Cellular Control Flashcards
Locus
Specific position on a chromosome, occupied by a specific gene
Allele
Alternate version of a gene
Phenotype
Observable characteristics of an organism
Genotype
Alleles present within cells of an individual, for a particular trait / characteristic
Dominant
Characteristic in which the allele responsible is expressed in the phenotype even in those with heterozygous genotypes
Codominant
A characteristic where both alleles contribute to the phenotype
Recessive
Characteristic in which the allele responsible is only expressed in the phenotype if there is no dominant allele present
Linkage
Genes for different characteristics that are present at different loci on the same chromosome are linked
Crossing Over
Where non-sister chromatids exchange alleles during prophase I of meiosis
Epistasis
The interaction of genes concerned with the expression of one characteristic. One gene may mask the expression of another gene
Gene
A length of DNA that codes for one (or more) polypeptides / proteins. Some genes code for RNA and regulate other genes.
Annealing
The term used to describe hydrogen-bond formation between complementary base pairs when sections of single-stranded DNA or RNA join together.
Annealing is seen when complementary sticky-ends join and where DNA probes attach to a complementary DNA section.
Apoptosis
Programmed cell death.
An orderly process by which cells die after they have undergone the maximum number of divisions
Chromosome mutation
Random change to the structure of a chromosome.
There are different types: - inversion, deletion, translocation, non-disjunction
The shuffling of alleles in prophase I is NOT an example of mutation
Inversion
A section of chromosome turns through 180 degrees
Deletion
A part of the chromosome is lost
Translocation
A piece of one chromosome becomes attached to another
Non-disjunction
Homologous chromosomes fail to separate properly at meiosis I or chromatids fail to separate at meiosis II.
If this happens to a whole set of chromosomes, polyploidy results
Cladistics
A method of classifying living organisms based on their evolutionary ancestry
Comparative genome mapping
The comparison of DNA sequences coding for the production of proteins / polypeptides and regulatory sequences in the genomes of different organisms of different species.
Comparisons include the search for sequences that make some species pathogenic whilst related organisms are not
Continuous variation
Genetic variation, also called quantitative variation, where there is a wide range of phenotypic variation within the population.
There are no distinct categories.
It is controlled by many genes.
Diploid
Having two sets of chromosomes (Eukaryotes and organisms)
Denoted by 2n
DNA Ligase
An enzyme capable of catalysing a condensation reaction between the phosphate group of one nucleotide and the sugar group of another.
This results in the DNA backbone molecules being joined together and is an essential part of recombinant DNA procedures
DNA Mutation
A change to DNA structure.
May be substitution of one base pair for another, inversion of a base triplet, deletion of a base pair or triplet of bases (on both strands), addition if a base pair or triplet of bases (on both strands),or a triple nucleotide repeat - a stutter
DRD4
Gene that codes for a dopamine receptor molecule
Exergonic
Chemical or biochemical reaction that releases energy
Gametes
Specialised sex cells
In many organisms the gametes are haploid and are produced by meio
Haploid
Eukaryotic cell or organism having only one set of chromosomes.
Denoted by n
Hardy-Weinberg Principle
The concept that both genotype frequencies and gene frequencies will stay constant from generation to generation, within a large interbreeding population where mating is random, there is no mutation and no selection or migration
Hayflick constant
The number of time that a normal body cell divides before undergoing apoptosis.
The number of divisions is about 50
Hemizygous
Cell or individual having only one allele for a particular gene
Heterozygous
Eukaryotic cell or organism that has two different alleles for a specific gene
Homeobox genes
Genes that control the development of the body plan of an organism
Homeotic selector genes
These direct development of individual body segments. They are master genes that control other regulatory genes
Homozygous
Eukaryotic cell or organism that has two identical alleles for a specific gene
Hox clusters
Groups of homeobox genes.
More complex organisms have more Hox clusters. This is probably due to a mutation that duplicated the Hox clusters
Hypostasis
Where two alleles interact to control the expression of one characteristic, one is epistatic and one is hypostatic.
Where a recessive allele at the first locus prevents the expression of another allele at a second locus, the alleles at the first locus are epistatic and the alleles at the second locus are hypostatic
Meiosis
Reductive division. The chromosome number is halved. It involves two divisions. It produces cells that are genetically different from each other and from the parent cell
Monogenic
Characteristic coded for by one gene
Monophyletic
A monophyletic group is one that includes an ancestral organism and all of its descendant species
Mutation
Structural change to genetic material - either to a gene or a chromosome
Necrosis
Disorderly, often accidental cell death
Operon
A unit consisting of genes that work together under the control of an operator gene
An example is the lac operon, which consists of two structural genes and an operator gene
Operon a were first found in prokaryotes but were later found in eukaryotes
Phylogenic group
Group of organisms that share evolutionary ancestry
Polygenic
Characteristic coded for by many genes.
Polygenic characteristics are more influenced by environmental factors than monogenic characteristics
Polyploid
Eukaryotic organisms or cells with more than two sets of chromosomes
Primer
Short, single stranded sequences of DNA, around 10 bases in length. They are needed, in sequences reaction and polymerase chain reactions, to bind to a section of DNA because the DNA polymerase enzymes cannot bind directly to single-stranded DNA fragments
Proto-oncogene
Gene that can undergo mutations to become an oncogene, which induces tumour formation (cancer)
Allele frequency
How common an allele is in a population
Gene pool
A measure the amount of variation of all the alleles in the population
Genome
Alleles within an individual
Genetic drift
Change in allele frequency
Can reduce genetic variation
Antigenic drift
Gradual change in antigen structure on a pathogen
Antigenic shift
Dramatic change in antigen structure
Can lead to new strains - Pandemic
Artificial selection
When humans choose the characteristic to breed for.
