Module 6 Flashcards
(205 cards)
1
Q
Substitution
A
= a nucleotide base is replaced with another
2
Q
Insertion =
A
an extra nucleotide base is inserted into the sequence causing ‘frameshift’ where all the subsequent bases are shifted down 1 place relative to the twin DNA strand
3
Q
Deletion
A
= the absence of a nucleotide, causing ‘frameshift’ where all the subsequent bases are shifted back 1 place relative to the twin DNA strand
4
Q
gene mutations can be
A
Neutral Harmful Beneficial
5
Q
gene mutations Neutral
A
○ May occur in phenotypically insignificant strand of DNA ○ May not result in change of polypeptide primary sequence (because DNA is degenerate) ○ May result in a change of polypeptide primary sequence that does not affect secondary/ tertiary/quaternary structure of protein therefore protein function unaffected ○ May results in a change of polypeptide secondary/tertiary/quaternary structure but where active site of protein remains the same therefore function still unaffected
6
Q
gene mutations Harmful
A
○ May result in change in final protein shape where protein and active site is deformed and therefore cannot fulfil function
7
Q
gene mutations Beneficial
A
○ May result in change in final protein shape where the protein performs its function better than it would have without the mutation ○ This is the basis of natural selection and evolution ○ The individual is better suited to survival and will pass on the mutation to its offspring ○ E.g. eye colour – Blue eyes was a mutation that occurred about 7000 years ago – In sunny areas, this would be harmful as the retina is more exposed – However in cloudy regions this was beneficial as it enabled people to see better – So the mutation was carried down generations and became widespread
8
Q
Point mutation
A
Mutations can affect 1 nucleotide base, or more than one adjacent bases • A point mutation is where only one base is affected • There are 3 types: silent, nonsense, missense
9
Q
Silent mutation
A
○ No change in amino acid sequence of polypeptide
10
Q
Missense mutation
A
○ The mutation changes the code for 1 amino acid ○ 1 amino acid in the sequence is changes
11
Q
nonsense mutation
A
○ The mutation changes the code turning the triplet into a stop codon ○ Instructs the end of polypeptide synthesis ○ The polypeptide is shorter than it would normally be
12
Q
Lac system genes
A
• Lac operon is a section of DNA within the bacterium DNA ○ Structural genes code for the enzymes ○ Operator region can switch the structural genes on and off ○ Promoter region is a length of DNA which the RNA polymerase can bind to begin the transcription of the genes • Regulator gene is not part of the operon and is some distance from it
13
Q
Lac operon in the absence of lactose
A
• Regulator gene is expressed and the repressor protein is synthesized ○ One site binds to lactose ○ One site binds to the operator region • Repressor protein binds to operator region ○ Covers part of the RNA polymerase binding site • RNA polymerase cannot bind to the promoter region ○ Structural genes are not transcribed to mRNA ○ Genes cannot pre translated ○ Enzymes not produced
14
Q
Lac operon in the presence of lactose:
A
• Lactose inducer binds to the other side of the repressor, changing its shape • Repressor can now bind to the operator region • Repressor is now able to break away from the operator region • Promoter region is unblocked • RNA polymerase is now able to bind to this region • This system acts as a molecular switch • The enzymes can now be translated
15
Q
Homeobox Genes
A
• Genes that turn on/off development of specific body parts • DNA sequence that is found within many genes • They are grouped together as homeotic genes in a ‘hox cluster’ • These genes are involved in the regulation of anatomical development ○ Very important therefore precisely conserved • More complex organisms have more hox clusters• Homeobox genes expressed in specific patterns in certain stages of development • Activated and expressed from anterior to posterior • Very similar across species and highly conserved ○ Indication that they first arose in early common ancestor • Regulate development of embryos along anterior-posterior axis ○ Determine where limbs branch off
16
Q
Apoptosis •
A
Programmed cell death • Occurs in multicellular organisms
17
Q
Sequence of events Apoptosis •
A
Enzymes break down cell cytoskeleton • Cytoplasm becomes dense with organelles tightly packed • Cell surface membrane changes and blebs form • DNA breaks into fragments • Cell breaks into vesicles • These are taken up by phagocytosis • Very quick process
18
Q
control Apoptosis
A
Controlled by a diverse range of cell signals • Nitric oxide can induce apoptosis
19
Q
Development
A
• Apoptosis causes limbs and appendages to separate ○ E.g. separation of human fingers — rather than being webbed • Weeds out ineffective T-lymphocytes during the development of the immune system
20
Q
Transcription factors
A
• Can be proteins or noncoding pieces of RNA • Coded for by about 8% of genome • Attach/detach from DNA to control which genes are expressed
21
Q
Introns mn Exons
A
• Post-transcriptional gene regulation • Regions of DNA that don’t code for genes are called introns — they separate… • Regions of DNA that are expressed, called exons • Both are transcribed, but resulting mRNA is modified to remove the introns
22
Q
• Homeobox genes
A
are found across all multicellular organisms
23
Q
• Hox genes
A
are a sub-type of Homeobox gene which are only found in animals
24
Q
Genotype =
A
genetic makeup of an individual
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Phenotype
= visual characteristics of an individual (not just external physical attributes — for example, being affected by Diabetes Mellitus is a phenotype) An individual’s phenotype is a result of its genotype and its phenotype. This is the basis of the nature vs nurture debate. It explains why genetically identical twins may have diverging phenotypes, especially as they get older and are exposed to more environmental stimuli.
