20: Gene expression Flashcards
What is a mutation?
Any change to the quantity or the structure of DNA
What is a gene mutation?
Any change to one or more nucleotide bases or rearrangement of bases in DNA
What is substitution of bases?
Type of gene mutation in which a nucleotide is replaced by another with a different base
What are the consequences of substitution?
Formation of one of three stop codons, stopping production early
Formation of a codon for a different amino acids, different polypeptide by one amino acid
Produces codon that is different but codes for same amino acid
What happens if stop codons are produced by gene mutation?
Production of polypeptide stopped short
Final protein is probably significantly different
Unlikely to perform normal function
What occurs to a polypeptide if the substitution causes a different amino acid to form?
Different polypeptide formed
Different shape of active shape could form so could not work
Why can a gene mutation sometimes produce the same amino acid?
Genetic code is degenerate so most produce more than one codon
Mutation has no effect on the polypeptide
What is the deletion of bases?
Loss of nucleotides from a base DNA sequence
What is the effect on DNA deletion?
Creates a frame shift as reading frame has shifted to the left
Gene now read in wrong triplets and code is altered
Most triplets will be different and leads to a non-functioning polypeptides
Why can deletions have variable effects?
Deletion at the start changes the polypeptide significantly
Deletion at end may have a lesser effect
What occurs when the duplication of bases occurs?
One or more bases are repeated
Produces a frame shift to the right
What occurs in the inversion of bases?
Group of bases become separated from DNA sequence and rejoin but in the inverse order
What occurs in addition of bases?
Extra base inserted in sequence
Similar effect to base duplication as frame shift is to the right
But if 3 added then there is no frame shift
What occurs to the polypeptide if there is an addition of 3 bases?
Polypeptide is different from what is should be
However not as different as if there was a frame shift
What occurs in the translocation of bases?
Group of bases become separated from DNA sequence on one chromosome and are inserted in the sequence on a different chromosome
What is the effect on translocation of bases?
Significant effects on gene expression leading to abnormal phenotype
Effects include development of certain cancers
What is a spontaneous mutation?
Permanent changes in DNA that occur without any outside influence
What is the average rate of mutations?
1 or 2 mutations per 100000 genes per generation
When do spontaneous gene mutations occur?
DNA replication
How is the genetic mutation rate increased?
Mutagenic agents or mutagens
What are some examples of mutagens?
High energy ionising radiation - alpha or beta particles and short wavelength radiation (UV and X-Ray)
Chemicals - NO2, benzopyrene, asbestos etc.
What are the advantages and disadvantages of mutations?
Genetic diversity - allows for natural selection and speciation
Produces organism which is less adapted to environment
Mutations in body cells lead to conditions such as cancer
What is the process whereby a cell becomes specialised?
Cell differentiation
Why is specialisation of a cell necessary?
No one cell can be totally efficient at all jobs
As each function requires a different cellular structure, enzymes etc.
What cells are present in early development?
All cells are identical at the start
Then they adapt as the organism matures
What is the origin of all cells of a human and what does this mean?
Derived by mitotic divisions of the zygote
All contain same genes
What are some genes that are permanently expressed in all cells?
Genes that code for enzymes in respiration, transcription, translation, membrane synthesis, tRNA and ribosomes
How do differentiated cells differ from each other?
Produce different proteins as different genes are expressed
What are totipotent cells?
Cells which can mature into any body cell
What are some examples of totipotent cells?
Fertilised eggs
What occurs to a cell in differentiation?
Only some genes are expressed in the cells
Only produces certain proteins for a function, doesn’t make others as it has no function
How are genes prevented from expressing?
Preventing transcription so production of mRNA
Preventing translation
What are stem cells?
The few cells in mature mammals which retain the ability to differentiate into other cells
Undifferentiated cells in adult animal tissues with the ability to form an identical copy
What is the process whereby stem cells form an identical copy of themselves?
Self-renewal
What are the origins of stem cells in mammals?
Embryonic stem cells
Umbilical cord blood stem cells
Placental stem cells
Adult stem cells
What are embryonic stem cells?
Stem cells from embryos in early stages of development
Pluripotent
What are umbilical cord blood stem cells?
Stem cells derived from umbilical cord blood and are similar to adult stem cells
What are placental stem cells?
Found in the placenta and develop into specific types of cells
What are adult stem cells?
Found in bone marrow from fetus to adult
Specific to a particular tissue/organ within which they produce cells to maintain and repair tissue throughout an organism’s life
Multipotent
What is a pluripotent stem cell?
