A Level Biology, 3.8 - The Control of Gene Expression

Cells are able to control their metabolic activities by regulating the transcription and translation of their genome. Although the cells within an organism carry the same coded genetic information, they translate only part of it. In multicellular organisms, this control of translation enables cells to have specialised functions, forming tissues and organs. There are many factors that control the expression of genes and, thus, the phenotype of organisms. Some are external, environmental factors, others are internal factors. The expression of genes is not as simple as once thought, with epigenetic regulation of transcription being increasingly recognised as important. Humans are learning how to control the expression of genes by altering the epigenome, and how to alter genomes and proteomes of organisms. This has many medical and technological applications. Consideration of cellular control mechanisms underpins the content of this section. Students who have studied it should develop an understanding of the ways in which organisms and cells control their activities. This should lead to an appreciation of common ailments resulting from a breakdown of these control mechanisms and the use of DNA technology in the diagnosis and treatment of human diseases.

____________ mutation: one or more bases are swapped for another

substitution

____________ mutation: one or more bases are removed

deletion

____________ mutation: one or more bases are added

addition

____________ mutation: one or more bases are repeated

duplication

__________ mutation: sequence of bases is reversed

inversion

____________ mutation: sequence of bases moved from one location in the genome to another; this could be movement within the same chromosome or movement to a different chromosome

translocation

____________ mutations are passed on to the offspring through the gamete with this genetic disorder being fertilised

hereditary

____________ have huge affect on the ______________ of a gene through changing the number of bases in the DNA code which means it is read in a diferent way

frameshift mutations / base sequence

Which type of mutations cause frameshift mutations?

addition / duplication / deletion

What increases the rate of mutations?

mutagenic agents

Mutagenic Agents

• Chemicals called ______________ can increase the rate of mutations through ______________ for a base during DNA replication, changing the base sequence in the new DNA

• Chemicals can ___________ or _______ bases

• Some types of ______________ can change the structure of DNA, which causes problems during replication

base analogs / substituting / delete / alter / radiation

What is an acquired mutation?

mutations that occur in individual cells after fertilisation

Mutations that occur in individual cells after fertilisation are called ________________. If these mutations occur in the genes that control the rate of cell division (by __________), it can cause uncontrolled cell division. If a cell divides uncontrollably, the result is a _________. Those that invade and destroy surrounding tissue are called cancers

acquired mutations / mitosis / tumour

What is the definition of a tumour?

abnormal cell mass

What are the two types of gene that control cell division?

tumour suppressor genes / proto-oncogenes

Normally, tumour suppressor genes __________ _____________ by producing ___________ that stop cells ___________ or cause _____________ to occur

slow cell division / proteins / dividing / apoptosis

______________ is a type of ________________. It’s where cells that are infected, damaged or have reached the end of their functional life are destroyed.

apoptosis / programmed cell death

Normally, proto-oncogenes _________ _____________ by producing certain proteins.

stimulate cell division

Cell Division and Cancer

• If a mutation occurs in a _____________________, the gene will be _____________;

  the protein it codes for isn’t produced and the cells divide uncontrollably (the rate of

  division increases) resulting in a tumour

• If a mutation occurs in a ________________, the gene can become ____________. This stimulates the cells to divide uncontrollably (the rate of division increases) resulting in a tumour. When mutatated, this is called an ___________.

tumour suppressor gene / inactivated / proto-oncogene / overactive / oncogene

Malignant vs Benign

• Malignant tumours are cancers. They usually grow rapidly and invade and

  destroy surrounding tissues. Cells can break off the tumours and spread to

  other parts of the body in the ________________ or _______________ system.

• Benign tumours are not cancerous. They usually grow slower than malignant

  tumours and are often covered in _____________ that stops cells invading other

  tissues. Benign tumours are often harmless, but they can cause blockages and

  put pressure on organs. Some benign tumours can become malignant.

bloodstream / lymphatic / fibrous tissue

What do fibrous tissue do in ________ tumours?

benign / stops cells invading other tissues

Normal vs Tumour Cells

• The nucleus is __________ and __________ than in normal cells. Sometimes the cells have more than one nucleus.