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mutagenic agents
– X-rays – Benzopyrene found in tobacco smoke – Viruses – Gamma rays
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chromosomal mutations
– Deletion: part of a chromosome is lost – Inversion: section of chromosome breaks off, then is re-inserted in the opposite direction – Translocation: section of chromosome breaks off then is re-inserted on a different chromosome – Duplication: part of a chromosome occurs twice – Non-disjunction: one pair of chromosomes fails to separate, so the gamete and zygote has an extra chromosome (e.g. Down’s syndrome)
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○ Aneuploidy
chromosome number is not a multiple of the haploid number for that organism
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Polyploidy
diploid gamete fertilised by a haploid gamete ○ Resulting zygote is triploid (3n chromosomes)
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how normal sexual reproduction causes genetic variation
– Meiosis produces genetically different gametes – Alleles shuffle around – Independent assortment of chromosomes – Contribute to genetic diversity – Random fusion of gametes at fertilisation
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gemertic variable can be caused by
Genetic variation caused by mutations ○ Caused by mutagenic agents ○ Caused by chromosomal mutations ○ Aneuploidy ○ Polyploidy
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Phenotypic factors
Variation caused by the environment alone ○ E.g. losing a limb in an accident
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Variation caused by the environment alone ○
E.g. losing a limb in an accident
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• Variation caused by the environment interacting with genes
○ Environmental conditions can affect the expression of some genes ○ This is called epigenetics ○ Genes are put in certain ‘modes’ where they might behave in a certain way ○ E.g. plants reacting to light ○ It is thought that epigenetics can be passed vertically (from parent to offspring)
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epigenetics
○ Environmental conditions can affect the expression of some genes
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Monohybrid
investigations that examine the inheritance of a single characteristic:
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Dihybrid
investigations that examine the inheritance of two characteristics:
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why are Linked genes more likely to be passed on together
since their loci are close together on the chromosome.
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Linkage
when two or more genes are located on the same chromosome
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Autosomal linkage
linked genes which are on non-sex chromosomes
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Sex linkage
linked genes are on sex chromosomes — therefore specific characteristic is more likely to be inherited in either male or female offspring • Genes are more likely to be X-linked ○ Found on X chromosome • This means female offspring will only show recessive genes if homozygous • Male offspring will show recessive X-linked genes even if only present on X chromosome • E.g. colour blindness more common in males
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Epistasis
interaction of non-linked genes where one masks the expression of the other
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Recessive epistasis •
Homozygous recessive alleles mask expression of another allele at different locus
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Codominance =
when both alleles present in the genotype contribute to the phenotype wg bloodtype and cow coat colour
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Chi-squared test =
statistical test to find out whether the difference between observed vs expected data is due to chance. • Genetic diagrams give us an indication of probable offspring genotypes • Due to the random nature of gamete fusion, these are rarely 100% accurate predictions
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When to use the chi-squared test:
The data are in categories (i.e. discrete variation) • The sample size is large enough to be representative • The data indicate absolute numbers: not percentages • No data values are equal to null
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How to apply the chi-squared test
. Define null hypothesis a. States that there is no significant difference between observed/expected data b. I.e. states that the difference is due to chance Apply the test:. Determine the number of degrees of freedom (number of categories — 1) . Determine the number of degrees of freedom (number of categories — 1) . Decide whether the result is significant
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Discontinuous variation
• Phenotypes are in distinct categories • E.g. blood types or sex ○ Cannot be ‘between’ blood type A and B • Determined by a single allele • Monogenic • Qualitative
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Continuous variation •
Phenotypes fall in a range • Smooth gradient between phenotypes, which are often distributed in a bell curve • Eg tail length in mice; birth weight; height; skin colour; heart rate • Controlled by more than one gene • Polygenic • Quantitative
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polygenic
, it is determined by the interactions of several genes and the alleles at those loci — in that one individual.