Found in embryos and can differentiate into almost any type of cell
Cannot form placenta
What is a multipotent stem cells?
Found in adults, can differentiate into a limited number of specialised cells
Develop into cells of a specific type
What are some examples of multipotent stem cells?
Adult stem cells and umbilical cord blood cells
What is a unipotent stem cell?
Only can differentiate into a single type of cell
Derived from multipotent stem cells and made in adult tissue
What is an induced pluripotent stem cell (iPS cell)?
Type of pluripotent cell that is produced from unipotent stem cells
Unipotent cell can be from almost any body cell
How are iPS cells formed?
Unipotent stem cell genetically altered to acquire characteristics of embryonic stem cells, which is a pluripotent cell
Done by inducing genes and transcriptional factors to express themselves
What do iPS cells show?
Shows that adult cells have genes from birth, just some are turned on/off
What are the differences of iPS cells and embryonic stem cells?
iPS not exact duplicates of embryonic cells
iPS are capable of self-renewal to provide limitless supply
Why is self-renewal of iPS important?
Replaces embryonic stem cells in medical research/treatment
This overcomes ethical issues
What is the use of pluripotent stem cells?
Regrow tissues damaged in an accident (skin graph from burns) or diseases
What are some potential uses of human cells produced from stem cells?
Heart muscle cells - heart attack
Skeletal muscle cells - muscular dystrophy
Beta cells of the pancreas - type 1 diabetes
Nerve cells - MS
Blood cells - leukemia
Skin cells - burns and wounds
Bone cells - osteoporosis
Cartilage cells - osteoarthritis
Retina cells of the eye - macular degeneration
What is oestrogen an example of?
Steroid hormones
How is the expression of a gene possible?
Transcriptional factor (TF) moves form cytoplasm into nucleus
Site on TF binds to a specific base sequence of DNA in the nucleus
Binding causes region of DNA to begin transcription by allowing RNA polymerase to bind
What occurs for a gene not to be active?
Site on the transcriptional factor that binds to DNA isn’t active
As cannot bind to DNA, cannot cause transcription and polypeptide synthesis
What is a transcriptional factor?
Proteins possessing domains that bind to the DNA of promoter or enhancer regions of specific genes
How does oestrogen switch on a gene?
Combining with a receptor site on transcriptional factor
Actives the DNA binding site which causes it to change shape
What is oestrogen?
Lipid-soluble molecule that has the ability to cause genes to be expressed
What is the process of gene expression by oestrogen?
Oestrogen diffuses through membrane
Oestrogen binds with site on TF,changing its shape
TF can then can now enter nuclear pore and bind to specific base sequences on DNA
This causes transcription of gene that makes up the portion of DNA
What is epigenetics?
Field that explains how environmental influences can subtly alter the genetic inheritance of an organism’s offspring
What are some environmental influences which can alter genetic information?
Diet
Stress
Toxins
What does epigenetics suggest could be looked at?
Formerly discredited theories such as Lamarckism
What are histones?
Proteins which DNA is wrapped around
Covered in chemicals called tags
What is the epigenome?
Chemical tags on histones which determines the shape of the DNA-histone complex
How does the epigenome influence whether genes are turned on/off?
Inactive genes are tightly packed to the histone
Active genes are unwrapped so DNA is exposed and can be transcribed
What is necessary to bind for DNA transcription?
Transcriptional factors
RNA polymerase
Is the epigenome fixed?
No
The epigenome can change
How can the epigenome be variable?
Chemical tags respond to environmental changes
So genes turned off/on by factors such as diet and stress
How is the epigenome of a cell formed?
Through the accumulation of the signals it has received during its lifetime
Where do signals for epigenome alternation come from before birth?
From cells of the fetus and the nutrition provided by the mother
How do environmental signals transfer its message to the nucleus?
Signals stimulate proteins to carry message inside the cell
Proteins cause other proteins in nucleus to attach to specific sequence on DNA
What is chromatin?
The complex formed by DNA and histones
What are the two processes which occur to affect chemical tags on the DNA sequence on chromatin?
Acetylation of histones
Methylation of DNA by attracting enzymes which add/remove methyl groups
Where is chromatin loosely-packed?
Where the association of histones with DNA is weak
What is a feature of loosely-packed chromatin?
DNA is accessible by transcription factors which can initiate production of mRNA
Where is chromatin tightly-packed?
Where the association of histones with DNA is stronger
What is a feature of tightly-packed chromatin?
DNA is not accessible by transcriptional factors
Gene is not expressed
How can a gene be turned off?