Only allow the individuals closest to the intended outcome to breed.
Repeat for a number of generations.
Reduces genetic variation. Leads to inbreeding, which reduces fitness (survivability + reproductive success) for most species
What characteristics can be bred for?
- Discontinuous
- Continuous (Only ones where enough of the variation is genetic - heritability is high) rather than environmental
Natural selection
Competing selection
- Selection pressures
Autosome
Non-sex linked chromosome
Prophase 1
Chromatin condenses and supercoils
Homologous pairs forms a bivalent
Crossing over occurs between non-sister chromatids
Nuclear envelope disintegrates
Nucleolus disappears
A spindle forms
Metaphase I
Bivalents line up across spindle equator
They are attached by the centromere to the spindle fibres
Bivalents are randomly assorted with each member of the homologous pair at opposite poles
Anaphase I
Homologous chromosomes in bivalents are pulled by the spindle fibres to opposite poles
Centromeres don’t divide
Chiasmata separate and lengths of chromatid that have crossed over remain with the chromatid
Telophase I
Two new nuclear envelopes form around each set of chromosomes at each pole
Cytokinesis occurs
Prophase II
Nuclear envelope reforms and breaks fown
Nuceolus disappears
Chromosomes condense
Spindles form
Metaphase II
Chromosomes move to the spindle equator
They attach to the spindle fibres by their centromeres
Chromatids of each chromosomes are randomly assorted
Anaphase II
Centromeres divide and the chromatids are pulled to opposite poles by the spindle fibres
The chromatids randomly segregate
Telophase II
Nuclear envelopes reform around the haploid nuclei
The two cells then divide into four haploid cells in animals
In plants a tetrad of four haploid cells is formed
Epistasis: Normal dihybrid cross ratio?
9:3:3:1
Recessive epistatic cross ratio?
9:3:4
Dominant epistatic cross ratio?
12:3:1
What is null hypothesis?
There is no significant difference between the observed and the expected result
What are the four possible bases in DNA?
Adenine, Thymine, Guanine, and Cytosine
What are the possible bases for RNA?
Adenine, Uracil, Cytosine, and Guanine
Which DNA bases pair together in complementary base pairing?
Adenine — Thymine
Cytosine — Guanine
What determines the order of amino acids in a protein?
The order of bases in a gene
What are three adjacent bases in mRNA called?
A codon
Where in the cell is mRNA made?
The nucleus
Describe the role of mRNA
mRNA carries the genetic code from the DNA in the nucleus to the cytoplasm, where it is used to make a protein during translation
Describe the role of tRNA
tRNA carries the amino acids that are used to make proteins to the ribosomes during translation
What are the two stages of protein synthesis called?
Transcription and translation
Where does the first stage of protein synthesis (transcription) take place?
The nucleus
Where does the second stage of protein synthesis (translation) take place?
At the ribosomes in the cytoplasm
When does RNA polymerase stop making mRNA?
When it reaches a stop codon
Explain why genetic code would not work if nucleotide bases were arranged in pairs, rather than triplets, to make the coding units
If the four nucleotide bases were arranged in pairs, the maximum number of different combinations would be 4^2, which is 16.
This is not enough to code for the 20 amino acids involved in protein synthesis, plus some stop codes
What is meant by degenerate code?
Each amino acid has more than one triplet base code.
This helps reduce the effect of point mutations
In which type of cell, prokaryote or eukaryote, would you expect protein synthesis to be faster?
Prokaryotes, as the mRNA does not have to exit a nucleus and the DNA in prokaryotes is naked - there are no histone proteins
What is the minimum number of different tRNA molecules that are needed for protein synthesis?
21 - one for each of the 20 amino acids and a stop
What is a mutation?
A change in the amount of, or arrangement of, the genetic material in a cell
Explain how the degenerate nature of DNA code reduces the effect of point mutations
All amino acids, except methionine, have more than one triplet of bases coding for them.some have as many as six.
So some point mutations will not change the amino acid that is added to the polypeptide at that position
Vitamin A is stored in the liver of all mammals. Suggest why pregnant women are advised not to eat liver.
It contains large amounts of vitamin A.
Retinoic acid is a derivative of vitamin A and too much retanoic acid, particularly in the early stages of pregnancy when the body plan is being organised, can interfere with the normal expression of homeobox genes and causes birth defects.
Explain what is meant by a morphagen
A morphagen is a substance that governs the pattern of tissue development by activating homeobox genes
What are transcription factors?
Transcription factors are some of the polypeptides expressed by homeobox genes, which bind to other genes further along the DNA from the homeobox genes, and switch them on.
They regulate the expression of other genes and so influence the development of the embryo
Explain the role of maternal-effect genes
They determine the embryo’s polarity - which end is the head and which is the tail
Explain the role of segmentation genes
They specify the polarity of each body segment
Explain the effect of making the inner mitochondrial membrane more permeable to hydrogen ion
If the proton gradient cannot be built up across the inner membrane then there will be less chemiosmosis and less formation of ATP.
