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Biology > Section 8 - The control of gene expression: 20. Gene expression > Flashcards

Section 8 - The control of gene expression: 20. Gene expression Flashcards

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1
Q

What are gene mutations

A

The rearrangement or changing of bases in the DNA base sequence, potentially changing the amino acid sequences coded for by the DNA, altering the structure of the formed protein

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2
Q

What are the main types of mutations that can occur within DNA

A
  • Substitution
  • Deletion
  • Addition/Insertion
  • Duplication
  • Inversion
  • Translocation
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3
Q

What is the difference between a Gene mutation and a Chromosome mutation

A
  • Gene mutations occur with a base (or group of bases) within a gene
  • Chromosome mutations occur with a gene (or group of genes) within a chromosome
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4
Q

What is a Substitution (mutation)

A

When one nucleotide (base) is replaced with another
- Could result in the formation of a stop codon, stopping the production of a polypeptide
- Could code for a different amino acid, altering the protein structure
- Due to the degenerative nature of the genetic code, new codon may code for the same amino acid (no effect)

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5
Q

What is a Deletion (mutation)

A

When a nucleotide (base) is lost from the sequence
- Will result in ‘Frame shift’
- ∴ More of an impact if occurs near the start of the gene
- Alters amino acid sequence, so effects the produced protein

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6
Q

What is an Addition/Insertion (mutation)

A

When a nucleotide (base) is added to the sequence
- Will result in ‘Frame shift’, as all following codons are changed
- ∴ More of an impact if occurs near the start of the gene
- Alters amino acid sequence, so effects the produced protein

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7
Q

What is a ‘Frame Shift’

A

When a nucleotide is lost/added to the DNA sequence, due to the codes all being read groups of 3 bases, all following codons are changed
- Results in a larger impact if the mutation occurs near start of gene
- Can completely change the structure of produced protein, potentially making it dysfunctional
- If any multiple of 3 bases are lost/added, frame shift will end at the last one

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8
Q

What is a Duplication (mutation)

A

When one or more base is repeated in the the sequence
- Results in ‘Frame Shift’
- Occurs when a section of one chromosome is removed and inserted into it’s homologous partner, giving it two copies of the same section
(other chromosome experiences deletion)

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9
Q

What is an Inversion (mutation)

A

When a group of bases is separated from the sequence and re-joins in the same position, but in reverse order
- Will alter the structure of the protein coded for, as section of the polypeptide chain is ‘backwards’

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10
Q

What is Translocation (mutation)

A

When a section of DNA is removed from one chromosome and inserted into another
- Results in simultaneous deletion and insertion in the two chromosomes
- ∴ Both will experience a ‘Frame Shift’

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11
Q

What are the main causes of mutation

A
  • Arise spontaneously during DNA replication
    • Occurs without outside influence
    • ~1-2 mutations per 100,000 genes (per generation)
  • Rate may be increased by Mutagenic Agents
    • High energy ionising radiation (eg. UV) can disrupt DNA structure
    • Chemicals can alter DNA structure or interfere with transcription (eg. Benzopyrene in Tobacco inactivates tumour suppressor genes, causing cancer)
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12
Q

What is cell differentiation

A

The process by which each cell develops into a specialised structure suited for it’s role

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13
Q

Why is cell differentiation important for multicellular organisms

A

As multicellular organisms develop, each cell will specialise for a particular role, allowing the whole organism function

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14
Q

How are cells different once they have specialied

A

Every cell has the exact same genes, but those that are expressed depends on the cell’s function
- Some genes are permanently expressed in all cells, such as those that code for vital respiratory enzymes
- Some genes are permanently not expressed in some cells, such as insulin producing genes in the cells lining the intestine
- Some genes are switched on/off as and when required

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15
Q

What are Totipotent cells

A

Cells which can mature into any body cells
eg. Early cells derived from fertilised egg
- These later differentiate for specialised functions

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16
Q

What are Stem cells

A

Cells that retain the ability to differentiate into other cells
- Specialisation is irreversible so stem cells are vital to replace damaged tissue
- Self replicate by mitosis to give more stem cells, and also specialise into different functioning cells
- Different types of stem cells can differentiate into more/less specialised cells

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17
Q

What are the main sources of Stem Cells (in mammals)

A
  • ‘Embryonic’ stem cells:
    • Come from embryos in the early stages of development
    • Can differentiate into almost any type of cell
  • ‘Umbilical cord blood’ stem cells
    • Derived from umbilical cord blood and are similar to adult stem cells
  • ‘Placenta’ stem cells
    • Found in the placenta and can only develop into specific types of cells
  • ‘Adult’ stem cells
    • Found in body tissue (foetus through to adult)
    • Specific to a particular organ or tissue
    • Produce cells to maintain and repair tissues throughout an organism’s life
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18
Q

