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biology a-level > Topic 8 The control of gene expression > Flashcards

Topic 8 The control of gene expression Flashcards

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1
Q

What are the types of mutuation?

A
  • Addition: when one or more bases are added.
  • Deletion: when one or more bases are removed.
  • Substitution: when one or more bases are swapped for one another.
  • Inversion: when a sequence of bases is reversed.
  • Duplication: when one or more bases are repeated.
  • Translocation: when a sequence of bases is moved from one location in the genome to another (within a
    chromosome or to a different chromosome).
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2
Q

Explain how mutations can lead to a non-functional protein

A
  • Some gene mutations (e.g. addition/deletion) result in a frame shift.
  • They change all the base triplets downstream from the mutation.
  • So they change the order of amino acids in the polypeptide downstream of the mutation.
  • Therefore the sequence of R groups is changed and the tertiary structure of the protein will be altered.
  • This is more likely to result in a non-functional protein.
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3
Q

Totipotent stem cells

A
  • TOTIPOTENT stem cells = cells which can mature into any type of body cell (including extra-embryonic
    tissue).
  • Have the ability to replicate in unlimited numbers.
  • Found in the early embryo (only present for approximately four days post-fertilisation).
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4
Q

Pluripotent stem cells

A
  • PLURIPOTENT stem cells = cells which can develop into any type of body cell, with the exception of extra-
    embryonic cells (e.g. placenta).
  • After the first few cell divisions. embryonic stem cells become pluripotent.
  • Can divide in unlimited numbers.
  • Can be used to treat human disorders e.g. neurodegenerative diseases.
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5
Q

Multipotent stem cells

A
  • MULTIPOTENT stem cells = cells which can differentiate to form a limited number of different cell types.
  • Found in mature mammals.
  • e.g. adult stem cells (such as bone marrow stem cell).
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6
Q

Unipotent stem cells

A
  • UNIPOTENT stem cells = cells which can only differentiate into one cell type.
  • Found in mature mammals.
  • e.g. damaged cardiomyocytes (heart muscle cells) can be replaced by new cardiomyocytes that develop from
    a supply of unipotent stem cells in the heart.
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7
Q

How do stem cells become specialised?

A
  1. Stem cells all contain the same genes (because they are derived from a fertilised egg cell which divides by
    mitosis).
  2. As the cell differentiates, some genes are expressed and others are not.
  3. mRNA is only transcribed from active genes and this mRNA is translated into proteins.
  4. The range of proteins that a cell produces, determine the structure and function of the differentiated cell.
  5. The cell has become specialised.
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8
Q

IPS

A
  • Adult body cells are made to express transcription factors that are normally associated with pluripotent
    stem cells.
  • These transcription factors attach to specific regions of target genes.
  • This stimulates transcription of genes that were previously inactive.
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9
Q

Role of oestrogen initiating transcription

A
  • Oestrogen is a steroid hormone → lipid-soluble, so can diffuse freely through the phospholipid bilayer.
  • In the cytoplasm of the target cell, oestrogen binds to the oestrogen receptor (a transcription factor), forming an
    oestrogen-oestrogen receptor complex.
  • This complex moves from the cytoplasm to the nucleus and binds to specific DNA sites near the target gene
    and initiates transcription (depending on the cell, it can also act as a repressor).
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10
Q

What is epigenetics?

A

Epigenetics = the process by which environmental factors can cause heritable changes in gene function
without changing the base sequence of the DNA (environmental factors e.g. diet, stress).

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11
Q

What effect does increased methylation have on the expression of a gene?

A
  • Methyl groups are attached to the DNA at CpG sites (CpG sites = where a cytosine and a guanine are next
    to each other in the DNA).
  • Increased methylation attracts proteins that condense the DNA-histone couples (by inducing the
    deacetylation of histones) → genes can’t be transcribed as transcription factors can’t bind to DNA to initiate
    transcription.
  • Result = gene is not expressed.
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12
Q

What effect does decreased acetylation of histones have on the expression of a gene?

A
  • Acetyl groups are removed from histone proteins → chromatin becomes highly condensed.
  • Genes can’t be transcribed because transcription factors can’t bind to DNA.
  • Result = gene is not expressed.
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13
Q

How can abnormal methylation cause the growth of tumours?