The cell will not be able to carry out active transport or bulk transport and cannot maintain its metabolism - particularly anabolic reactions such as protein synthesis
Explain why apoptosis does not damage the nearby cells or tissues
Because the hydrolytic enzymes are enclosed in vesicles and these are ingested by phagocytes
Suggest how ineffective T lymphocytes would differ from effective lymphocytes
Ineffective lymphocytes would have no receptors on their cell surface membranes and could not recognise antigens
Suggest how harmful T lymphocytes would differ from effective lymphocytes
Harmful T lymphocytes would have receptor on their cell surface membranes, with shapes complementary to self antigens, causing autoimmunity - the immune system attacking your own tissues
What is a bivalent?
A homologous pair of chromosomes, each consisting of two sister chromatids, paired up for meiosis
What is the minimum number of genetically different gametes that can be theoretically be produced by a human?
2^23
Explain why sexual reproduction has increased the diversity of living organisms on Earth
Because gamete production by meiosis and fertilisation increases diversity.
During meiosis there is crossing over, Independant assortment of chromosomes and chromatids.
Fertilisation combines genetic material from two unrelated organisms
Which ratio suggests recessive epistasis?
9:3:4
What ratios suggests dominant epistasis?
12:3:1 or 13:3
What ratio suggests epistasis by complementary action?
9:7
What factors can alter the amount of genetic variation within a population?
Size of population
Randomness of mating
Mutation
Competition
Selection
Explain why the Hardy-Weinberg principle does not need to be used to calculate the frequency of codominant alleles
Because both alleles contribute to the phenotype, the genotype of all frequencies of all phenotypes are known
What biotic factors limit population growth?
Predators
Diseases/Pathogens
Food availability
Mate availability
What abiotic factors limit population growth?
Temperature
Water availability
Soil type
Habitat availability
Shelter
Explain why inbreeding amongst animals, such as dogs or race horses, may be harmful
The characteristics selected as useful for humans may make the animal less adapted to its natural environment
Explain why marriages between relatives may not be desirable
If there is a genetic defect in the family’s gene pool, the chances of two individuals, both carriers, mating and producing an affected individual are increased
Explain why, in small populations, where marriage with outsiders is discouraged, there may be high incidences of genetic disorders
If one person in the original small group of settlers carried a recessive allele, it could be passed on to his offspring and grandchildren.
Cousins may marry so two carriers may mate. The frequency of this allele will increase within the population.
This is know as the founder affect
Suggest why the phylogenetic species concept should be used to classify bacteria
Because bacteria do not reproduce sexually, the biological concept is not appropriate.
Their biochemistry, morphology, ecological niche, can all be studied and analysed
How is cladistics different from taxonomic classification systems?
It focuses on evolution, rather than on similarities between species
It places great importance on using objective and quantitative analysis
It uses DNA and RNA sequencing
It uses computer programmes and the data obtained from nucleic acid sequencing to generate cladograms that represent the evolutionary tree of life
It makes no distinction between extinct and extant species and both may be included in cladograms
Explain which classification system should be used to classify a newly discovered fossil organism
The phylogenetic (cladistic) system, as we can’t deduce anything about their sexual reproduction and ability to produce fertile offspring, but we can deduce information about morphology, genes, and ecological niche
Explain the meaning of the term genetic code
The sequence of the bases on a gene is a code with instructions for the construction of proteins. It has a number of characteristics:
It is a triplet code- three bases code of an amino acid
It is a degenerate code- All amino acids bar one have more
than one code
Some codes don’t code for amino acids but are ‘stop’
codons- they indicate the end of the polypeptide chain
It is widespread but not universal- Codons generally always
code for the same amino acid in every organism, but this is
not always the case.
Describe the way in which a nucleotide sequence codes for the amino acid sequence in a polypeptide
- Free RNA nucleotides are activated, two extra phosphoryl groups are added to make ATP, GTP, CTP and UTP.
- The gene to be transcribed unwinds and unzips. To do this the length of DNA that makes up the gene dips into the nucleolus & the hydrogen bonds between the nucleotide bases break.
- Activated RNA nucleotides binds, using Hydrogen Bonds, with their complementary exposed bases on the template strand. This is catalysed by RNA polymerase
- The two extra phosphoryl are released, releasing energy for bonding two adjacent nucleotides The mRNA produced is complementary to the nucleotide base sequence on the template strand of DNA and therefore is a copy of the base sequence on the coding strand of DNA
- The mRNA is released from the DNA and passes out of the nucleus through a pore in the nuclear envelope to a ribosome
Describe how the sequence of nucleotides within a gene is used to construct a polypeptide, including the roles of messenger RNA, transfer RNA and ribosomes
- A molecule of mRNA binds to a ribosome. Two codons are attached to the small subunit of the ribosome and exposed to the large subunit.
The first exposed mRNA codon is always AUG. Using ATP energy and an enzyme, a tRNA molecule with the amino acid methionine and the anticodon UAC forms hydrogen bonds with this codon
- A seconds tRNA molecule, bearing a different amino acid, binds to the second exposed condon with its complementary anticodon
- A peptide bonds forms between the two adjacent amino acids. This is catalysed by an enzyme in the small ribosomal sub unit
- The ribosome now moves along the mRNA reading the next codon. A third tRNA brings another amino acid and a peptide bonds forms between it and the dipeptide. The first tRNA leaves and is able to collect and bring another of its amino acids.