• They have an _____________ shape.

• They don’t produce all the ___________ needed to function correctly.

• They have different ____________ on their surface.

• They don’t respond to __________________________.

• They divide (by mitosis) more frequently than normal cells.

larger / darker / irregular / proteins / antigens / growth regulating processes

What are 2 examples of factors that cause tumour growth?

abnormal methylation / increased oestrogen exposure

Methylation

• Means adding a methyl (-______) group onto something.

• Methylation of DNA is an important method of regulating gene expression - it can control whether or not a gene is ______________ (copied into mRNA) and _______________ (turned into a protein).

• When methylation is happening normally, it plays a key role in many processes in the body.

• It’s only when it happens too much (_________________) or too little (_________________) that it becomes a problem.

• The growth of tumours can be caused by abnormal methylation of certain cancer-related genes.

CH3 / transcribed / translated / hypermethylation / hypomethylation

When ___________________ are __________________, the genes are not ______________ - so the proteins they produce to slow cell division aren’t made. This means that cells are able to divide uncontrollably by mitosis and tumours can develop.

tumour suppressor genes / hypermethylated / transcribed

What is a reason for cancer being caused by tumour suppressor genes?

hypermethylation

When ___________________ are __________________, they act as ______________ - increasing the production of the proteins that encourage cell division. This stimulates cells to divide uncontrollably, which causes the formation of tumours.

proto-oncogenes / hypomethylated / oncogenes

What is a reason for cancer being caused by proto-oncogenes?

hypomethylation

What do HRT drugs do? Why are they used for treating?

increase oestrogen (& usually also progesterone) / menopause symptoms

Theories why Oestrogen can Contribute to the Development of Breast Cancers

• Oestrogen can stimulate certain _____________ to divide and replicate which increases the chance of mutations occurring.

• ƒOestrogen’s ability to stimulate division could also mean that if cells do become cancerous, their rapid replication could be further assisted by oestrogen, helping tumours to form quickly.

• Other research suggests that oestrogen is actually able to _______________ mutations directly into the _____ of certain breast cells.

breast cells / introduce / DNA

What is the term for when characteristics are affected by different genes?

polygenic

What are the 4 types of stem cell?

totipotent / pluripotent / multipotent / unipotent

Totipotent cells

• Where are they found?

• How do they remain unspecialised?

• What can they develop into?

embryonic development / translate only DNA part / any body cell & supportive structures

Multipotent cells

• Where are they found?

• What can they develop into?

mature mammals / limited cell types

Pluripotent cells

• Where are they found?

• What do they develop into?

• What have they lost in terms of the ability to become in comparison to totipotent cells?

• What are they used for?

embryos / unlimited any body cell / cells that make placenta / treating human disorders

Unipotent cells

• Where are they found?

• What can they develop into?

mature mammals / 1 cell type

What is the name for the heart muscle cells that make up a lot of the tissue in our hearts? What has recent research shown? What has this come from?

cardiomyocytes / regenerative capability / replacement derived from small supply of cardiac unipotent stem cells

What are the main sources of stem cells?

adult / embryonic / induced pluripotent

What are induced pluripotent stem cells produced from?

specialised adult somatic cells

Production of Induced Pluripotent Stem Cells

• Somatic cells are converted to iPS cells by _________________ using appropriate _________________________.

• This makes somatic cells become __________________ so they can be used to treat disease.

activating genes / protein transcription factors / unspecialised

What are activators?

transcription factors that stimulate gene expression by interacting w RNA polymerase, allowing DNA binding

What are repressors?

transcription factors that inhibit gene expression by interacting w RNA polymerase, stopping DNA binding

How do peptide hormones regulate transcription?

bind to cell surface membrane to trigger secondary messenger response

How do lipid-soluble steroid hormones regulate hormones?

pass through phospholipid membrane to interact directly w DNA

Oestrogen

1. Enters cytoplasm of cell by passing through phospholipid bilayer.

2. Binds to receptors on _______________ which causes them to change shape and _________________________ forms - this can enter ___________.