A
  • If a tumour suppressor gene is hypermethylated (increased methylation), the genes are not transcribed,
  • So proteins that should be produced to slow cell division, are not made.
  • Result = uncontrolled cell division by mitosis → development of tumours.
    *
  • If a proto-oncogene is hypomethylated (decreased methylation), they act as oncogenes, increasing the
    production of proteins that cause cell division.
  • Result = uncontrolled cell division by mitosis → development of tumours.
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14
Q

What is RNAi

A
  • RNAi = small, double stranded RNA molecules that prevent the translation of mRNA.
  • one type of RNAi is siRNA (small interfering RNA).
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15
Q

How does RNAi using siRNA work?

A
  • Double stranded RNA is cut into smaller sections of siRNA by an enzyme.
  • The double stranded siRNA unwinds and becomes single stranded.
  • After transcription is complete, mRNA’s leave the nucleus and enter the cytoplasm BUT before the mRNA
    can be translated, a single strand of the siRNA binds to its target mRNA → base sequence of the siRNA
    is complementary to part of the base sequence in the target mRNA.
  • This results in the target mRNA being cut into fragments → it can no longer be translated.
  • The mRNA fragments are degraded.
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16
Q
  • How can tumours arise as result of DNA mutations?
A
  • If a mutation occurs in a tumour suppressor gene,
  • Proteins that stop cells dividing might not be produced.
  • If a mutation occurs in a proto-oncogene,
  • It can turn the proto-oncogene into an oncogene → causes the production of too many proteins that cause
    cells to divide.
  • Both cases result in uncontrolled cell growth → resulting in a tumour.
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17
Q

Benign tumours

A
  • Not cancerous
  • Non invasive
  • Slow growing
  • Cannot move to other parts of the body
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18
Q

Malignant tumours

A
  • Cancerous
  • Grow rapidly
  • Can invade and destroy surrounding cells
  • Can move to other parts of the body via the blood or the lymphatic system
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19
Q

How might oestrogen contribute to the development of breast cancer?

A
  • Oestrogen can stimulate some breast cells to divide and replicate.
  • If more replication is taking place, the chances of new mutations (that could cause cancer) increases.
  • Already cancerous cells will also replicate → accelerates tumour formation.
  • Oestrogen may directly cause mutations in certain breast cells, which increases the chance of cancer-causing
    mutations being introduced.
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20
Q

Why might a woman have increased exposure to oestrogen?

A
  • Earlier menstruation / later menopause than normal.
  • Oestrogen-containing drugs such as HRT.
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21
Q

What is a genome?

A

All the genetic material in an organism.

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22
Q

What is a proteome?

A

The full range of proteins that a cell/organism is able to produce.

23
Q

Why is it possible for an organism of one species to produce a protein from the DNA of another species?

A
  1. Genetic code is universal.
  2. Transcription and translation mechanisms are similar in different species.
  3. Therefore, the recipient organism is able to produce proteins from the transferred DNA.
24
Q

Three methods by which fragments of recombinant DNA can be produced:
1. Conversion of mRNA to cDNA using REVERSE TRANSCRIPTASE.

A
  • Reverse transcriptase = an enzyme which can make complementary DNA from an RNA template.
  • mRNA that is complementary to the required DNA fragment is isolated from cells.
  • The mRNA is mixed with DNA nucleotides and reverse transcriptase.
  • The reverse transcriptase uses the mRNA as a template to synthesise a new strand of cDNA.
  • (because cDNA is synthesised using mRNA as a template, it DOES NOT contain INTRONS - this is an
    advantage if the DNA fragment is to be inserted into a bacterial cell - prokaryotic DNA does not contain
    introns therefore they lack the ability to splice pre-mRNA).
  • Why is mRNA for a gene easier to obtain than a DNA fragment containing the target gene?
  • Most cells only contain 2 copies of each gene, whereas cells contain many mRNA molecules which are
    complementary to the gene (if the gene is being actively transcribed).
25
Q

RESTRICTION ENDONUCLEASES

A
  • Restriction endonucleases = enzymes that cut DNA molecules at a specific sequence of bases called a
    recognition site.
  • Palindromic sequences = a nucleotide sequence that is the same reading from the 5’-3’ direction on one
    strand, as it is reading from the 3’-5’ direction on the complementary strand.
  • Sticky ends = after digestion by a restriction endonuclease, the ends have one strand overhanging the other,
    forming a short single-stranded segment.
26
Q

Why do restriction endonucleases only cut DNA at specific places?

