totally efficient at all functions, because they each require different cellular structure, enzymes and other proteins.

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16
Q

What are the origins of cells?

A

All the cells are derived by mitotic division of the zygote.
So they all contain the exact same genes, and so capable of making everything the body can produce.
But, only certain genes are expressed in any one cell at any one time.

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17
Q

How does gene expression vary?

A

Some genes are permanently expressed in all cells, e.g. the genes that code for enzymes involved in respiration, transcription, translation, membrane synthesis, ribosome and tRNA synthesis.
Other genes are expressed when they are needed.

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18
Q

What are differentiated cells?

A

They each produce different proteins.
The proteins a cell produces are coded for by the genes that are expressed.

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19
Q

What are totipotent cells?

A

Cells e.g. fertilised eggs, which can mature into any body cell.
The early cells derived from the fertilised egg are also totipotent.

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20
Q

How is gene expression prevented?

A

It would be wasteful to produce proteins not needed for the specialised cells.
So to conserve energy and resources, a variety of stimuli ensure these genes are not expressed.
By: preventing transcription and so preventing the production of mRNA, and by preventing translation.

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21
Q

Can specialised cells develop into other cells?

A

Xylem vessels, which transport water and red blood cells, are so specialised that they lose their nuclei once mature.
As the nucleus contains the genes, these cells cannot develop into other cells.
Only stem cells can differentiate into other cells.

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22
Q

What are stem cells?

A

Undifferentiated dividing cells in adult animal tissues that need to be constantly replaced.
So they have the ability to divide to form an identical copy of themselves by self-renewal.

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23
Q

Where do stem cells originate from?

A

Embryos in the early stages of development, can develop into any cell in the initial stages of development.
Umbilical cord blood stem cells are similar to adult stem cells.
Placenta stem cells develop into specific types of cells.
Adult stem cells are found in the body tissues of the foetus through to the adult. They are specific to particular tissue or organ and produce the cells to maintain and repair tissues throughout it’s life.

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24
Q

What are the types of stem cells?

A

Totipotent stem cells found in the early embryo. The embryo divides and matures into slightly more specialised pluripotent stem cells.
Pluripotent, multipotent then unipotent stem cells.

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25
Q

What are pluripotent stem cells?

A

Found in embryos and can differentiate into almost any type of cell.
E.g. embryonic stem cells and fetal stem cells.

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26
Q

What are multipotent stem cells?

A

Found in adults and can differentiate into a limited number of cells.
Usually develop into cells of a particular type.
Stem cells in the bone marrow can produce any type of blood cell.
E.g. adult stem cells and umbilical cord blood stem cells.

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27
Q

What are unipotent stem cells?

A

Can only differentiate into a single type of cell.
They are derived from multipotent stem cells and are made in adult tissue.

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28
Q

What are induced pluripotent stem cells?

A

iPS cells are a type of pluripotent cell produced from unipotent stem cells.
The body cell is genetically altered in a lab to make them acquire the characteristics of embryonic stem cells.

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29
Q

How are iPS cells made?

A

To make the unipotent cells acquire the new characteristics involves inducing genes and transcriptional factors within the cell to express themselves.
This shows that adult cells retain the same genetic information that was present in the embryo, because the genes are capable of reactivation.

30
Q

How are iPS cells different from embryonic?

A

They express some of the same genes that expressed in embryonic stem cells, but are not exact duplicates of them.
They can potentially divide indefinitely to provide a limitless supply, and so could replace embryonic in medical research, overcoming the ethical issues.

31
Q

What are the uses of pluripotent cells?

A

The cells can be used to regrow tissues that have been damaged by accident e.g. skin grafts for serious burn damage, or from disease e.g. neuro-degenerative like parkinsons.

32
Q

What are the potential uses of human cells?