- The polypeptide chain grows until a stop codon is reached, for which there are no corresponding tRNAs and the polypeptide chain is complete
Mutations cause changes to
The sequence of nucleotides in DNA molecules
Explain how mutations can have beneficial, neutral or harmful effects on the way a protein functions
Beneficial
The mutation changes the sequence of amino acids and therefore the phenotype, but this gives the organism an advantageous characteristic
E.g. Paler skin in more temperate climates absorbs more vitamin D
Neutral
It is a mutation in a non-coding region of the DNA
It is a silent mutation- although the base triplet has changed, it still codes for the same amino acid and so the protein is unchanged.
Harmful
The mutation changes the sequence of amino acids and therefore the phenotype, and the resulting characteristic is harmful
E.g. paler skin in a hotter climate burns more easily
Cyclic AMP activates proteins by…
Altering their three-dimensional structure
When lactose is absent in lac operon…
- The regulator gene is expressed and the repressor protein is synthesised. It has two binding sites. One binds to lactose and one that binds to the operator region
- In binding to the operator region, it covers part of the promoter region where RNA polymerase normally attaches
- RNA polymerase cannot bind to the promoter region so the structural genes cannot be transcribed into mRNA
- Without mRNA the genes cannot be translated and the enzymes cannot be synthesised
When lactose is present in lac operon…
- Lactose binds to the other site on the repressor protein, causing the molecule to change shape. This prevents the other binding site from binding to the operator region. The repressor dissociates from the operator region
- The leaves the promoter region unblocked. RNA polymerase can now bind to it and initiate the transcription of mRNA.
- The operator- repressor- inducer system acts as a molecular switch. It allows synthesis of the structural genes
- As a result, the bacteria can now use the lactose permease enzyme to take up lactose from the medium into their cells. They can then convert it to glucose and galactose using the β-galactosidase enzyme. These sugars can then be used for respiration
Explain genetic control of protein production in a prokaryote using the lac operon
E. coli grown in a culture medium with no lactose can be placed in a growth medium with lactose.
At first they cannot metabolise the lactose because they only have tiny amounts of the enzymes needed to catalyse the reaction.
A few minutes after the lactose is added, E. coli increases the rate of synthesis of these enzymes by about 1000 times, so lactose must trigger the production of them - it is the inducer.
Explain that the genes that control development of body plans are similar in plants, animals and fungi, with reference to homeobox sequences
Homeotic genes are similar in plants, animals and fungi.
These genes control the development of body plans and are expressed in specific patterns and in particular stages of development depending on when they are activated.
The homeobox is a sequence of DNA that codes for a region of 60 amino acids, and the resulting protein is found in most, if not all, eukaryotes.
The region binds to DNA so that they can regulate transcription.
In animals the homeobox is common in genes concerned with the control of developmental events, such as segmentation, the establishment of the anterior-posterior axis and the activation of genes coding for body parts such as limbs
Outline how apoptosis (programmed cell death) can act as a mechanism to change body plans.
Apoptosis is an integral part of plant and animal tissue development.
It is a series of biochemical events that leads to an orderly and tidy cell death, in contrast to cell necrosis, which leads to the release of harmful hydrolytic enzymes.
Apoptosis ensures that the rate of cells produced by mitosis is the same as the rate of cells dying, so the number of cells remains constant. Not enough apoptosis leads to cancer.
Apoptosis causes the digits (toes and fingers) to separate from each other during development.
- Enzymes break down the cell cytoskeleton
- The cytoplasm becomes dense with organelles tightly packed
- The cell surface membrane changes and blebs form
- The Chromatin condenses and the nuclear envelope breaks. DNA breaks into fragments
- The cell breaks down into vesicles that are taken up by phagocytosis. The cellular debris is disposed of so that it does not damage other cells or tissue.
Describe the behaviour of chromosomes during prophase I
- The chromatin condenses and supercoils
- The chromosomes come together in their homologous pairs to form a bivalent.
Each member of the pair has the same genes at the same loci.
Each pair consists of one maternal and one paternal chromosome
- The non sister chromatids wrap around each other and attach at points called chiasmata
- They may cross over and swap sections of chromatids with each other
- The nucleolus disappears and the nuclear envelope breaks down
- A spindle forms
Describe the behaviour of chromosomes during metaphase I
- Bivalents line up across the equator of the spindle, attached to spindle fibres at the centromeres
- The bivalents are arranged randomly (random assortment) with each member of the homologous pair facing opposite poles
Describe the behaviour of chromosomes during anaphase I
- The homologous chromosomes in each bivalent are pulled by the spindle fibres to opposite poles
- The centromeres do not divide
- The chiasmata separate and the lengths of chromatid that have been crossed over remain with the chromatid to which they have become newly attached
Describe the behaviour of chromosomes during telophase I
Telophase I
1. In most animal cells two new nuclear envelopes form- one around each set of chromosomes at each pole and the cell divides by cytokenesis.