A

Different restriction endonucleases recognise and cut at a different specific recognition site, because the shape of the
recognition site is complementary to the enzyme’s active site.

27
Q

How can restriction endonucleases be used to produce DNA fragments?

A
  • DNA sample is mixed with the specific restriction endonuclease, which cuts the DNA fragment out via a hydrolysis
    reaction.
  • the cut leaves sticky ends, which can be used to join the DNA fragment to another fragment of DNA with the same
    sticky ends (using DNA ligase).
28
Q

GENE MACHINE

A
  • Fragments of DNA can be made without a DNA template:
  • Design the required sequence → can be designed so DNA has no introns / has sticky ends → machine produces
    oligonucleotides (short sections of DNA, about 20 nucleotides long) → joined to make a DNA fragment.
  • Advantage of using a gene machine = the DNA sequence does not have to appear naturally - any
    sequence can be made.
29
Q

Summary of gene transfer and cloning

A

Isolation
Insertion
Transformation
Identification
Growth

30
Q

IN VIVO CLONING: 1. ISOLATION of the DNA fragment containing the gene of interest

A
  • Restriction endonuclease is (generally) used to isolate the DNA fragment (because restriction
    endonucleases leave sticky ends).
  • To enable transcription of the gene of interest to occur → extra lengths of DNA must be added:
  • A PROMOTER REGION → sequence of DNA added at the start of the gene that acts as a
    binding site for RNA polymerase and so initiates transcription.
  • What would happen if there was no promoter region? The DNA fragment would
    not be transcribed and therefore no protein would be made.
  • A TERMINATOR REGION → sequence of DNA added at the end of the gene to release RNA
    polymerase and stop transcription at the right point.
  • End result = isolated fragment of DNA containing the gene of interest.
31
Q
  1. INSERTION of the DNA fragment into a vector (e.g. a plasmid) using DNA ligase.
A
  • Plasmid is cut open with the SAME restriction endonuclease that was used to isolate the DNA
    fragment containing the gene of interest (so the plasmid and the fragment have complementary
    sticky ends).
  • DNA fragment and cut plasmid are mixed together, along with DNA ligase.
  • DNA ligase joins the sticky ends of the DNA fragment to the sticky ends of the plasmid DNA, by
    catalysing condensation reactions which form phosphodiester bonds (forming the sugar-phosphate
    backbone).
  • End result = recombinant plasmid carrying the gene of interest.
32
Q
  1. TRANSFORMATION of the host cell - DNA fragment is taken up by the host cell.
A
  • Mix the plasmids and bacterial cells in a solution containing calcium ions and then heat shock
    (sudden change in temperature) → this makes the bacterial cell membranes more permeable
    (allows the plasmids to pass through into the cell more easily).
  • End result = transformed bacterial cells containing the recombinant plasmid which contains
    the gene of interest.
33
Q
  1. IDENTIFICATION of host cells that have successfully taken up the DNA (using marker genes).
A
  • Bacteria which have taken up the recombinant plasmid need to be identified because NOT ALL
    bacterial cells will contain the DNA fragment with the gene of interest.
  • This is done using MARKER GENES (antibiotic resistance genes, fluorescent markers e.g. GFP,
    enzyme markers) to identify which of the bacteria have accepted the gene of interest.
  • Example:
  • Plasmid contains a marker gene that produces a green fluorescent protein (GFP).
  • The gene of interest is inserted into the middle of the GFP gene, so any bacterial cell that
    takes up the plasmid with the gene of interest WILL NOT be able to produce GFP protein.
  • Bacterial cells that have not taken up the plasmid will continue to fluoresce.
  • ADVANTAGE = results are obtained quickly.
34
Q
  1. CULTURING of the host cells containing the gene of interest.
A
  • Identified transformed cells are allowed to divide - producing many copies of the desired gene
    and therefore large quantities of the protein encoded by the gene.
35
Q