A

Heart muscle cells to repair heart damage from heart attacks.
Skeletal muscle cells for muscular dystrophy.
ß cells of pancreas for type 1 diabetes.
Nerve cells for parkinsons, multiple sclerosis, strokes, alzheimers, paralysis from spinal cord injury.
Blood cells for leukaemia, inherited blood disease.
Skin cells for burns and wounds.
Bone cells for osteoporosis.
Cartilage cells for osteoarthritis.
Retina cells for macular degeneration.

33
Q

How is gene expression controlled by controlling transcription?

A

To start transcription, the gene is switched on by transcription factor molecules that move from the cytoplasm to the nucleus.
The transcription factor has a site that binds to the specific base sequence of DNA.
When it binds, it causes the DNA region to start transcription.
mRNA is produced and then translated to a polypeptide.
When a gene is not expressed, the site on the transcriptional factor is not active, so it cannot cause transcription.

34
Q

How does oestrogen affect gene transcription?

A

Oestrogen is a lipid-soluble molecule so diffuses through the phospholipid bilayer.
In the cytoplasm, oestrogen binds with a site on a receptor on the transcriptional factor - the shapes are complementary.
By binding, the oestrogen changes the shape of the DNA binding site on the transcription factor, which can now bind to DNA.
The transcription factor can now enter the nuclear pores and bind to specific base sequences on DNA.
Transcription is stimulated on the gene that makes up the portion of DNA.

35
Q

What is epigenetics?

A

Environmental factors such as diet, stress and toxins, cause heritable changes in gene function without changing the base sequence of DNA.
It can explain, and maybe cure illness such as autism and cancer.

36
Q

What is the epigenome?

A

Both the DNA and the histones it’s wrapped around are covered in chemicals or tags.
These tags form a second layer the epigenome, which determines the shape of the DNA-histone complex.
It keeps inactive genes in a tightly packed arrangement so they cannot be read - epigenetic silencing.
It also unwraps active genes so the DNA is exposed and easily transcribed.

37
Q

How has the epigenome changed in its lifetime?

A

The epigenome is the accumulation of signals its has recieved in its lifetime and so acts like a cellular memory.
In early development, the signals come from within the cells of the fetus and the nutrition from the mother is important in shaping the epigenome.
After birth, environmental factors, as well as hormones also influence it.

38
Q

How does the environment affect the epigenome?

A

The 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.

39
Q

What does the protein bound to DNA change?

A

Acetylation of histones leading to the activation or inhibition of a gene.
Methylation of DNA by attracting enzymes that can add or remove methyl groups.

40
Q

What is the DNA-histone complex?

A

Where the association of histones with DNA is weak, the complex (chromatin) is less condensed. The DNA is accessible by transcription factors, and produce mRNA.
Where the association is stronger, the chromatin is more condensed, and DNA is inaccessible.
So condensation inhibits transcription, and is brought about by decreased acetylation of the histone or methylation of DNA.

41
Q

What is acetylation?

A

Where an acetyl group is transferred to a molecule.
The group donating is acetylcoenzyme A.
Deacetylation is where an acetyl group is removed.

42
Q

What is decreased acetylation?

A

This increases the positive charges on histones and so increases their attraction to the phosphate groups on DNA.
The association of DNA and histones is stronger, so DNA is inaccessible to transcription factors, so gene expression is inhibited.

43
Q

What is increased methylation of DNA?

A

Methylation is the addition of a methyl group (CH3) to a molecule.
The methyl group is added to the cytosine bases of DNA.
It inhibits transcription by:
prevents binding of transcriptional factors to DNA.
Attracting proteins that condense the DNA-histone complex (by inducing deacetylation) and making DNA inaccessible to transcription factors.

44
Q

How is epigenetics inherited?

A

Female rat offspring who recieved good care when young, respond better to stress later on and nurture their offspring better.
Good maternal behaviour transmits epigentic information onto their offspring’s DNA without passing through an egg or sperm.

45
Q

What is an example of epigenetic inheritance in humans?