3. Complex binds to ______________ of DNA which activates _____________ thus stimulating ________________.

transcription factors / oestrogen-oestrogen receptor complex / nucleus / promoter region / transcription / protein synthesis

RNA Interference

• Small, _____________, ___________ RNA molecules that stop mRNA from target genes being translated into proteins through binding to the molecule and breaking it down.

• What are the two types?

non coding / double stranded / siRNA + miRNA

siRNA

• Once mRNA has been ____________, it leaves the nucleus for the cytoplasm.

• In the cytoplasm, double-stranded siRNA associates with several proteins and unwinds.

• One of the resulting single strands of siRNA is selected and the other strand is ________________.

• Single strand of siRNA binds to ______________ target mRNA.

• Proteins associated with siRNA cut mRNA into _____________________, which moves into a ______________ which degrades them.

transcribed / degraded / complementary / fragments / processing body

miRNA

• When miRNA is first transcribed, it exists as a long, folded strand. It is processed into a double stand, and then into two single strands, by enzymes in the cytoplasm.

• __________________ physically blocks the _____________ of the target mRNA. The mRNA is then moved into a _______________ where it can either be stored or degraded.

• When it’s stored, it can be returned and translated at another time.

miRNA-protein complex / translation / processing body

What is the chemical layer that surrounds chromatin called?

epigenome

How does the epigenome making chromatin more condensed affect transcription?

prevents transcription factors binding to DNA so transcription inhibited

How does the epigenome making chromatin less condensed affect transcription?

allows easier access to transcription factors so transcription promoted

What are epigenetic markers?

groups that don’t alter base sequence but influence chromatin structure

What does increased acetylation cause? What does increased methylation cause?

chromatin less condensed / chromatin more condensed

Epigenetic Markers - Increased Methylation

• Methyl groups bind to a ______ site on DNA (areas in DNA where __________________ are together in the base sequence).

• Methyl groups cause the chromatin to __________.

• ______________________ can’t reach the DNA.

• Methylation __________ transcription.

CpG / cytosine + guanine / condense / transcription factors / inhibits

What are CpG sites?

DNA areas where cytosine & guanine together in base sequence

Where and how does the methyl group attach as an epigenetic marker?

cytosine by DNA methyltransferases

Epigenetic Markers - Decreased Acetylation

• Acetyl groups (___________) are removed from histone proteins.

• Removal of acetyl groups increases the ______________ on histone proteins. This increases the attraction to ________________ on DNA.

• Decreased acetylation causes the chromatin to _____________.

• ___________________ can’t reach the DNA.

COCH3 / positive charge / phosphate groups / condense / transcription factors

Which enzyme is responsible for removing the acetyl groups?

histone deacetylase

________________ - genes can be switched 'on' or switched 'off'; genes that are switched on will be expressed, and levels of gene expression can be measured.

microarrays

What are the important features of the genome?

exons / introns / reg genes

What have been the uses of genome projects?

medical advances / biotechnology / evolutionary relationships / further genome sequencing

_________________: faulty alleles in a person’s cells are replaced by working versions of those alleles.

gene therapy

What are the sections of DNA that are transferred called? What is the organism that receives these called? What is produced?

fragments / transgenic / recombinant DNA

Producing DNA Fragments - Reverse Transcriptase

• mRNA isolated from cells.

• Mixed with ________________________.

• The enzyme uses the mRNA as a ___________ to synthesise new strands of __________.

free DNA nucleotides / template / cDNA

Label the Steps of Making DNA Fragments Using Reverse Transcriptase (1→3)

mRNA strands isolated / cDNA made from mRNA templates / many mRNA cDNA copies produced

Producing DNA Fragments - Restriction Endonuclease

• DNA sample is incubated with the specific restriction endonuclease, which cuts the DNA fragment out via a ____________ reaction.

