UNIT 8 - Gene expression, Mutations and Gene technology Flashcards
what is a mutation
a change in the DNA base sequence
what is a substitution mutation
are when a base on the code is copied incorrectly and is substituted for another.
what is a deletion mutation
when a base is removed from the sequence causing a frame shift in the sequence to the left
what is an addition/insertion mutation
extra base is inserted in the sequence that has a similar effect to a base deletion that causes a frame shift to the right
what is a duplication mutation
One or more base is repeated, and it produces a frame shift to the right
what is an inversion mutation
a group of bases become separated from the DNA rotate and go back in causing it to be reversed and therefore effecting the amino acid that is sequenced for
what is a translocation mutation
a group of bases is moved from one location to another within the chromosome to a different chromosome
what is a mutagenic agent and an example
Mutagens are outside factors that can increase the mutation rate
e.g. gamma rays, alpha and beta particles
how do mutagenic agent increase the mutation rate
- They can act as a base which can be substituted for a base during DNA replication
- alter base sequence by deleting alternate bases
- changing the DNA structure like UV radiation causing adjacent bases that we dont want
what is an hereditary mutation
If a gamete containing a mutation is fertilised it will be present in the new foetus
what is a benefit of mutations
increases genetic diversity necessary for survival
what are stem cells
unspecialised cells that can make a new copy of itself or become specialised
what genes are permanently expressed
enzymes involved in respiration , transcription and translation
what is cell speciation
The process by which a cell develops into a specialised cell suited to its role by genes being expressed and it is irreversible
what does totipotency mean and where are they found
has the ability to give rise to all types of cells
normally fertilised egg
what is pluripotency and where are they found
Can still specialise to become anybody cells but lose the ability to make up the placenta
found in a mature embryo from the IVF process
what is multipotency and where are they found
Found in adults and can differentiate into a limited number of specialised cells
Bone marrow can become any type of blood cell
what is unipotency and where is it found
Can only differentiate into a single type of cell
Made in adult tissue
what are induced pluripotent cells and why are they made
made to express a series of transcriptional factors normally associated with pluripotent stem cells and these cause the adult body cell to express the genes and divide indefinately and become a stem cell
what are the uses of pluripotent stem cells
can be used to regrow tissues that have been damaged like burns and ones affected by parkinsons
what is a transcription factor
something that controls the transcription of genes
where are transcription factors found
they are proteins in the cytoplasm
how do transcription factors work
they move into the nucleus and attach themselces to the DNA by the promotor region of a specific base sequence near their target zone
what are activator
increase the rate of transcription as they help RNA polymerase bind to the promoter region
what are repressors
inhibit or slow the rate of transcription and they bind to the promoter region and prevent RNA polymerase from binding
outline how Oestrogen has an effect on gene transcription
- oestrogen is lipid soluble and can diffuse through phospholipid membrane and diffuse into the ctyloplasm
- oestrogen binds to an oestrogen receptor on a transcription factor forming a complex and changing the shape of the transcription factor
- transcription factor diffuses through the nuclear pore and gets to the DNA in the nucleus where it binds to a promotor region on a specific base sequence and this stimulates transcription of the gene
what is epigenetics and how is it influenced
inheritable changes in gene function without changes to the base sequence of DNA
-the environment can influence gene expression without changing the base sequence e.g. diet, stress
what is the epigenome
Epigenome is all the chemical modifications to all histone proteins and DNA in an organism
how do epigenetic markers work
- attach or remove chemical groups and this alters how easilt transcription enzymes and other proteins interact with the DNA
what happens to epigenetic markers between generations
Most epigenetic markers are removed between generations after fertilisation however some are passed on to the offspring
what is epigenetic silencing
when the histone DNA complex is too condensed to be transcribed
what happens when the association of histones with DNA is strong
the complex is more condensed and accessible by transcription factors which cannot initiate production of mRNA so the gene is switched off.