There is a brief interphase and the chromosomes uncoil
- In most plant cells the cell goes straight from Anaphase I to Meiosis II
Describe the behaviour of chromosomes during meiosis II
This occurs at right angles to Meiosis I
Prophase II
1. If a nuclear envelope has reformed, it breaks down again
2. The nucleolus disappears, chromosomes condense and
spindles form
Metaphase II
1.The chromosomes arrange themselves on the equator of
the spindle. They are attached to spindle fibres at the
centromeres
2. The chromatids of each chromosome are randomly
assorted
Anaphase II
1. The centromeres divide and the chromatids are pulled to
opposite poles by the spindle fibres. The chromatids
randomly segregate
Telophase II
1. Nuclear envelopes reform around the haploid daughter
nuclei
2. In animals, the two cells now divide to give four daughter
cells
3. In plants, a tetrad of four haploid cells if formed
Explain how meiosis and fertilisation can lead to variation through independent assortment
Meiosis:
Crossing over ‘shuffles’ alleles
Random distribution and subsequent segregation of
maternal and paternal chromosomes in the homologous
pairs during meiosis I leads to genetic reassortment
Random distribution and segregation of the chromatids at
meiosis II leads to genetic reassortment
Random mutations
Fertilisation
Randomly combining two sets of chromosomes, one from
each of two genetically unrelated individuals
Describe the interactions between loci (epistasis)
Epistasis is the interaction of different gene loci so that one gene locus makes or suppresses the expression of another gene locus.
Recessive Epistasis
The homozygous presence of a recessive allele prevents
the expression of another allele at a second locus
E.g. flower colour in Salvia:
The alleles for purple (B) and pink (b) can only be expressed in the presence of the allele A. When the genotype is aa– the phenotype is white
Dominant Epistasis
A dominant allele at one gene locus masks the expression
of alleles at the second gene locus
E.g. feather colour in poultry:
If the dominant allele A is present, the chickens will be white; even if the dominant allele of the second gene, B/b is present. The genotype must be aaB- for any colour to be expressed
Describe the differences between continuous and discontinuous variation
Discontinuous variation describes qualitative differences between phenotypes - they fall into clearly distinguishable categories with no intermediates.
E.g. blood type is either A, B, AB or O
Continuous variation is quantitative differences between phenotypes - there is a wide range of variation within the population with no distinct catagories
E.g. height
Explain the basis of continuous and discontinuous variation by reference to the number of genes which influence the variation
Discontinuous variation
Different alleles at a single gene locus have large effects on
the phenotype.
Different gene loci have different effects on the trait
Continuous variation
Different alleles at the same gene locus have small effects
Different gene loci have the same, often additive effect on
the trait
A large number of gene loci may have a combined effect on
the trait
Explain that both genotype and environment contribute to phenotypic variation.
While an organism may have the genetic potential to achieve a certain characteristic, e.g. length of corn cob, the environment also has an influence. The corn cob may have the genetic potential to be 12cm long, but the plant may be short of water, light or certain minerals, meaning that the cob is shorter, as the environmental factors have limited the expression of the genes.
Explain why variation is essential in selection
So that when the environment changes, there will be individuals that are better adapted, so they will survive and reproduce passing on the advantageous alleles to their offspring and allowing the species to continue
Explain,with examples, how environmental factors can act as stabilising or evolutionary forces of natural selection
In unchanging conditions, stabilising selection maintains existing adaptations and so maintains existing allele frequencies.
In changing conditions, directional selection alters allele frequencies.
A mutation may be disadvantageous in existing conditions, and so is removed in stabilising selection, but if the conditions change, the mutation might be advantageous and selected for, meaning that selection becomes an evolutionary force
Explain how genetic drift can cause large changes in small populations
Genetic drift is a change in allele frequency that occurs by chance because only some of the organisms in each generation reproduce.
It is particularly noticeable when a small number of individuals are separated from the rest of the large population.
They form a small sample of the original population and so are unlikely to be representative of the large population’s gene pool.
Genetic drift will alter the allele frequency still further.
Explain the role of isolating mechanism in the evolution of new species, with reference to ecological (geographic), seasonal (temporal) and reproductive mechanisms
If two sub-populations are separated from each other, they will evolve differently as they have different selection pressures, so different alleles will be eliminated or increased within each sub population.
Eventually the sub populations will not be able to interbreed and so will be different species.
The sub populations may be split by various isolating mechanisms
Geographical barriers e.g. rivers or mountains
Seasonal barriers e.g. climate change throughout the year
Reproductive mechanisms e.g. their genitals, breeding seasons or courtship rituals may be different
Explain the significance of the various concepts of the species, with reference to the biological species concept and the phylogenetic (cladistic/evolutionary) species concept
The biological species concept
A species is ‘a group of similar organisms that can interbreed and produce fertile offspring and it reproductively isolated from such other groups’
But
Not all organisms reproduce sexually
Members of the same species can look very different to each other Males can look different to females
Isolated populations may appear to be very different from each other
The phylogenetic species concept
A species is ‘a group of organisms that have similar morphology, physiology, embryology and behaviour, and occupy the same ecological niche’.
This classification shows the evolutionary relationships, or phylogeny. The phylogenetic linage is called a clade
Compare and contrast natural selection and artificial selection
Natural selection
The organisms best adapted for their environment are more likely to survive and pass on the favourable characteristics to their offspring
Artificial selection
Humans select the organisms with the useful characteristics
Humans allow those with useful characteristics to breed and prevent the ones without the characteristics from breeding
Thus, humans have a significant impact on the evolution of these populations or species
Describe how artificial selection has been used to produce the modern dairy cow
Each cow’s milk yield is measured and recorded
The progeny of bulls is tested to find out which bulls have produced daughters with high milk yields
Only a few good-quality bulls need to be kept are the semen from one bull can be used to artificially inseminate many cows
Some elite cows are given hormones so they produce many eggs
The eggs are fertilized in vitro and the embryos are implanted into surrogate mothers
These embryos could also be clones and divided into many more identical embryos
Describe how artificial selection has been used to produce bread wheat
Wheat can undergo polyplody- the nuclei can contain more than one diploid set of chromosomes.