• Sometimes the cut leaves ________________ - small tails of unpaired bases at each end of the fragment.

• These can be used to bind (_________) the DNA fragment to another piece of DNA that has sticky ends with complementary sequences

hydrolysis / sticky ends / anneal

Label the Steps of Making DNA Fragments using Restriction Endonucleases (1→2)

recognition sequence / restriction endonuclease

Producing DNA Fragments - Using a Gene Machine

• The sequence for the target gene is obtained from a ___________.

• First nucleotide in sequence fixed to _____________.

• ____________________ are added throughout the synthesis to make sure the correct nucleotides are added (for the correct base sequence) and no _____________ are produced.

• _____________________ (short sections of DNA) produced. Once these are complete, they are broken off from the support and all the protecting groups are removed. They can then be joined together to make longer DNA fragments.

database / support / protecting groups / side branches / oligonucleotides

What are palindromic base pairs?

antiparallel base pairs

What are recognition sequences?

specific palindromic sequences that restriction endonuclease recognises

How can DNA fragments be produced?

reverse transcriptase / restriction endonuclease / using gene machines

What are the different techniques of gene cloning?

in vivo / in vitro

What are the 3 stages of in vivo cloning?

making recombinant DNA / transforming cells / identifying transformed cells

In Vivo Cloning - Making Recombinant DNA (Stage 1)

1. _____________ cut open by __________________ which cut the DNA at specific _____________________. This leaves single-stranded ends of DNA called the ______________.

2. _______________ joins sticky ends on DNA fragment and vector DNA together.

vector DNA / restriction endonucleases / recognition sequences / sticky ends / DNA ligase

What is the process of joining sticky ends on DNA fragment and sticky ends on vector DNA called?

ligation

In Vivo Cloning - Transforming Cells (Stage 2)

• The vector with the _______________ transfers gene into ___________ (these cells have been ‘transformed’).

  • If the vector is a plasmid , the host cells take up the recombinant DNA via ______________ (host bacterial cells placed in ice-cold caclcium chloride to make cell walls more permeable, plasmids added and mixture is heated to _____°C for ____________).

  • If the vector is a ______________ (virus), the recombinant DNA is injected into host cells.

recombinant DNA / host cells / heat-shock / 42 / 1 minute / bacteriophage

Other than heat-shock, how else can bacteria be encouraged to take up DNA in the process of in vivo cloning?

electroporation

In Vivo Cloning - Identifying Transforming Cells (Stage 3)

• ______________ inserted into vectors along with gene to be cloned.

• Transformed cells will produce colonies where all the cells contain the cloned gene and the marker gene.

  • The marker gene can code for _________________ - host cells are grown on agar plates containing the specific antibiotic, so only transformed cells that have the marker gene will survive and grow.

  • Marker gene can code for ___________________ - when the agar plate is placed under a UV light only transformed cells will fluoresce.

• Identified transformed cells are allowed to grow more, producing lots and lots of copies of the cloned gene.

marker genes / antibiotic resistance / fluorescence

If you want the transformed host cells to produce the protein coded for by the DNA fragment, what do you need to do?

ensure vector contains specific promoter & terminator regions

What are promoter/terminator regions?

DNA sequences that tell RNA polymerase where to start/stop producing mRNA

In Vitro Cloning - _________

• Reaction mixture containing _________________________________ set up.

• The DNA mixture is heated to _____°C to break the hydrogen bonds between the two strands of DNA.

• The mixture is cooled to _______ °C so that the primers can bind (anneal) to the strands.

• The reaction mixture is heated to ________°C, so DNA polymerase can work. The DNA polymerase lines up free DNA nucleotides alongside each template strand and joins the nucleotides together. Specific base pairing means new complementary strands are formed.