IN VITRO CLONING advantages and disadvantages of PCR

A
  • Advantages of PCR vs in-vivo cloning: many copies of a DNA sequence can be made in hours / works with a
    very small starting sample.
  • Disadvantages of PCR vs in-vivo cloning: higher chance of contamination (where a sample of unwanted
    genetic material is also replicated) / equipment required is more expensive.
36
Q
  • How are DNA fragments amplified using in-vitro cloning i.e. PCR?
A
  1. Reaction mix is made up containing the DNA sample, free nucleotides, primers and DNA polymerase.
  2. DNA mixture is heated to 95oC to break the hydrogen bonds between complementary bases and
    separate the two strands.
  3. Mixture is cooled to 50-65oC, so the primers can bind (anneal) to the strands.
    * Primers allow DNA polymerase to attach.
    * Two different primers are required because the sequences at the beginning and end of the target
    sequence are different.
  4. Mixture is heated to 72oC, which is the optimum temperature for the thermostable DNA polymerase
    to work at (the DNA polymerase is thermostable, so it is not denatured during the 95oC step).
  5. DNA polymerase lines up free nucleotides alongside each template strand and specific base pairing
    results in new complementary strands forming.
  6. Cycle repeats, with the original and the new stands acting as templates for each new cycle, resulting in
    exponential amplification of the DNA fragment.
37
Q

Why does the number of copies of DNA produced begin to level off/plateau as the PCR proceeds?

A

Nucleotides
have been used up / primers have been used up - so no reagents left to synthesise the complementary strands with.

38
Q

Ways in which PCR differs from transcription?

A
  1. Transcription uses RNA polymerase, PCR uses DNA
    polymerase.
  2. Transcription uses RNA nucleotides (uracil), PCR uses
    DNA nucleotides.
  3. Transcription uses one template strand, PCR uses both
    strands as templates.
  4. Transcription uses start/stop codons, PCR uses primers.
39
Q

Ways in which PCR differs from semi-conservative
replication?

A
  1. PCR can only replicate short DNA fragments, semi-
    conservation replication can replicate entire DNA.
  2. PCR use 95oC to separate strands, semi-conservative
    replication uses DNA helicase.
  3. PCR uses primers, semi-conservative replication does not
    require primers.
40
Q

Cons of recombinant DNA technology

A
  • Monoculture of transformed crops → whole crop susceptible to the same disease because the plants are
    genetically identical.
  • If recombinant crops interbreed with wild plants → super-species that are resistant to herbicides might develop.
  • Uncontrolled spread of recombinant DNA/contamination of organic crops by wind-blown genetically-modified
    seeds → organic farmers would lose income.
  • Large companies control the technology → forcing smaller companies out of business.
  • Consumers may unknowingly buy GM products if products are not labelled correctly.
  • Concerns that the technology could be used to make designer babies.
  • Debate over who owns genetic material from humans once it has been removed from the body - the donor or
    the researcher.
41
Q

Benefits of recombinant DNA technology

A
  • Crops could be produced that are resistant to drought/disease → reduces the risk of famine.
  • Transformed crops could be used to produce drugs.
  • Medicines could be produced more cheaply.
  • Recombinant DNA technology could be used in gene therapy to treat disease.
42
Q

GENE THERAPY

A
  • Gene therapy = altering defective genes inside cells to treat e.g. genetic disorders and cancer.
  • Defective genes = mutated alleles.
  • To treat a disease caused by 2 mutated recessive alleles → add a working dominant allele.
  • To treat a disease caused by 1 mutated dominant allele → silence the dominant allele by inserting a piece of DNA
    into the middle of the allele so the gene doesn’t produce a functional protein.
43
Q

Somatic therapy:

A

altering alleles in body cells (doesn’t affect the individuals sex cells, so offspring could
still inherit the disease).

44
Q

Germ line therapy:

A

altering alleles in sex cells (so every cell of any offspring produced from these cells will
be affected by the gene therapy). This is currently illegal.