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Directional selection
• Environment favours individuals at one extreme of the bell curve • E.g. faster cheetahs are able to survive better • The mean changes ○ Mean sprint speed of cheetahs becomes faster and faster over time
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Stabilising selection
• Environment favours individuals close to a specific value which doesn’t change • Individuals with extreme phenotypes are less likely to survive • E.g. birth mass ○ Too heavy = birth problems ○ Too small = developmental problems • The mean stays the same • Standard deviation becomes smaller over time
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Genetic drift
• Occurs when population is small to begin with • Small gene pool • Chance mutations that are not beneficial or harmful might cause changes in allele frequency The isolated population can ‘drift’ and become very different to the parent population
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Genetic bottleneck
• When a population shrinks and then increases again • E.g. when disease spreads through a population and few survive • The new population has reduced genetic diversity as their genes derive from a few individuals • However in the case of disease, they will have acquired resistance to the disease which allowed their ancestors to survive the epidemic
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Founder effect
• If a new population is established from very few ‘founding’ individuals, there will be little genetic diversity • Small gene pool • Specific type of genetic drift
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EXAM TIP
Be clear that genetic bottleneck and genetic drift occur as a result of random mutations — not the other way round. Random mutations occur irrespective of the size of the population, but if the population is notably small, they affect a larger proportion of it, and therefore have a greater effect and are more likely to be carried into future generations.
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Hardy-Weinberg Principle predicts.
the ongoing frequencies of alleles and genotypes within a closed, freely and randomly breeding population
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Hardy-Weinberg Principle • Assuming:
○ Large population ○ No migration or immigration ○ No mutation to new alleles ○ Random mating, with respect to the genotype of the organism
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Speciation
the formation of a new species. • Parent species must be split into 2 groups • Requires the isolation of one group which will go on to become new species • Different selection pressures on each group • Speciation occurs when individuals from the 2 groups have significant genetic differences ○ Can no longer interbreed
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Isolating mechanisms
Geographical isolation ○ 2 groups separated geographically ○ Eg. ocean/mountains/rivers ○ 2 groups do not meet and cannot interbreed ○ ‘Allopatric speciation’ = speciation in different countries
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Reproductive isolation
Biological/behavioural changes arise from mutation ○ Mutation only affects some individuals in the species population ○ E.g. mutation causes individuals to become active at night rather than in the day – Changes foraging behaviour – These individuals only meet/breed with individuals also active at night
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artificial selection.
selection of genes for optimal economic yield This is where farmers and breeders select individuals from a population with desirable traits — e.g. cereal with resistance to drought, or cows with high milk yields
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Natural selection =
selection of genes which adapt a species to surviva
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Hybrid vigour
• Excessive selective cross-breeding can cause inbreeding depression • Breeding of related individuals • Gene pool diversity reduced • Chances of expression of recessive harmful gene increased • To avoid this problem, breeders must maintain a resource of genetic material • They outcross individuals from different varieties ○ Often with wild types • The resulting F1 are heterozygous at many loci • This is hybrid vigour • Decreased genetic variety = increased widespread susceptibility to disease
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The Ethics of Artificial Selection ...dogs
Domesticated animals are less able to defend themselves against predators • They are also often less able to hunt prey ○ E.g. dogs who became scavengers and were no longer under the selection pressure to be able to hunt as a pack • Livestock animals are biomorphically different and this may not support a happy life ○ E.g. chickens which grow too rapidly — bones unable to support weight ○ Pigs vulnerable to low temperatures during the winter because of reduced fat percentage • Pedigree dogs subject to narrow gene pool and therefore often have higher susceptibility to certain diseases ○ E.g. Boxer: cancer, heart disease ○ Labrador: abnormal hip and shoulder joints, lameness ○ West Highland Terrier: dry eye, skin irritation
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DNA can be manipulated in several ways:
• DNA profiling • Genomic sequencing • Genetic engineering • Gene therapy
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Gene Sequencing Process:
• Genomes mapped to identify which part of the genome they have come from • Microsatellites can be used to identify which region they are from • Samples of the genome are sheared into section around 100,000 base pairs long • Sections placed into separate bacterial artificial chromosomes (BACs) and transferred to E-coli cells • As the cells grow in culture, many copies of the sections are produced • These are clone libraries • The cells containing the specific BACs are taken and cultured • DNA is extracted and cut up by restriction enzymes • Fragments separated using electrophoresis • Each fragment is sequenced using an automated process • Computer regions compare overlapping regions form the cuts made by different restriction enzymes
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Automated DNA sequencing
Reaction mixture contains: ○ DNA polymerase ○ Single stranded DNA fragments ○ Free DNA nucleotides – Some have fluorescent markers ○ Primers • If fluorescent markers are added to the chain, DNA polymerase is thrown off • The strand cannot have any more nucleotides • Process: ○ Primer anneals at the 3’ end, allowing DNA polymerase to attach ○ DNA polymerase adds free nucleotides, so the strand grows ○ A modified nucleotide is added ○ Enzyme is thrown off ○ Reaction stops ○ In every strand the final nucleotide has a specific colour ○ As these strands are run through a machine, a laser reads the colour sequence – Move in increasing size order – Sequence of colours and so bases can be displayed
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High throughput sequencing =
methods of rapid, inexpensive gene sequencing developed in 21st century
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Pyrosequencing
Type of high throughput sequencing developed in 1996 • Involves synthesising a single strand of DNA complementary to the one being sequenced • Process: ○ DNA cut into fragments of 300-800 base pairs ○ Fragments are degraded into single-strand DNA (ssDNA) ○ Fragments incubated with primer, APS,luciferin, and several enzymes, including DNA polymerase ○ Nucleotides added are ATP, TTP, CTP, GTP ○ Nucleotides form chains complementary to the DNA fragments ○ They dephosphorylate: i.e. ATP -> adenosine; TTP thymine, etc ○ APS + pyrophosphate ATP ○ Visible light is released in this reaction and detected by a camera ○ Light patterns detected indicate amount of ATP and therefore DNA sequence ○ 10-hour run = 400 million bases are read
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Applications of DNA SequencingComparisons between species
• Thanks to gene sequencing we can identify the presence of genes throughout many species • Humans share 99% of genes with chimpanzees • Few genes are unique to our species • Pigs have similar gene for insulin as humans ○ Therefore pig insulin used to be used to treat diabetes in humans • FOXP2 is a gene found in humans, mice and chimpanzees ○ However it is mutated in humans ○ Allows speech • Identifying genetic similarities helps us track evolutionary paths/relationships of species
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applications of DNA Sequencing comparisons between individuals
Almost all humans share 99.9% similar DNA — the 0.1% makes us each unique • These 0.1% differences arise from substitutions ○ Called ‘single nucleotide polymorphisms’ or ‘SNPs’ ○ Epigenetics is the study of how methylation of DNA causes changes in the expression of some genes • E.g. parent/child genetic matching
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Predicting amino acid sequences
• Easier to sequence DNA than polypeptides • Can read amino acid sequence directly from DNA • According to triplets and codons • Need to know what part of DNA codes for introns/exons
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Synthetic biology
= designing useful biological devices and systems • E.g. biomedicine, food production
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Applications of DNA Sequencing
Comparisons between species Comparisons between individuals Predicting amino acid sequences synthetic biology
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DNA profiling
g refers to the practice of DNA analysis that confirms the identity of an individual.
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DNA profiling process:
DNA obtained from individual — e.g. mouth swab • DNA cut by restriction enzymes at specific sites • Fragments are separated by gel electrophoresis • Banding pattern can be seen • Banding pattern compared to another individuals’ which has been treated with the same restriction enzymes • Related individuals will have more similar banding patterns
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DNA profiling in forensic science
Establish innocence of suspects • Identify Nazi war criminals hiding in South America • Identify victims’ body parts after air crashes/terrorist attacks
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DNA profiling in analysis of disease
• Protein electrophoresis can identify type of Hb produced by an individual • Diagnose sickle cell anaemia
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EXAM TIP
DNA profiling and DNA sequencing is not the same thing. DNA profiling doesn’t necessarily involve the reading of individual nucleotides or genes.
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PCR
The polymerase chain reaction, a technique used to amplify DNA which makes it more suitable for analysis. Millions of copies of sample of DNA are made and the base sequence is retained.