What are the different types of Stem Cells

A
  • Totipotent stem cells
  • Pluripotent stem cells
  • Multipotent stem cells
  • Unipotent stem cells
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19
Q

What are Totipotent stem cells

A

Stem cells that can differentiate into any type of cell
- Found in early embryo (ie. zygote)

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20
Q

What are Pluripotent stem cells

A

Stem cells that can differentiate into almost any type of cell
- Found in embryo
- eg. Embryonic/Foetal stem cells

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21
Q

What are Multipotent stem cells

A

Stem cells that can differentiate into a limited number of cells
- Found in adults
- eg. Bone marrow stem cells can produce any type of blood cell
- eg. Adult/umbilical cord blood stem cells

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22
Q

What are Unipotent stem cells

A

Stem cells that can differentiate into a single type of cell
- Derived from multipotent stem cells in adult tissue
- eg. Cardiomyocytes can divide to produce new heart cells (to repair damage to the muscle)

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23
Q

What are induced pluripotent stem cells (iPS cells)

A

A type of pluripotent stem cell produced from unipotent stem cells (almost any body cell)
- Body cells are genetically altered, by inducing genes and transcriptional factors to express genes that were otherwise ‘switched off’
- ∴ Acquire the characteristics of an embryonic stem cell (pluripotent)
- However, unlike embryonic stem cells, these iPS cells can self replicate, dividing to give a potentially limitless supply
∴ Could help overcome the ethical issues of using embryonic stem cells

24
Q

How are pluripotent stem cells used to treat human disorders

A

Many possible medical uses:
- Regrow damaged tissue
- Cure diseases (Muscular degeneration, Alzheimer’s, Parkinson’s, etc)

25
Q

What are the main ethical issues with stem cell research (arguments for/against)

A

Early embryonic stem cells have the greatest ability to specialise into any cell, but their use requires them to be ‘harvested’ from human embryos (less than 14 days old).
This presents some ethical issues:

For
- Justified, as research will provide information leading to the treatment of diseases
- Embryos can be sourced from IVF

Against
- Research may provide information on reproductive cloning which can be used illegally
- Embryos should be treated as human life
- Development in research may lead to the use of foetuses/new-borns

∴ Currently, research is focused on Adult stem cells (bone marrow), with the aim of making them behave more like embryonic stem cells

26
Q

What are the two main ways that Gene expression is controlled by an organism

A
  • Controlling transcription (transcriptional factors)
  • RNA interference
27
Q

What is a transcriptional factor and how does it control gene expression

A

A molecule with a complementary binding site to a particular base sequence, which triggers the DNA to begin transcription when it binds
- Binds to promoter region on DNA strand
- The transcriptional factor allows the ‘RNA Polymerase’ enzyme to bind
- Transcriptional factor must be activated by hormones (eg. Oestrogen) before it can bind
- ∴ Allows for hormonal control of gene expression

28
Q

What is the process by which the hormone ‘Oestrogen’ stimulates the transcription of a gene

A
  • Oestrogen is lipid-soluble, so diffuses easily into the cell
  • Once in the cytoplasm, the oestrogen binds to a receptor site on the transcriptional factor
  • This changes the shape of the DNA binding site on the transcriptional factor (activating it)
  • The transcriptional factor can now enter the nucleus and bind to the specific DNA sequence
  • This allows the ‘RNA polymerase’ enzyme to bind, stimulating the transcription of the gene, forming mRNA
29
Q

What is RNA interference and how does it effect gene expression

A

RNA interference is the process by which mRNA is broken down before it is coded into a polypeptide, inhibiting the expression of a gene
- Occurs in Eukaryotes (+ some prokaryotes)
- Done by siRNA molecules (small interfering RNA)
- Allows for control of gene expression even after the mRNA has been produced

30
Q

What is the process of RNA interference (RNAi)

A
  • Double stranded RNA (dsRNA) is produced from single stranded mRNA, with the complementary strand synthesis by the enzyme ‘RNA-dependant RNA polymerase’ (RdRp)
  • The dsRNA is cleaved into small sections by the enzyme ‘DICER’
  • These small fragments are cells ‘small interfering RNA’ (siRNA), and have several overhanging bases on each end
  • The siRNA then associates with an enzyme to firm an ‘RNA induced silencing complex’ (RISC)
  • The original strand is degraded, leaving the complementary strand in the RISC
  • The complex can now bind to specific mRNA that fits with the complementary strand, causing it to be broken down
  • ∴ Proteins are no longer coded for by the gene that produced this mRNA
31
Q

