all topic 7

what does gene expression do?

control how different tissues and organs are produced

what must happen for a gene to be expressed?

production of mRNA
translation of mRNA
polypeptide protein production

which methods of controlling gene expression are epigenetic modification?

destruction of mRNA
DNA methylation
histone acetylation

how do DNA regulatory sequences and transcription factors control gene expression?

typically turn a gene on by allowing RNA polymerase to attach to transcription factors attached to regulatory sequences

what do promoters do?

enable RNA polymerase to bind to the gene

what do enhancers do?

stimulate promoters causing an increase in the rate of transcription

why do both types of regulatory sequences lie upstream of the gene they regulate?

ensure the correct gene is read and transcribed

what does alternative splicing produce?

isoforms

what are isoforms?

different arrangements of exons in mature mRNA transcribed from a single gene, which results in different polypeptides

how does alternative splicing control gene expression?

alternative splicing turns genes off if done incorrectly and on if done correctly

what is post-transcriptional modification of mRNA?

alternative splicing results in different arrangements of exons in mature mRNA, which creates different polypeptides and these turn genes on or off if done correctly or incorrectly

how is mRNA destroyed?

small non-coding sections of RNA ensure that mRNA can be destroyed so it never gets translated

what is the complex that destroys mRNA?

RISC - RNA induced silencing complex

what does miRNA (microRNA) do?

causes mRNA to be hydrolysed and causes disruption of mRNA so it can't be translated and results in no gene expression

what happens after mRNA binds to RISC?

mRNA is degraded if bases extensively match
mRNA is disrupted by forming bulges if bases do not extensively match

what happens if mRNA is hydrolysed or bulged?

cannot be translated, so the gene is not expressed

how is siRNA (small inhibitory RNA) formed?

a dicer (type of RNA hydrolyse) hydrolysed the dsRNA (double stranded RNA) and forms lengths of 20 bases - these small pieces are siRNA

how does siRNA hydrolyse mRNA?

siRNA binds to protein and forms a RISC, which unwinds the siRNA - one strand is lost and the other remains bound in the RISC
siRNA strand binds to target mRNA strand and mRNA is hydrolysed

how is histone acetylated?

histone are grouped into nucleosomes and have tails containing leucine
leucine can be acetylated by CoA

how does acetylation change gene expression?

acetylation causes nucleosomes to become more loosely packed, which frees/exposes the gene and allows transcription factors and RNA polymerase to access it

what happens if there is no histone acetylation?

nucleosomes are tightly packed and transcription factors and RNA polymerase cannot access the gene

how does DNA methylation change gene expression?

prevents base sequence from being transcribed when cytosine is methylated in vertebrates

where does methylation normally happen?

in a base sequence where C is next to G (CpG)

where is CpG commonly located and what effect does this have?

near promoter regions, which prevents activation of RNA polymerase and target gene is silenced

what do restriction enzymes do?

hydrolyse phosphodiester bonds to form double stranded fragmemts of DNA

what do restriction enzymes do in bacteria?

protect against bacteriophages by restriction multiplication of phage viruses

why are sticky ends needed?

because they bind to other DNA molecules, whereas blunt ends don't

what must happen before a DNA fragment can be cloned?

it must be added to a vector

why are plasmids used as a vector?

more numerous, easier to isolate, and easier to reintroduce
when the plasmid replicates, any copies will be passed on to daughter cells during binary fission

why is the same restriction endonuclease used to cut the plasmid and the DNA fragment?

ensures the sticky ends created are complimentary and the plasmid and DNA fragment can join together

which enzyme joins the plasmid and the DNA fragment and what is this process called?