Decreased acetylation of histones
Methylation of DNA
What is acetylation?
Process whereby an acetyl group is transferred to a molecule
What is deacetylation?
Removal of the acetyl group from a molecule
What does decreased acetylation on histones cause?
Increases positive charge on histones
Increases attraction to negative charge of phosphate groups in DNA
Becomes more tightly packed, gene is switched off
What is methylation?
Addition of a methyl group (CH3) to a molecule
What molecule undergoes methylation?
Cytosine bases of DNA
What is the effect of methylation?
Prevents binding of transcriptional factors to DNA
Attracts proteins that condense chromatin (by causing deactylation of histones)
What is epigenetic inheritance?
Epigenetic tags which are passed from parent to offspring
How can a mothers diabetes affect a fetus?
Fetus exposed to high concentrations of glucose
Causes epigenetic changes in fetus DNA
Increases chance of fetus developing diabetes
What occurs to epigenetic tags in sperm and eggs?
Specialisation erases majority of epigenetic tags
When do epigenetic changes occur?
Occur as part of normal development
What can epigenetics be related to?
Diseases such as some types of cancers
How can the methylation of cancer cells be different?
Sections of DNA near promoter regions usually have no methylation
Region is highly methylated in cancer cells
What is siRNA?
Small interfering RNA
How can mRNA translation be prevented?
Breaking down mRNA before it is translated to a polypeptide
What is the mechanism whereby siRNA is involved in the break down of mRNA?
Enzyme cuts long dsRNA to siRNA
1 of 2 siRNA strands combine with the enzyme
siRNA guides enzyme to mRNA by complementary base pairing
Enzyme cuts mRNA into smaller sections, so can’t code for polypeptide
Gene has effectively not been expressed
In what organisms are siRNA used to inhibit gene expression?
Eukaryotes
Prokaryotes
What is cancer?
A group of diseases that damage genes that regulate mitosis and the cell cycle
Leads to unrestrained growth
What is a tumour?
Abnormal growth of cells caused by unrestrained growth
What are the types of tumour?
Malignant
Benign
What is a benign tumour?
A non-cancerous tumour
What is a malignant tumour?
A cancerous tumour
What are the characteristics of benign tumours?
Can grow to a large size Grows slowly Cell nucleus appears normal Cells often differentiated Surrounded by a capsule of dense tissue so remain as a compact structure Cells adhere by producing chemicals Less likely to be lethal but can affect organ function Localised effect on the body Usually can be removed by surgery rarely reoccur after treatment
What are the characteristics of malignant tumours?
Can grow to large size
Grows rapidly
Nucleus often looks larger and darker (abundance of DNA)
Cells are unspecialised
Do no produce adhesion chemicals, so spreads to other regions
Not surrounded by capsule, so grow finger-like projections into surrounding tissue
More likely to be lethal
Have systemic (whole body) effects like weight loss and fatigue
Removal involves chemo or radiotherapy and surgery
More frequently reoccurs after treatment
What is a primary tumour?
A tumour which remains from the tissue in which they arise
What is metastasis?
The spread of cancer when cells break off a malignant tumour
Why are malignant tumours more likely to be life threatening?
Grows finger-like projections into tissue and replaces normal tissue
Spreads throughout the body
What is cancer shown to derive from?
A single mutant cell
How does cancer form?
Single cell mutates to cause uncontrolled mitosis
Further mutation in descendant cell causes cells to become different in growth and appearance
What genes play a role in cancer?
Oncogenes
Tumour suppressor genes
What is a proto-oncogene?
A gene which stimulates a cell to divide when growth factors attach to a protein receptor on cell surface membrane
Activates genes causing DNA replication and cell division
What is an ocogene?
Mutation of a proto-oncogene which is permanently activated
How can a oncogene form?
Receptor protein on cell-surface membrane becomes permanently activated, even without growth factors
Oncogene may code for growth factor in excess, stimulating excess cell division
What is the result of oncogenes forming?
Out of control mitosis
Tumour or cancer forms
Are oncogenes inherited?
Some cancers caused by inherited mutations of proto-oncogenes
Majority involves acquiring the mutation
What is the function of a tumour suppressor gene?
Slow cell division
Repair mistakes in DNA
Cause apoptosis in cells
Therefore prevents tumour formation
What occurs if tumour suppressor genes becomes inactivated?
Cells can grow out of control
Cells are structurally and functionally different from normal cells
Most die but those that survive divide and form tumours
What are some examples of tumour suppressor genes?