what happens when the association of histones with DNA is weak
the complex is less condensed so this means the DNA is accessible by transcription factors to make mRNA so the gene can be expressed/ switched on
outline what methylation is and what it does
methylation is the addition of a methyl group to a cytosine base of DNA and this changed the structure of DNA making it hard for transcriptional machinery to interact with the gene and therefore the gene isnt expressed and this can cause genes to be switched off
what is epigentic silencing
when a histone DNA complex is too condensed to be transcribed
outline what acetylation is and what it does
acetylatino is a process of transferring an acetyl group to a molecule from acetyle CoA and when histones are acetylation the chromatin is less condensed so the transcriptional machinery can access DNA allowing transcription
what are the two genes that affect cancer
tumour supressor gene
protooncogene
what are 3 things that help us treat disease with epigenetic therapy
use drugs to inhibit enzymes involved in acetylation of histones or DNA methylation
epigentics diagnostic testing helping us detect disease early
use drugs to inhibit enzymes and reactivate genes that have been silenced
how does RNA interference work
- enzyme cuts large double stranded molecules into smaller sections called interfering RNA by hydrolysis (siRNA)
- one of the two strands combines with an enzyme using energy from ATP to separate the two strands
- the siRNA molecule guides the enzyme to mRNA by pairing up its complimentary bases
- the enzyme associated with the siRNA cuts the mRNA into smaller sections and this means it is no longer capable of being translated into a polypeptide chain and the gene will not be expressed
- the fragments are then broken down into RNA nucleotides by enzymes
what does miRNA do in RNA interference
- enzyme cuts large strand of double stranded RNA into smaller pieces
- one of the two strand combines with an enzyme to form a complex
- the miRNA guides the enzyme to the mRNA where it binds by complementary base pairing and prevents translation
where does RNA interference occur
cytoplasm
how can siRNA be used it treat cancer
siRNA can be used to target oncognes that have been expressed or unregulated reducing the number of proteins produced that can lead to cancer or maintain cancerous growth
how can siRNA be used to treat viruses
signals for the degradation of viral genetic material stopping the virus from using the hosts cellular machinery to replicate itself
how is finding the proteome of a bacteria and viruses helpful in medical research
you can identify the protein antigens on the bacteria and virus cells helping in the development of vaccines and helps monitor outbreaks
what is recombinant DNA
transferring a fragment of DNA from one organism to another
what are the three methods of making DNA fragments
using reverse transcriptase
using restriction endonucleases
using a gene machine
how do you use reverse transcriptase to make DNA fragments
Mix mRNA with DNA nucleotides and reverse transcriptase and the reverse transcriptase uses mRNA as a template to synthesise a single strand of cDNA
DNA polymerase forms a second strand of DNA using cDNA as a template
how do you use restriction endonucleases to make DNA fragments
each endonuclease cuts the DNA strand at a specific sequence called the recognition sequence and sometimes they would cut between opposite base pairs and laves two straight edges but others make sticky ends by cutting the DNA at angles
when do you use reverse transcriptase to make DNA fragments and why
in prokaryotes as they have fewer strands of DNA and only have exons
how do you use a gene machine for making DNA fragments
- get the amino acid sequence
- mRNA codons are looked up and complementary DNA triplets are worked out
- the DNA sequence is entered into the computer to check for biosafety and security
- The first nucleotide in the sequence is fixed to a support like a bead
- Nucleotides are added step by step in the correct order in a cycle process where protective groups are added to make sure the nucleotides are joined at the right points to prevent unwanted branching
- Short sections are called oligonucleotides are produced and are broken from the support and the protective groups are removed
what does in vitro cloning mean and what do we use
gene copies are made outside of a living organism using Polymerase chain reaction
what does in vivo cloning mean and what do we use
gene copies are made inside of a living organism where the organisms divides and replicates the DNA creating multiple copies of the DNA
normally use a vector and bacteria
what are the three ways to use recombinant DNA
in agriculture to get crops to produce a higher yield, be more nutritious, famine resistant e.g. golden rice being developed to reduce vitamin A deficiency in Asia and Africa
in industry to produce enzymes quickly and cheaper e.g. enzymes in cheese making we take from cows stomachs when they are dead we no longer need to kill the cows