A

Mothers with gestational diabetes expose the foetus to high glucose concentrations.
These cause epigenetic changes in the daughter’s DNA, increasing the likelihood of developing gestational diabetes herself.

46
Q

How do epigenetics cause diseases?

A

Altering any of the epigenetic processes can cause abnormal activation or silencing of genes.
Activating a normally inactive gene can cause cancer.

47
Q

How is methylation linked to cancer?

A

Tissues with cancer had less DNA methylation, so had higher gene activity.
The promoter regions of DNA in cancer cells become highly methylated causing genes that should be active to switch off.
Increased methylation of genes that help repair DNA and so prevent cancers has lead to these genes switched off, so DNA is not repaired, and can lead to cancer.

48
Q

How can diseases be treated with epigenetics?

A

Treatments use drugs to inhibit certain enzymes involved in histone acetylation or DNA methylation.
e.g. drugs that inhibit enzymes that cause methylation can reactivate silenced genes.
The drugs must be specifically targeted to cancer cells, otherwise they could activate gene transcription on normal cells, and causing more cancer.

49
Q

What is epigenetics in diagnosis?

A

The development of diagnostic tests that help detect the early stages of cancer, brain disorders and arthritis.
The tests can identify the level of DNA methylation and histone acetylation at an early stage.
This allows those to seek early treatment and so a better chance to cure.

50
Q

What is siRNA?

A

Small interfering RNA breaks down mRNA before its coded information can be translated.
An enzyme cuts large double stranded molecules of RNA to smaller sections of siRNA.
One of the strands combines with an enzyme.
The siRNA guides the enzyme to an mRNA by complementary base pairing on the mRNA.
Once in position, the enzyme cuts the mRNA into smaller sections, and cannot be translated, and the gene not expressed.

51
Q

What is cancer?

A

A group of diseases caused by the genes that regulate mitosis and cell cycle.
This causes unrestrained growth of cells, and so a tumour forms, which continues growing in size.

52
Q

What are benign tumours?

A

Can grow to a large size.
Grow very slowly.
The cell nucleus has a relatively normal appearance.
Cells are well specialised.
Can usually be removed by surgery alone.
Rarely reoccur after treatment.

53
Q

What are functional characteristics of benign tumours?

A

Cells produce adhesion molecules that make them stick together and so remain within the original tissue.
Tumours are surrounded by a capsule of dense tissue and so remains a compact structure.
Less likely to be life threatening but can disrupt functioning.
Tend to have localised effects.

54
Q

What are malignant tumours?

A

Can grow to a large size.
Grow rapidly.
Cell nucleus is larger and darker due to an abundance of DNA.
Cells become unspecialised.
Removal involves radiotherapy, chemo, and surgery.
More likely to reoccur after surgery.

55
Q

What are the functional characteristics of malignant tumours?

A

Cells do not have adhesion molecules so spread to other regions of the body – metastasis – form secondary tumours.
Tumours aren’t surrounded by a capsule so can grow projections into surrounding tissue.
More likely to be life-threatening, the abnormal tissue replaces the normal.
Often have whole body effects, weight loss and fatigue.

56
Q

What are oncogenes?

A

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 activates the genes that cause DNA to replicate and cell division.
The oncogene can become permanently activated.

57
Q

Why can oncogenes be permanently activated?

A

The receptor protein on the membrane can be permanently activated, so cell division is switched on without growth factors.
The oncogene may code for a growth factor that is then produced excessively, stimulating excessive division.

58
Q

What are tumour suppressor genes?

A

They slow down cell division, repair mistakes in DNA, and tell cells when to die - apoptosis.
It so prevents the formation of tumours.
If it mutates, the gene is inactivated, so stops inhibiting cell division and cells can grow out of control, usually structurally and functionally different from normal.
Most die, but the survivors make clones and form tumours.
Example of gene is TP53, BRCA1, BRCA2.

59
Q

How do tumour suppressor genes become mutated?