• Two new copies of the fragment of DNA are formed and one cycle of PCR is complete. The cycle starts again - the mixture is heated to 95 °C and this time all four strands (two original and two new) are used as templates.

PCR / DNA sample, free nucleotides, primers & DNA polymerase / 95 / 65 / 72

What are the key temperatures in the polymerase chain reaction of in vitro cloning?

95 / 65 / 72

In the polymerase chain reaction of in vitro cloning, why is the mixture heated to 95°C?

break hydrogen bonds between DNA strands

In the polymerase chain reaction of in vitro cloning, why is the mixture cooled to 65°C?

so primers can anneal to strand

In the polymerase chain reaction of in vitro cloning, why is the mixture heated to 72°C?

so DNA polymerase can work

What happens to the amount of DNA each PCR cycle?

doubles

How can recombinant DNA technology be used?

agriculture / industry / medicine

What are the types of gene therapy? Where do they alter alleles?

somatic - adult body cells / germ line - sex cells

Gene Therapy

• Used to treat diseases that are caused by a ______________ in a gene.

• The insertion used depends on the ____________________ of the gene that causes the disease.

  • If the mutation is in the recessive allele, a ____________ dominant allele is inserted into the genome. The dominant allele counteracts the mutant alleles.

  • If the mutation is in the dominant allele, an allele that '____________' the mutant allele is inserted in the genome.

mutation / allele interactions / wild-type / silences

What are the techniques used to diagnose disease using DNA probes?

electrophoresis / microarrays

Label the Image (1→3)

DNA probe / label / probe hybridises to complementary gene part

DNA Probes

• Section of __________________ that is complementary to DNA of the ______________. If present, it will bind to DNA probe through __________________.

• DNA probes labelled with _____________ or _______________. If present, this label detected.

• What are the techniques used to do this?

single-stranded DNA / target allele / hybridisation / radioactive phosphate / fluorescent tag / electrophoresis & microarrays

Using DNA Probes for Medical Diagnosis - ___________________

1. A sample of DNA is digested into ________________ using ___________________.

2. The separated DNA fragments are then transferred to a _____________________ and incubated (through ‘____________’) with a fluorescently labelled DNA probe. If the allele is present, the DNA probe will _________________.

3. The membrane is then exposed to UV light and if the gene is present there will be a ___________________.

electrophoresis / fragments / restriction enzymes / nylon membrane / washing over / hybridise / fluorescent band

Using DNA Probes for Medical Diagnosis - _____________

• Use many DNA probes at once.

• Slide with many indents - each indent contains the DNA probes for a specific gene.

• The fluorescently labelled DNA sample is _____________.

• Any DNA fragments that are complementary to the probes will ______________.

microarrays / washed over / hybridise

________________ can be used to identify….

• if an individual is a __________ of a genetic disease.

• if an individual is at greater risk of developing a disease.

• how likely an individual is to respond to a particular ________.

genetic screening / carrier / drug

_________________ aims to determine…

• if ____________ is advisable.

• what the results of screening mean.

• how to prevent or treat a _____________ identified through screening.

genetic counselling / screening / condition

What can genetic fingerprinting be used for?

genetic relationships / genetic variability / forensic science / medical diagnosis / breeding

What are the steps of producing genetic fingerprints?

PCR to make DNA fragments / gel electrophoresis to separate DNA fragment / genetic fingerprint analysis

Producing Genetic Fingerprints

1. DNA sample extacted from individual and _______________ using ______. ____________ are used that bind to either side of the VNTR repeats so the whole repeat is coped many times.

2. _____________ labelled using fluorescent labels and inserted into a well in a gel which is covered in _______________ that conducts electricity. Current passed through gel so _______________ DNA fragments move toward ________________.

3. _____________ analysed, the length (in nucleotides) of DNA fragments corresponds to the number of __________ the person has at each locus.

amplified / PCR / primers / DNA fragments / buffer solution / negative / positive electrode / DNA ladder / VNTRs