in medicine drugs and vaccines are made using recombinant DNA which makes them more affordable e.g. insulin
what are the concerns about transformed organisms in agriculture
in agriculture farmers might plant only on type of crop and this can cause the whole crop to be vulnerable to the same disease as they are genetically identical
reduced biodiversity
people are concerned about the possibility of superweeds that are resistant to herbicides as the transformed crops could interbreed with weeds that are resistant to herbicides leading to an uncontrolled spread of recombinant DNA
organic farmers can have their crops contaminated by wind blown seeds from the modified crops which in tern means that they cant sell their crops as organic and may lose their income
what are the concerns about using transformed organisms in industry
without proper labelling people may think that they dont have a choice about eating food made using genetically modified organisms
some people are worried that the process used to purify proteins could lead to the introdiction of toxins into the food industry
large biotechinical companies control some forms of genetic engineering and this increases their power and may force smaller companied out of buisness
what are the concerns of using transformed organisms in medicine
companies who own genetic engineering tech may limit the use of the tech that could be saving lives and this is unethical
some people worry this use of tech could go to far and start designing babies
recombinant DNA tech also creates ownership issues over who owns the DNA is it the person is came from or the company that is using it in technology
what is gene therapy
involves the altering the defective genes/ mutated alleles inside cells to treat gentic disorders and cancer
what can you do in gene therapy when a disorder is caused by two mutated recessive alleles
add a working dominant allele to supplement the recessive faulty alleles
in gene therapy if the disorder is caused by a mutated dominant allele what could you do
you can silence the dominant allele by interrupting it with DNA in the middle so it doesn’t work anymore
what are the two types of gene therapy
somatic and germ line
what is somatic gene therapy and what is the limitation
this involves altering the alleles in the body cells that are most affected by the disorder
doesn’t affect the individuals sex cells so any offspring can still inherit the disease
what is germ line gene therapy and what are the limitations
involves altering the alleles in the sex cells and this means that every cell of any offspring from these cells will be affected by the gene therapy and they wont suffer from the disease
limitation is it isnt legal in humans
what are the ethical issues surrounding gene therapy
some people are worried the tech could be used in other ways than for medical treatment like treating cosmetics and aging
others worry that there is the potential to do more harm then good by using the technology like risking the overexpression of genes
what are DNA probes
Short strands on DNA complementary to the base sequence of the target allele to help identify them
how do you screen for multiple different genes at the same time
use a DNA microray where a sample is washed over the array which the DNA sequences that match the probes will stick too and then you wash it to remove any fluorescently labelled DNA that hasnt stuck and then visualise under UV light
what are the uses for screening with DNA probes
- used to identify inherited conditions like huntingtons disease
- used to help determine how a patient will respond to specific drugs like breast cancer can be treated by Herceptin but it is only effective against a specific type
- used to identify health risks like inheriting particular mutated alleles increases your risk of developing certain types of cancer so a person may make better life choices to reduce the risk
what is the limitation of genetic screening
some people are concerned it may lead to discrimination by insurance companies and employers if people are known to have a high risk of developing disease
what is genetic counselling
advising patients and their relatives about the risks of genetic disorders
what are VNTRs
variable number tandem repeats are base sequences that dont code for proteins and repeat next to each other over and over
what is genetic fingerprinting
the number of times a VNTRs at different places in the genome being compared between individuals
what are the uses of genetic fingerprinting
- determining genetic relationships
- determining genetic variability within a population
- in forensic science
- for medical diagnosis
- in animal and plant breeding
how can you use genetic fingerprinting in determining genetic relationships
we inherit VNTR base sequences from our parents as roughly half comes from them and this means the more bands on a genetic fingerprint that match the more closely related two people are