Modern bread wheat is hexaploid, having 42 chromosomes in the nucleus of each cell, meaning that the cells are bigger.
Outline the differences between reproductive and non-reproductive cloning
Reproductive cloning is the production of offspring which are genetically identical to either the mother (nuclear transfer), or the other offspring (splitting embryos)
Non-reproductive cloning is the use of stem cells in order to generate replacement cells, tissues or organs which may be used to treat particular diseases or conditions of humans
Describe the production of natural clones in plants using the example of vegetative propagation in elm trees
The English Elm is adapted to reproduce asexually following damage to the parent plant.
New growth in the form of basal sprouts appears within two months of the destruction of the main trunk
These suckers grow from meristem tissue in the trunk close to the ground where the least damage is likely to have occured
Describe the production of artificial clones of plants from tissue culture
A small piece of tissue is taken from the plant to be cloned, usually from the shoot tip- this is called the explant
The explant is placed on a nutrient growth medium
Cells in the tissue divide but do not differentiate. Instead they form a mass of undifferentiated cells called a callus
After a few weeks, single callus cells can be removed from the mass and placed on a growing medium containing plant hormones that encourage shoot growth
After a further few weeks, the growing shoots are transferred onto a different growing medium that encourages root growth
The growing plants are then transferred to a greenhouse to be acclimatised and grown further before they are planted outside
Discuss the advantages and disadvantages of plant cloning in agriculture
Advantages
Very many genetically identical plants can be produced from one original plant
Plants can be produced at any time of the year and air-freighted around the world
Callus can be genetically engineered
Disadvantages
Because all of the plants are genetically identical, they are all susceptible to a newly mutated pathogen or pest, or to changing environmental conditions
The process is labour intensive- it is more difficult to plant plantlets than to sow seed
Describe how artificial clones of animals can be produced
Nuclear transfer
A nucleus from an adult differentiated cell is placed in an enucleated egg cell.
The egg then goes through the stages of development using the genetic information from the inserted nucleus
Splitting embryos
Cells from a developing embryo are separated out, with each one going on to produce a separate, genetically identical organism
Discuss the advantages and disadvantages of cloning animals
Advantages
High value animals, e.g. cows giving a high milk yield, can be cloned in high numbers
Rare animals can be cloned to preserve the species
Genetically modified animals- e.g. sheep that produce pharmaceutical chemicals in their milk- can be quickly reproduced
Disadvantages
High value animals are not necessarily produced with animal welfare in mind. Some strains of meat producing chickens jave been developed that are unable to walk
As with plants, excessive genetic uniformity in a species makes it unlikely to be able to cope with, or adapt to, changes in the environment
It is still unclear whether animals cloned using the nuclear material of adult cells will remain healthy in the long term
Explain why microorganisms are often used in biotechnological processes
Grow rapidly in favourable conditions, with a generation time of as little as 30 minutes
Often produce proteins or chemicals that are given out into the surrounding medium and can be harvested
Can be genetically engineered to produce specific products
Grow well are relatively low temperatures, much lower than those required in the chemical engineering of similar processes
Can be grown anywhere in the world and are not dependent on climate
Tend to generate products that are in a more pure form than those generated via chemical processes
Can often be grown using nutrient materials that would otherwise be useless or even toxic to humans
Describe how enzymes can be immobilised
Adsorption
Enzyme molecules are mixed with the immobilising support
and bind to it due to a combination of hydrophobic
interactions and ionic links.
Covalent bonding
Enzyme molecules are covalently bonded to a support,
often by covalently linking enzymes together and to an
insoluble material using a cross-linking agent
Entrapment
Enzymes are trapped, for example in a gel bead or network
of cellulose fibres.
Substrate and product molecules can pass through the
material to the enzyme, but the enzyme cannot pass
through to the solution
Membrane separation
Enzymes are physically separated from the substrate
mixture by a partially permeable membrane. The substrate
and product molecules can pass through the membrane,
but the enzymes cannot
Explain why immobilised enzymes are used in large-scale production
Enzymes can be recovered easily and used many times
The product is not contaminated by the enzyme
Protection by the immobilising material means the enzyme is more stable in changing temperatures or pH
Enzyme activity can be controlled more easily
Compare and contrast the processes of continuous culture and batch culture
Batch Culture
Growth rate is slower because nutrient level declines with
time
Easy to set up and maintain
If contamination occurs, only one batch is lost
Less efficient- fermenter is not in operation all of the time
Very useful for processes involving the production of
secondary metabolites
Continuous Culture
Growth rate is higher as nutrients are continuously added
to the fermentation tank
Set up is more difficult, maintenance of required growing
conditions can be difficult to achieve
If contamination occurs, huge volumes of product may be
lost
More efficient- fermenter operates continuously
Very useful for processes involving the production of
primary metabolites
Describe the differences between primary and secondary metabolites
Primary metabolites are substances produced by an organism as part of its normal growth.
The production of primary metabolites matches the growth in population of the organism
Secondary metabolites are substances produced by an organism that are not part of its normal growth.