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Principles of PCR
• DNA consists of 2 antiparallel chains • Each strand has 3’ end and 5’ end (according to direction of phosphate backbone) • DNA only grows from the 3’ end • Complementary base pairs
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Process PCR
• DNA Replication in Test Tube ○ Needed: – DNA to be replicated – DNA polymerase – Excess of A/T/G/C bases – Primers • Separating DNA strands ○ Heated to 95c ○ Causes strands to separate • Primers ○ Cooled to 55c ○ Primers are able to attach • DNA replication ○ Heated to 72c ○ DNA replication can now occur • Thermostable DNA polymerase ○ Taq polymerase used ○ Thermus aquaticus ○ Bacteria that lives in deep, warm oceans
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PCR Overall Process
○ Everything added ○ Heated to 95c – H bonds broken ○ Cooled to 40c – Allows primers to join ○ Increase temperature to 72c – Allow DNA to replicate ○ DNA is replicated ○ Heated again and process repeated
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Difference between PCR and normal DNA replication
○ Strand separation – In the cell DNA helicase separates DNA strands – In PCR, heat and temperature do this ○ Primers – Required to allow DNA polymerase to begin – In cells, they are made by DNA polymerase – In PCR they are synthesised separately and added
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Problems wPCR
• Any contamination will be amplified
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UsesPCR
Cloning • Electrophoresis • Gene Probes
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Electrophoresis
c = uses electric currents through agarose gel to separate DNA fragments according to size • DNA samples treated with restriction enzymes to cut them into fragments • DNA samples placed into wells of the gel • Gel is immersed in a tank of buffer solution • Phosphate groups make DNA negatively charged, so DNA diffuses through the gel towards the positive electrode • Shorter lengths of DNA move faster than longer lengths, so move further • Position of fragments can be shown by a dye that stains DNA molecules • DNA fragments are complementary to the piece of DNA that is being investigated • Probe is labelled: ○ Using a radioactive marker ○ Fluorescent marker that emits a colour on exposure to UV light • Copies of the probe will anneal to any complementary single strand • Probes are useful in locating specific sequences, for example: ○ Locate a desired gene for genetic engineering ○ Identify the same gene on different genomes ○ Identify the presence or absence of an allele
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DNA Probes
short, single-stranded pieces of DNA
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Genetic engineering = recombinant DNA technology = genetic modification
involves the manipulation and combination of genes from different organisms.
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Genetic engineering = recombinant DNA technology = genetic modification process
1. Specific gene is isolated and copied 2. Gene is placed inside vector (e.g. plasmid) 3. Vector carries gene to target cell 4. Recipient cell now has recombinant DNA and expresses newly acquired gene
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Isolating a required gene Genetic engineering
mRNA coding for the specific gene is obtained • Reverse transcriptase forms a single strand of complementary DNA (cDNA) based off the mRNA • Adding primers and DNA polymerase catalyses the formation of double stranded DNA • Gene is then synthesised ○ Automated polynucleotide synthesis if gene sequence known ○ PCR if gene sequence unknown • DNA probe used to locate gene • Gene isolated by restriction enzymes
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Genetic engineering Placing the gene inside a vector
Cut plasmid at specific site using restriction enzymes • Cuts made by restriction enzymes match the ends of the isolated gene ○ The complementary ends are called sticky ends • DNA ligase catalyses insertion of gene into plasmid • Gene can also be sealed in an attenuated virus
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Genetic engineering
• Several methods of achieving this • Heat shock ○ Bacteria subject to fluctuating temperatures between 0C and 42C ○ Cell walls and cell membranes become more permeable ○ Recombinant DNA enters cell more easily • Electroporation ○ High voltage applied to cell and the membrane becomes more permeable • Electrofusion ○ Electrical fields cause DNA to enter cells • Transfection ○ Gene inserted into bacteriophage which infects bacterial cell
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The ethics of Genetic Manipulation Pathogens • Benefits Hazards
* GM viruses which have no harmful effect can be used to make vaccines. • Gene therapy
* In gene therapy, gene modification can increase risk of cancer
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The ethics of Genetic Manipulation Mice • Benefits Hazards
* GM mice used for medical research, e.g. breast and prostate cancer
* Welfare concerns
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The ethics of Genetic Manipulation Golden Rice Benefits Hazards
* GM rice contains beta carotene to reduce rates of blindness in children suffering from Vit A deficiency
* Originally there were concerns that new seeds would have to be bought each year but the manufacturers have developed schemes so farmers can keep and re-sow seeds
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The ethics of Genetic Manipulation Plantains • Benefits Hazards
* GM plantain has higher zinc content as local consumers have low-meat diet making them zinc deficient
* People fear artificially present DNA can harm our own genomic sequence — however DNA that we ingest orally is digested by lytic enzymes
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The ethics of Genetic Manipulation Microorganisms • Benefits Hazards
* GM E. coli makes human insulin to treat diabetics and human growth hormone
* GM microorganisms must be carefully contained, as if they are released into the wild, their genes will spread and will affect entire ecosystems