45
Q

DNA probes

A
  • What is a DNA probe? Short, single stranded sections of DNA (approximately 20 bases in length) that are
    fluorescently or radioactively labelled.
  • Why are DNA probes 20 nucleotides long and not shorter? It is unlikely that a sequence of 20 bases will
    occur else where in the DNA, whereas a shorter sequence may occur elsewhere and so a shorter primer may
    bind to multiple DNA sequences (would not be SPECIFIC).
  • Have a specific base sequence → only bind to complementary DNA.
46
Q

Genetic screening

A
  • Analysing an individual’s DNA for the presence of a particular gene (e.g. a mutated allele associated with a
    genetic disorder).
  • Take a sample of the patient’s DNA and make it single stranded (so the DNA probe can bind).
  • Add a specific DNA probe that is complementary to the allele associated with the disease that is being
    screened for.
  • If the allele is present - DNA probe will bind and will be seen as a fluorescent band.
47
Q
  • Benefits of genetic screening:
A
  • Identify inherited conditions
  • Determine how a patient will respond to a particular drug
  • Identify health risks e.g. certain alleles are associated with an increased risk of certain diseases - patient could
    modify lifestyle if they knew they carried one of these alleles.
48
Q
  • Negatives of genetic screening:
A
  • Discrimination by employers / insurance companies.
  • Knowledge of whether you will develop a life-threatening disease would cause stress.
  • Decision may have to be made whether to abort a pregnancy based on the results of genetic screening.
49
Q
  • Results of genetic screening can be used for:
A
  • Genetic counselling = advising patients and relatives about the risks of genetic disorders.
  • Personalised medicine = medicine that is tailored to an individual’s DNA.
  • Genes determine how an individual responds to a particular drug.
  • Doctors can prescribe the drugs that will be effective for you.
50
Q

VNTRs and Genetic fingerprinting

A
  • VNTRs = variable number tandem repeats
  • Non-coding base sequences that repeat next to each other over and over again → VNTRs occur in lots of places
    in the genome BUT the number of times VNTRs are repeated, differs between individuals.
  • The more closely related a person is to someone, the more similar their VNTRs will be.
  • Genetic fingerprinting compares the number of times a sequence is repeated at different places in the genome
    in different individuals - the probability of two individuals having identical VNTRs is incredibly low.
51
Q

Describe how genetic fingerprinting could be carried out on a sample of DNA? Step 1 - getting required section of DNA

A
  1. Sample of DNA is collected (e.g. from blood / body cells). If the sample of DNA is small, PCR could be used to
    make many copies/amplify the area of the DNA that contains VNTRs.
  2. DNA is cut into fragments using the SAME restriction endonuclease, which cuts close to, but not within,
    the repeated regions of DNA.
52
Q

Describe how genetic fingerprinting could be carried out on a sample of DNA? STEP 2 - Gel electrophoresis

A
  1. The fragments of DNA are separated according to size and charge, using GEL ELECTROPHORESIS.
    * Larger fragments move more slowly through the gel, the smallest fragments travel the furthest distance.
    * DNA is negatively charged, so it moves towards the positive electrode (anode) when an electric current is
    passed through the gel.
  2. Gel is immersed in alkali to separate the double strands into single strands.
  3. Radioactive (or fluorescent) DNA probes are added which bind to the VNTRs.
  4. DNA bands are transferred to a nylon membrane.
  5. An X-ray film is put over the nylon membrane and the film is exposed by the radiation from the radioactive
    probe (if using fluorescent probes, the positions are located visually using UV light).
  6. The positions of the probes correspond to the position of the DNA fragments, therefore the position of the
    bands is unique to every individual (except identical twins).
53
Q
  • What are the uses of genetic fingerprinting?
A
  • Forensic science e.g. linking a person to a crime scene.
  • To prevent inbreeding of plants or animals.
  • Genetic fingerprints can determine how closely individuals are related. The closer the match between their
    genetic fingerprints, the closer they are related. To avoid inbreeding → animals whose fingerprints differ
    the most should be mated.
  • To diagnose cancer or genetic disorders.
  • To investigate the genetic variability of a population.

biology a-level (7 decks)

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