A

Some cancers are caused by inherited mutations, but most are acquired.
E.g. over half of cancers display abnormalities of the TP53 gene, which codes for P53 protein.
P53 is involved in apoptosis, which is activated when a cell is unable to repair DNA.
If the gene for P53 isn’t functioning correctly, the damaged DNA cells continue to divide and cause cancer.

60
Q

What’s the difference between oncogenes and tumour suppressor?

A

Oncogenes cause cancer as a resut of the activation of proto-oncogenes, whereas tumour suppressor genes cause cancer when they are inactivated.

61
Q

What is hypermethylation?

A

Hypermethylation occurs in a specific region (promoter) of tumour suppressor genes.
This inactivates the tumour suppressor.
So transcription of the promoter region of suppressor genes is inhibited.
The tumour suppressor gene is therefore silenced.
This leads to increased cell division and the formation of a tumour.

62
Q

What are the abnormal forms of methylation?

A

Abnormal methylation occurs in the tumour suppressor gene BRCA1 which develops into breast cancer.
Hypomethylation (decreased) occurs in oncogenes, which activates them and forms tumours.

63
Q

How does oestrogen concentration effect breast cancer?

A

After menopause, the risk of breast cancer increases due to increased oestrogen concentrations.
Because the fat cells of breasts produce more oestrogen, and these trigger it.
Once the tumour develops, it further increases oestrogen concentration, leading to increased development of tumour.
White blood cells drawn to the tumour also increase oestrogen production.

64
Q

How does oestrogen cause a tumour?

A

If the gene that oestrogen acts on (by releasing an inhibitor molecule that prevents transcription) is one that controls cell division and growth, it will be activated and its continued division produces a tumour.
Oestrogen causes proto-oncogenes in breast tissue to develop into oncogenes.

65
Q

What is genome sequencing?

A

The human genome has over 3 million base pairs organised into around 20,000 genes.
Sequencing this was done by bioinformatics - the science of collecting and analysing biological data such as genetic codes.
Computers read, store and organised biological data at a faster rate.
It utilises algorithms to analyse and interpret data.

66
Q

What is whole genome shotgun sequencing?

A

Used to determine the complete DNA base sequence of an organism.
WGS sequencing involves researchers cutting the DNA into many small, easily sequenced sections and using algorithms to align overlapping segments to assemble the entire genome.

67
Q

What are the medical advancements from human genome sequencing?

A

E.g. over 1.4 million single nucleotide polymorphisms (SNPs) have been found.
These are single base variations in the genome that are associated with disease and disorders.
Medical screening allows quick identification to treat them.
It has also established evolutionary links between species.

68
Q

What is the proteome?

A

The proteome is all the proteins produced by the genome.
All the proteins produced in a given type of cell (cellular proteome) or organism (complete proteome) at a given time, under specified conditions.

69
Q

What is the knowledge from genome sequencing of simple organisms used for?

A

The knowledge will hopefully cure disease and provide information to exploit genes.
E.g. genes from organisms that withstand toxic environmental conditions have potential uses in cleaning up pollutants or in manufacturing biofuels.

70
Q

Why is determining the proteome of prokaryotes easy?

A

The vast majority of prokaryotes have just one, circular piece of DNA that is not associated with histones.
There are none of the non-coding introns of DNA found in eukaryotes.

71
Q

How can the knowledge of bacteria proteomes be applied?

A

The identification of those proteins that act as antigens on the surface of human pathogens.
These antigens can be used in vaccines against diseases caused by these pathogens.

72
Q

What is the genome and proteome sequencing of complex organisms?

A

The problem is translating knowledge of the genome into the proteome.
This is because the genome of complex organisms contains non-coding genes and others that have a role in regulating other genes.
In humans, only 1.5% code for proteins.
There is the problem of whose DNA is used, as everyone has different base sequences on their DNA.

Biology A2 (16 decks)

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