TP53
BRCA1
BRCA2
Are mutations to tumour suppressor genes inherited?
Majority are acquired mutations
What is the difference between oncogenes and tumour suppressor genes in terms of causing cancer?
Oncogenes cause cancer as result of activation of proto-oncogenes
Tumour suppressor cells cause cancer when they are deactivated
How is methylation associated with cancer?
Abnormal DNA methylation is common in the development of a variety of tumours
What is hypermethylation?
Increased methylation
How does hypermethylation lead to cancer?
Hypermethylation occurs at promoter region of tumour suppressor genes
Leads to no transcription and no protein produced
Protein cannot prevent cell division and no control of mitosis
Uncontrolled mitosis causes tumour
What occurs to BRCA1 to cause cancer?
Hypermethylation of the promoter region of the gene causes it to not be expressed
Leads to development of breast cancer
What is hypomethylation and how does it cause cancer?
Reduced methylation
Occurs in ocogenes, leading to activation and tumour formation
What is oestrogen used for in women?
Regulating the menstrual cycle
Increases in conc after the menopause
What occurs to risk of breast cancer in women after the menopause?
Increased risk of breast cancer
Due to high conc of oestrogen from breast cells
How can high oestrogen concentrations contribute to cancer developments?
Oestrogen activates genes
Increases conc after the menopause and increases further after cell division
Causes proto-oncogenes to develop into oncogenes leading to breast cancer
What is the genome of an organism?
Complete map of all the genetic material in an organism
How long is the human genome roughly?
Over 3 billion base pairs
Around 20000 genes
How long did it take to sequence the human genome?
13 years
What is bioinformatics?
Science of collecting and analysing complex biological data such as genetic codes
Uses computers to store and process data fast, using algorithms to analyse data
What is whole-genome shotgun (WGS) sequencing?
Cutting DNA into small, easily sequenced sections
Computers used to align overlapping sections to assemble entire genome
Do sequencing techniques stay standard?
No they are constantly updated
Increased automation led to rapid sequencing of whole genomes
What are single nucleotide polymorphisms (SNPs)?
Single-base variations in the genome that are associated with disease and disorders
How has medicine been affected by the human genome project?
Medical screening allows quick identification of potential medical problems
Early intervention for treatment can occur
How can the genome be used for taxonomy?
Allows establishment of evolutionary links between species
What is the proteome?
All of the proteins produced in a given cell type or organism
Why is the proteome not all proteins an organism can produce?
Proteins are only produced when genes are switched on
Differs from cell to cell
Why are bacteria having their genomes sequenced?
Information could aid to cure disease and provide info for genes that can be exploited
What project is currently sequencing different bacteria?
Human microbiome project
Why is finding the proteome of a prokaryotic organisms easy?
Most prokaryotes have just one circular piece of DNA which isn't associated with histones No introns (non-coding) DNA
What proteins are of interest in pathogenic bacteria?
Antigens on surface of membrane
Could be used for vaccines if protein made
Why is it a challenge to find the proteome from genome in complex organisms?
Introns (non-coding) DNA present
Genes present that regulate other genes
1.5% of genes in humans code for proteins
What is a hereditary mutation?
Mutations present in gametes which cause a genetic disorder/cancer
Passed onto offsprings
How do mutagens increase the rate of mutations?
Acting as a base
Altering bases
Changing structure of DNA
How are embryonic stem cells obtained?
Embryos created using IVF (fertilised out of womb)
4/5 day old embryos have stem cells removed and rest is destroyed
Can divide unlimited times
What are the benefits of stem cell therapies?
Save lives - many people on organ transplant list die, stem cells could grow organs
Improve quality of life - e.g. replace damaged cells in blind people
How are adult stem cells derived?
Removed in bone marrow
Simple operation with little risk but high discomfort
How can transcriptional factors be introduced to make iPS?
Infecting them with a specifically-modified virus
Virus integrates its DNA with the desired gene into the adult body cells
What is the ethical issue with embryonic stem cells?
Destroys embryo which could become a womb
People believe that when the embryo is fertilised, they have the right to live
What is the alternative to embryos which have been fertilised by actual sperm?
Artificially activated to start dividing
Therefore wouldn’t form a fetus if put in a womb
Why do scientists not use adult stem cells always?
Can’t develop into all specialised cell types that embryonic stem cells can
Why are iPS ethically useful?
Flexible as embryonic stem cells
Obtained for adult tissue so no ethical issues
Why are iPS useful when made from the persons cells who needs it?
Used to grow new tissue or organ
Patient would not reject it