how can you use genetic fingerprinting in determining genetic variability within a population
the greater the number of bands that don’t match on a genetic fingerprint the more genetically different individuals are and this means you can compare the number of repeats at several places in the genome for a population to find out how genetically varied that population is
how can you use genetic fingerprinting in forensic science
get samples of DNA collected from crime scenes and replicate them in a PCR to compare them to samples of DNA of possible suspects which can link them to crime scenes
how do you use genetic fingerprinting for medical diagnosis
used to refer to a unique pattern of several alleles that can be used to diagnose genetic disorders and cancer
how do you use genetic fingerprinting in animal and plant breeding
it can be used to prevent interbreeding which decreases the gene pool and can be used to prove pedigree in animal breeding
outline the steps of in vitro cloning
PCR
Needs: thermocycler, DNA fragment, DNA polymerase (taq) , nucleotides and primers
- temp increased to 95 to break hydrogen bonds between DNA fragments to form single stranded DNA molecules
- temp decreases to 55 to allow primers to attach/ annealing
- temperature is increased to 72 to allow DNA polymerase to attach complimentary nucleotides to make a new strand of DNA using the single stranded one as a template
outline the steps on in vivo cloning
Create DNA fragments
Inserting DNA into vector
-Restriction endonucleases cut the DNA at the recognition site to create sticky ends
-A promoter region must be added so that DNA polymerase to bind
-A terminator region is added to make DNA polymerase detach
-Plasmid cut open with the same RE to create complimentary sticky ends that align
-Add DNA ligase joins the plasmid and DNA fragment
Inserting DNA into host cell
-Insert the vector into the host cell where the gene will be expressed to create the protein required
- Make the membrane of the host cell more permeable by mixing Ca2+ and heat shocking which makes the vector more able to enter the host cell cytoplasm
Identification of transformed cells
- Three issues can occur: the recombinant DNA doesn’t get inside the cell, the plasmid rejoins with itself before DNA entered, DNA fragment may have stuck to itself instead of inserting into the plasmid
- Marker genes can be used to identify which bacteria successfully took up the recombinant plasmids and the three types are: antibiotic resistance genes, genes coding for enzymes and genes that code for fluorescent proteins
outline the steps of locating alleles with gene probes
A sample of patients DNA is removed and heated to make it single stranded and then mixed with DNA probe that is complimentary and if the patient has the allele you can identify using UV light or X-rays
outline the steps to forming genetic fingerprints
- DNA is collected and then amplified using PCR
- the DNA is cut into fragments using restriction endonucleases that will cut at the variable tandem repeats
- gel electrophoreses separated fragments according to their length
- DNA is then transferred onto a nylon membrane and a probe that is either radioactive or fluorescent is added
- tandem repeats are measured and therefore the individual can be identified as it will be unique to them
why would only one band show when there are usuallly 2
homozygous strands that are the same size
explain how strands of DNA are seperated in PCR
by heating which breaks the hydrogen bonds between bases
why are primers used in PCR
they tell the DNA polymerase where to bind and help start the reaction
suggest why 2 different primers may be used
one primer is for the start of the fragment to start the reaction and the other is at the end which is where the reaction will stop
what is a variable tandem repeat
Regions found in the non-coding part of DNA that contain variable numbers of repeated DNA sequences that are known to vary between different people
explain how DNA could be present on a toothbrush
cells will be on the toothbrush which contain the persons DNA
give one way that the PCR differs from DNA replication in a cell
in PCR the DNA is heated to break the hydrogen bonds where are in normal DNA replication DNA helicase breaks the hydrogen bonds
why might testing in criminal cases often take longer and why
get a very small sample of DNA which will need to be amplified in PCR
might be contaminated which will then need DNA that is required to be identified
explain why radioactive DNA probes are used to locate specific DNA fragments
DNA is invisible on gel so probe helps identify it
describe how a geneticist would attempt to insert copies of a gene into plasmids
- use the same restriction endonuclease to cut plasmid and DNA fragments
- complimentary sticky ends
- add ligase to join the sticky ends
suggest one advantage of using fluorescent gene to identify transformed bacteria
can quickly identify the transformed bacteria using UV light
what do we use to find an unknown segment of DNA
restriction mapping