What is Epigenetics

A

The process by which environmental factors can cause heritable changes in gene function, without changing the DNA base sequence
- eg. Diet, stress, toxins, etc. can subtly alter the gene expression of an organism’s DNA

32
Q

What is the Epigenome of a cell

A

The accumulation of all the signals (epigenetic tags) a cell has received during it’s life
- Environmental factors cause chemical tags to attach to both DNA and histones, changing the shape of the complex
- The DNA code is fixed, but the epigenome is flexible as chemical tags respond to environmental factors

33
Q

How is the DNA-histone complex (chromatin) effected by epigenetics

A

Environmental factors cause chemical tags to attach to the chromatin
- Can cause the complex to become more condensed (tightly coiled, due to strong association of histones with DNA)
- ∴ DNA is inaccessible to transcriptional factors, so gene is inactivated
- Called ‘Epigenetic silencing’
- Can cause the complex to become less condensed (less tightly coiled, due to weaker association of histones with DNA)
- ∴ DNA is accessible to transcriptional factors, so gene is activated

34
Q

What are the two processes (types of tags) that can effect gene expression through epigenetics

A
  • Acetylation: Process where an acetyl group is associated with the histone protein
  • Methylation: The process where a methyl group is associated with the DNA base sequence
35
Q

What is the effect of Acetylation of the chromatin on gene expression

A
  • Acetyl groups (COCH(3)) are added to lysine amino acids on histone protein (donated by Acetyl CoA)
  • Usually, Lysine has a positive R-group which forms an ionic bind with the negative phosphate backbone of DNA
  • However, is acetylation occurs, the negative acetyl group causes the lysine R-group to become negative, removing the bond between the DNA and histone
  • ∴ Acetylation causes the DNA to be less tightly wound, so is accessible to transcriptional factors and the gene is ‘switched on’
36
Q

What is the effect of Methylation of the chromatin on gene expression

A
  • Methyl groups (CH(3)) are added to a carbon molecule on the cytosine base of the DNA sequence
  • These methylated bases then attract histone proteins to bind to the DNA, condensing the DNA histone complex so it is inaccessible to transcriptional factors
  • Also, the Methyl groups on the DNA are simply in the way, so transcriptional factors can no longer bind
  • ∴ Methylation causes transcription to be inhibited, and the gene is ‘switched off’
37
Q

What epigenetic changes will stop gene expressions (inhibit transcription)

A
  • Decreased Acetylation
  • Increased Methylation
38
Q

How is the Epigenome inherited

A

During the earliest stages of development, specialised cellular mechanisms in the sperm and egg ‘search’ the genome and remove epigenetic tags.
However, a few tags are missed and pass unchanged from parent to off-spring

39
Q

How can epigenetics lead to diseases

A

Epigenetic processes can lead to abnormal activation and silencing of genes, potentially leading to the development of diseases such as cancer
- eg. Inactivation of a ‘protective’ gene
- May lead to some cancers being inherited

40
Q

How can diseases be treated with epigenetic therapy

A

1) Drugs are used to inhibit enzymes involved in Acetylation and Methylation
- eg. Drugs that inhibit methylation can reactivate silenced genes, allowing damaged DNA to be repaired
- However, must specifically target cells, as activating transcription in normal cells may lead to the development of cancer
2) Diagnostic tests
- Levels of Methylation and Acetylation can indicate if a disease is developing
- This allows for earlier treatment of diseases such as cancer, brain disorders, arthritis, etc.

41
Q

What are Cancers

A

A group of diseases that result in uncontrolled and unregulated cell growth, leading to the development of a tumour
- Caused by damage to the genes that regulate mitosis and the cell cycle
- Avoidable depending on life style (risk can be reduced)
- Treatable if diagnosed early enough

42
Q

What are the two type of tumours

A
  • Benign = Non-cancerous
  • Malignant = Cancerous
43
Q

What are the main features of Benign Tumours

A
  • Can grow to large size
  • Grow very slowly
  • Normal looking nuclei
  • Cells are often well differentiated (specialised)
  • Cells produce adhesion molecule, so stick together and remain in original tissue (primary tissue)
  • Surrounded by capsule, containing it in compact structure
  • Less likely to be life threatening (although can inhibit organ function)
  • Tend to have localised effect
  • Can be removed with surgery
  • Rarely occur after treatment
44
Q