The production of secondary metabolites usually begins after the main growth period of the organism and so does not match the growth in population of the organism
Explain the importance of manipulating the growing conditions in a fermentation vessel in order to maximise the yield of product required
The growing conditions can be manipulated and controlled in order to ensure that the microorganism is growing in its optimum conditions, and so the yield can be maximised
Temperature
Too hot and enzymes will be denatured, too cold and growth
will be slowed
Type and addition of nutrient
This depends on whether the product is a primary or a
secondary metabolite
Oxygen concentration
Most organisms are grown under aerobic conditions so
there must be a sufficient supply of oxygen to prevent the
unwanted products of anaerobic respiration and a reduction
in growth rate
pH
Changes in pH can reduce the activity of enzymes and
therefore reduce growth rates
Explain the importance of asepsis in the manipulation of microorganisms.
Asepsis is the absence of unwanted microorganisms which could:
Compete with the culture microorganisms for nutrients and
space
Reduce the yield of useful products from the culture.
microorganisms
Cause spoilage of the product
Produce toxic chemicals
Destroy the culture microorganisms and their products
Outline the steps involved in sequencing the genome of an organism
Genomes are mapped to identify which part of the genome that they come from. Information that is already known is used, such as the location of microsatellites
Samples of the genome are mechanically sheared into smaller sections of around 100,000 base pairs
These sections are places in separate Bacterial Artificial Chromosomes (BACs) and transferred to E. coli cells. As the cells are grown in culture, many copies of the sections are produced- referred to as Clone Libraries
Cells containing specific BACs are taking and cultured. The DNA is extracted from the cells and restriction enzymes used to cut it into smaller fragments. The use of different restriction enzymes on a number of samples gives different fragment types
The fragments are separated using electrophoresis
The many copies of the fragments are put in a reaction mixture containing DNA polymerase, free DNA nucleotides and primers, with some of the nucleotides containing a florescent marker.
The primer anneals to the 3’ end of the template strand, allowing DNA polymerase to attach
DNA polymerase adds free nucleotides
If a modified nucleotide is added, the polymerase enzyme is thrown off and the reaction stops on that template strand
As the reaction proceeds, many molecules of DNA are made. The fragments generally differ in size, as different numbers of nucleotides will have been added
As the strands run through a machine, a laser reads the colour sequence. The sequence of colours, and therefore the sequence of bases can then be displayed
Outline how gene sequencing allows for genome-wide comparisons between individuals and between species
The identification of genes for proteins found in all or many living organisms gives clues to the relative importance of such genes to life
Comparing the DNA of different species shows evolutionary relationships
Modelling the effects of changing DNA can be carried out
Comparing genomes from pathogenic and similar but non-pathogenic organisms can be used to identify the genes or base-pair sequences that are more important in causing the disease, so more effective drugs can be developed
The DNA of individuals can be analysed to reveal the presence of alleles associated with particular diseases
Define the term recombinant DNA
A section of DNA, often in the form of a plasmid, which is formed by joining DNA sections from two different sources
Explain that genetic engineering involves the extraction of genes from one organism, or the manufacture of genes, in order to place them in another organism (often of a different species) such that the receiving organism expresses the gene product
The required gene is obtained
A copy of the gene is placed in a vector
The vector carries the gene to the recipient cell
The recipient expressed the gene through protein synthesis
Describe how sections of DNA containing a desired gene can be extracted from a donor organism using restriction enzymes
A DNA probe can be used to locate the gene on DNA fragments and the gene can be cut from a DNA fragment using a restriction enzyme
Restriction enzymes cut through DNA at specific points, only where a specific base sequence occurs, normally about 10 base pairs long.
The enzyme catalyses a hydrolysis reaction which breaks the sugar phosphate backbone of the DNA at different places. The gives a staggered cut which leaving some exposed bases called sticky ends
Outline how DNA fragments can be separated by size using electrophoresis
DNA samples are treated with restriction enzymes to cut them into fragments
The DNA samples are placed into cells cut into the negative electrode end of the gel
The gel is immersed in a tank of buffer solution and an electric current is passed through the solution for a fixed period of time, usually around two hours
DNA is negatively charged because of its phosphoryl groups. It is attracted to the positive electrode.
Shorter lengths of DNA move faster than longer lengths, so move further in the fixed time that current is passed through the gel
The position of the fragments can be shown by using a dye that stains DNA molecules
Describe how DNA probes can be used to identify fragments containing specific sequences
A DNA probe is a short single-stranded section of DNA that is complementary to the section of DNA being investigated.
The probe is labelled in one of two ways:
Using a radioactive marker so that the location can be
revealed by exposure to photographic film
Using a fluorescent marker that emits a colour on exposure
to UV light
Copies of the probe are added to a sample of DNA fragments and will anneal to any fragment where a complementary base strand is present
Outline how the polymerase chain reaction (PCR) can be used to make multiple copies of DNA fragments
The DNA sample is mixed with a supply of DNA nucleotides and DNA polymerase
The mixture is heated to 95°C. This breaks the hydrogen bonds holding the strands together, so the samples are now single stranded
Primers (short lengths of single stranded DNA) are added
The temperature is reduced to 55°C to allow the primers to bind and form small sections of doubl stranded sections
DNA polymerase can bind to these double-stranded sections
The temperature is raised to 72°C. The enzyme extends the double stranded section by adding nucleotides to the unwound DNA
When the DNA polymerase reaches the other end of the DNA, a new, double stranded DNA molecule is generated
The whole process can be repeated many times so the amount of DNA increase exponentially
Explain how isolated DNA fragments can be placed in plasmids, with reference to the role of ligase
The plasmids and the fragments are both cut with the same restriction enzyme so they have complementary sticky ends
The base pairs anneal and DNA ligase joins together the phosphate sugar backbones to form recombinant DNA
State other vectors into which fragments of DNA may be incorporated
Liposomes
Viral DNA e.g. bacteriophages
Hybrid vectors with the propertied of both plasmids and bacteriophages
Explain how plasmids may be taken up by bacterial cells in order to produce a transgenic microorganism that can express a desired gene product
Large quantities of the plasmid are mixed with bacterial cells
Calcium salts are added, and the temperature of the culture is lowered to freezing before the being quickly raised to 40°C.