DNA ligaments joins the two fragments together in a process called annealing

what is annealing?

formation of phosphodiester bonds between plasmid and DNA fragments following alignment of the complimentary base pairs

how is the transfer of recombinant DNA encouraged?

soaking in ice cold sodium chloride followed by heat shock at 42oC for two minutes

promoters

regulatory sequence which lie close to target genes
start transcription by enabling RNA polymerase to bind to the gene

enhancers

regulatory sequence that lie at a distance from target genes
stimulate promoters causing an increase in the rate of transcription

why do regulatory sequences lie upstream of the gene they regulate?

so that the correct gene is read and transcribed

alternative splicing

different arrangements of exons in mature mRNA transcribed from a single gene, which results in different polypeptides

sticky ends and blunt ends

sticky ends bind more readily to other DNA molecules
blunt ends are made into sticky ends during in vivo methods of DNA amplification

why are plasmids used as a vector?

more numerous, easier to isolate, easier to reintroduce
replicates and any copies will be passed on to daughter cells during binary fission

how can the transfer of recombinant DNA be encouraged?

soaking in ice cold sodium chloride followed by heat shock at 42oC for 2 minutes - discovered by trial and error

transformation

once a plasmid has been taken up by bacteria

DNA ligase

an enzyme which catalyses the formation of phosphodiester bonds between DNA fragments which is used to join okazaki fragments in the lagging strand during replication
DNA ligase can be used to join fragments cut by restriction endonucleases during genetic engineering

gene gun

a method of injecting DNA combined with metals into a cell (typically a plant cell) using propulsion

knockout mice

laboratory mice which have had gene(s) removed or inactivated and are used in studies to identify the function of the knockout genes and the effect of harmful mutations in those genes

marker genes

specific detectable genes which are inserted along with other genes during the creation of a transgenic organism so that the organisms which successfully took up the other genes can be identified

recombinant DNA

artificially modified DNA which is made by the combination of genes from different sources

restriction endonucleases

enzymes which break double stranded DNA at specific sequences which are used in genetic engineering

transgenic organism

an organism which has had foreign genetic material inserted into its genome

vector (gene technology)

a carrier such as a virus or gene gun which is used for insertion of foreign DNA into an organism

induced pluripotent stem cells (iPS cells)

pluripotent stem cells produced artificially by the reprogramming of somatic cells through the introduction of genes

multipotent stem cell

a type of stem cell which has the ability to differentiate into any cell type within a certain tissue in the body

pluripotent stem cell

a type of stem cell which has the ability to differentiate into any cell type in the body

totipotent stem cell

a type of stem cell which has the ability to differentiate into any type of cell in the body or in the placenta

stem cell

an undifferentiated cell that can divide indefinitely to produce a given range of specialised cells+

DNA methylation

the addition of methyl groups to DNA molecules as a method of epigenetic modification

epigenetic modification

heritable changes to gene expression brought about without changing the original sequence of bases that compose the DNA molecules

gene expression

the transcription (and often subsequent translation) of genes

histone acetylation

the addition of negative acetyl groups to histones which loosens their binding to DNA, allowing for transcription

histone deacetylation

the removal of negative acetyl groups from histones which means the histone proteins can bind more tightly to DNA which restricts transcription

histone modification

changes made to histone proteins through the addition or removal of chemical groups which affect gene expression

histone proteins

positively charged proteins which bind to and package DNA and can be a target of epigenetic modification

non-coding RNA

RNA molecules which have been transcribed but are not translated to produce proteins

post-transcriptional modification

the production of mature mRNA from pre-mRNA through splicing

transcription factors

proteins which bind to regulatory regions of DNA and control DNA transcription

DNA amplification

the production of many copies of DNA from a small starting amount

DNA profiling

a method of comparing DNA sequences by splitting DNA sections into fragments and comparing the fragments with each other for genetic identification or determining genetic relationships

gene sequencing

the process of determining the specific order of nucleotides in a sequence of DNA

genome

all the genetic information within an organism

genomics

the study of structure and function of the genome

polymerase chain reaction (PCR)

a laboratory technique used to amplify DNA using Taq polymerase, primers, free nucleotides and a buffer