What are the main features of Malignant Tumours

A
  • Can grow to large size
  • Grow rapidly
  • Larger and darked nuclei (abundant DNA)
  • Cells become de-differentiated (unspecialised)
  • Cells don’t produce adhesion molecule, so can spread in process called metastasis (forms secondary tumours)
  • No capsule, so grows finger-like projections into surrounding tissue
  • More likely to be life threatening (replaces normal tissue)
  • Have systemic effect on whole body
  • Requires radio/chemo therapy
  • More frequently reoccur after treatment
45
Q

What are are Proto-oncogenes

A

Genes that stimulate cells to divide when growth factors attach to a protein receptor on the cell-surface membrane
- ∴ Regulate cell division, preventing uncontrolled growth and the development of a tumour

46
Q

What are Oncogenes

A
  • Mutations of Proto-oncogenes (although some are inherited)
  • If a proto-oncogene mutates into an oncogene, it can become permanently activated, so cells can continue to divide without growth factors
  • Oncogenes may also code for growth factors that are then overproduced, leading to more cell division
  • ∴ Oncogenes cause cells to divide rapidly and out of control, leading to the development of tumours
47
Q

What are tumour suppressor genes

A

Genes that slow down cell division, repair mistakes in DNA and cause programmed cell death (apoptosis)
- ∴ Maintain normal rates of cell division, preventing the formation of tumours
- If a tumour suppressor gene is mutated, it can become inactivated
∴ Cells can begin to grow out of control, causing cancer

48
Q

What is the effect of hypermethylation (increased methylation) of tumour suppressor genes

A
  • Hypermethylation of the promoter region means that transcriptional factors can no longer attach
  • ∴ Tumour suppressor gene is inactivated, leading to increased cell division and the development of tumours
49
Q

What is the effect of hypomethylation (decreased methylation) of Oncogenes

A

Activates them (transcriptional factors can attach), leading to the formation of tumours

50
Q

How can an increased Oestrogen concentration lead to the development of breast cancer

A
  • The hormone ‘Oestrogen’ allows genes to be expressed by binding to and activating transcriptional factors
  • If this gene controls cell division and growth, oestrogen over-activating it could lead to continued cell division and the formation of a tumour
  • eg. Oestrogen can cause proto-oncogenes in breast tissue to develop into oncogenes
    • In post menopausal women, breast tissue produces more oestrogen
      ∴ Increased risk of tumour
    • One tumour develops, there is a further increase in oestrogen (+ white blood cells increase production of the hormone)
      ∴ Further increase in tumour development
51
Q

What are genome projects

A

Projects to determine the entire DNA nucleotide base sequence of an organism
(eg. Humans, in the human genome project 1990-2003)
- Map the DNA base sequences that make up genes (DNA sequencing)
- Map the genes on the individual chromosome
- ∴ Entire genome is determined

52
Q

What is ‘Whole-genome shotgun’ (WGS) sequencing

A
  • DNA is cut into small sections to be easily sequenced
  • Computer algorithm is used to align overlapping segments to assemble the entire genome
53
Q

What are some examples of the uses of information from genome projects

A
  • Medical uses
    • eg. Over 1.4 million ‘single nucleotide polymorphisms’ have been found in the human genome
      (SNPs = single base variations associated with diseases)
    • ∴ Medical screening now allows these diseases to be identified
  • Evolutionary links can be made between organisms based on their DNA
  • etc.
54
Q

What is the Proteome

A

All the proteins in a given type of cell (cellular proteome) or organism (complete proteome) at a given time, under specific conditions

55
Q

How do you determine the genome and proteome of simple organisms (eg. Bacteria)

A

Genome:
- Genome of microbes can be sequenced to provide knowledge on and help cure human diseases

Proteome:
- Majority of prokaryotic cells have just one circular piece of DNA, with no associated histones and no non-coding sections
- ∴ Proteome can be determined from the sequenced DNA
- Knowledge of bacterial proteome has many applications, such as the use of antigen proteins in vaccines

56
Q

How do you determine the genome and proteome of complex organisms (eg. Humans)

A

Genome:
- Genome can be mapped in projects such as the ‘human genome project’

Proteome:
- Difficult to determine
- Non-coding genes
- Genes that only regulate other genes
(In humans, only ~15% of genes code for proteins)
- Also, all individuals (except identical twins) have a different base sequence, so will have a different proteome
- ∴ The human proteome project is currently underway to overcome these issues, but determining the human proteome is currently not possible

Biology (21 decks)

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