This increases the rate at which plasmids are taken up by bacterial cells to around 0.25%
Describe the advantage to microorganisms of the capacity to take up plasmid DNA from the environment
Genetic variation
In the case of antibiotic resistance genes, survival in the presence of these chemicals
Outline how genetic markers in plasmids can be used to identify the bacteria that have taken up a recombinant plasmid
Not all bacteria take up the plasmid.
Some of the bacteria take up a plasmid that has not seals
with a copy of the gene, but just sealed up on itself to reform
the original plasmid
A plasmid is used which carries genes which make any bacteria receiving them resistance to two different antibiotics. The resistance genes are known as genetic markers
The plasmids are cut by an enzyme which has its resistance site in the middle of one of the resistance genes (G1), so that if the required gene is taken up, the resistance gene for one of the antibiotics does not work, but it other (G2) does
The DNA is placed in the plasmids, and the plasmids in bacteria cells
The bacteria are grown on an agar plate to produce a colony
Some cells from the colonies are transferred onto agar that has been made from the antibiotic that remains intact, meaning that all bacteria that have taken up a plasmid will grow.
Some cells are transferred onto agar that has been made from the second antibiotic. Only the bacteria which have taken up a plasmid that is not recombinant will grow.
By keeping track of which colonies are which, we now know that any bacteria which grow on the agar containing the first antibiotic, but not on the agar containing the second antibiotic must have taken up the recombinant plasmid
The required colonies can now be identified and be grown on a large scale
Outline the process involved in the genetic engineering of bacteria to produce human insulin
- mRNA from human insulin is extracted from pancreas cells
- Reverse transcriptase uses mRNA as a template to make single stranded cDNA, and this is made double stranded by DNA polymerase
- A single sequence of nucleotides (GGG) is added to each end of the DNA to make sticky ends
- Plasmids are cut open when a restriction enzyme
- Cut plasmids have a single sequence of nucleotides (CCC) asses to each to make sticky ends
- Plasmids and the insulin gene are mixed so that sticky ends form base pairs
- DNA ligase links sugar-phosphate backbones of plasmid and insulin gene
- Plasmids are mixed with bacteria in the presence of calcium ion
- Bacteria take up plasmids and multiply to form a clone
- Genetically engineered bacteria transcribe and translate the human gene to make insulin
Outline the process involved in the genetic engineering of ‘Golden Rice
Two genes from the Daffodil and one from the bacterium Erwina urefovora were inserted into TI plasmids and taken up by the bacterium Agrobacterium tumefaciens.
This introduced the genes into rice embryos
The resulting rice plants produced seeds with β-carotene in the endosperm, which is yellow.
Vitamin A is produced in our bodies from β-carotene
Outline how animals can be genetically engineered for xenotransplantation
Pigs have been engineered to lack the enzyme α-1,3-transferase, which is a key trigger for rejection of organs in humans
The human nucleotidase enzyme has been grafted into pig cells in culture.
It reduces the number of immune cell activities involved in xenotransplant rejection
Explain the term gene therapy
Any therapeutic technique where the functioning allele of a particular gene is placed in the cells of an individual lacking the functioning alleles of that particular gene.
Can be used to treat some recessive conditions, but not dominant conditions
Explain the differences between somatic cell gene therapy and germ line cell gene therapy
Somatic cell gene therapy
The functioning allele of the gene is introduced into target cells - ∴ techniques are needed to get the gene to the target location, or the specific cells must be removed, treated and then replaced
Introduction into somatic cells means that any treatment is short-lived and has to be repeated regularly. The specialised cells containing the gene will not divide to pass on the allele
There are difficulties in getting the allele into the genome in a functioning state. Genetically modified viruses have been tried, but the host becomes immune to them so cells will not accept the vector on second and subsequent treatments. Liposomes are used but these may be inefficient
Genetic manipulations are restricted to the actual patient
Germline cell gene therapy
The functioning allele of the gene is introduced into germline cells- delivery techniques are more straightforward
Introduction into germline cells means that all cells derived from the germline cells will contain a copy of the functioning allele. The offspring may also contain the allele
Although more straightforward, it is considered unethical to engineer human embryos. It is not possible to know whether the allele has been successfully introduced without any unintentional changes to it which may damage the embryo
Genetic manipulations could be passed on to the patient’s children
Discuss the ethical concerns raised by the genetic manipulation of animals (including humans), plants and microorganisms
Religious objections
Objections to tampering with an organism’s natural genotype
Fears of unforeseen effects of the gene
Fears of the consequences of escape into the wild
Growing GM plants might damage the environment
Eating GM plants might be bad for health