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Gene therapy
is the use of gene technology to treat genetic disorders, which usually involves adding a functional copy of a gene to cells which only contain a dysfunctional copy
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Somatic Cell Gene Therapy
• During growth, cells become specialized • In these specialised cell, genes are switched on and off • Although the cell has a full genome, not all of it is active ○ Adding Genes – Some diseases caused by faulty alleles – Engineering a functional copy of that gene into the cell means that the polypeptide can be produced – Functional gene product created ○ Killing Cells – Cancerous cells can be made to express certain genes and create proteins – These can make the cells vulnerable to attack by the immune system – Targeted cancer treatments
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Germ line Cell Therapy
• Gene engineered into sperm or egg • Ensures all cells in the adult organism will have a copy of it • Illegal in humans
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Cloning =
process leading to the formation of a clone
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Clones
genetically identical copies of an organism
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Advantages of natural cloning
• Same environment suitable for parent and offspring • Rapid • Reproduction doesn’t require two parents or sexual reproduction
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Disadvantages of natural cloning
• Offspring overcrowding • No genetic diversity/variation • Therefore selection is impossible • Entire population vulnerable to environmental changes
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Reproductive Cloning
• Cloning that makes another organism
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Non-reproductive Cloning
Therapeutic cloning • Goal is to produce embryonic stem cells • Stem cells taken from blastocysts
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Cloning in Plants: Natural Vegetative Propagation
Generation of multiple offspring from one plant without sexual reproduction
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Cloning in Plants: Natural Vegetative Propagation Advantage
Only one parent required • Saves resources
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Cloning in Plants: Natural Vegetative Propagation Disadvantages
• One disease can affect the whole population
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Natural Vegetative Propagation Process
Many plants can reproduce asexually following damage to the parent plant • Root sucker, or basal sprouts, appear within 2 months • These grow from meristem tissue, where damage is least likely to have occurred • The offspring are genetically identical to the parent plant
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Micropropagation and tissue culture
the use of plant cuttings to produce clones. This process produces many genetically identical plants from just one plant, e.g. Elm trees
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Micropropagation and tissue culture Process
• Cells taken from shoot tip with sterile forceps • These are explants • Explants placed in nutrient agar • Cells proliferate to form a big ball of cells, called a callus • Cells are then treated with shoot stimulating hormones • Cells grow into plantlets • Treated with root-stimulating hormones • Plants grow • Plants are planted into compost
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Micropropagation and tissue culture Advantages
• Farmers know what the crop will be like • Reduced costs as all crop is ready for harvest at the same time • All crop has ideal features • Faster than selective breeding • Horticulture and agriculture
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Micropropagation and tissue culture Disadvantages
All plants susceptible to the same pest or disease
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Natural does not happen as frequently in animals as in plants because most animals reproduce sexually, creating genetic variation and diversity. However there are a few exceptions: what are they
Identical twins ○ Zygote divides early in development to form 2 separate cells ○ Each cell is genetically identical and grows into an individual organism • D. pulex and A. pisum ○ Species which reproduce asexually to produce clones
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copying genome for
○ Conservation ○ Exploitation ○ Experimentation
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Embryo Twinning
Cleaving of embryo is repeated • Used in artificial cloning in animals • All organisms produced are genetically identical ○ E.g. Cloned herds of cattle in America
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Somatic Cell Nuclear Transfer
Nucleus of an adult egg placed in an enucleated egg • Organism produced is genetically identical to that from which the nucleus was taken • This is how Dolly the Sheep was created
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cloning Advantages
• High-value animals can be cloned in large numbers • Rare animals can be cloned to preserve the species • Genetically modified animals can be quickly produced
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cloning Disadvantages
• Animal welfare may be forgotten • Reduced genetic diversity may decrease ability to cope with change • Long term health of cloned animals is still unclear
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features that make Microorganisms useful in biotechnology
Grow rapidly in favorable conditions, with generation time of less than 30 minutes • Metabolites can be harvested • Can be genetically engineered to produce specific products • Can grow well at low temperatures • Can be grown anywhere in the world and are not dependent on climate • Tend to generate more pure products • Economic considerations
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Example uses of microorganisms
• The Production of food ○ Cheese and yoghurt ○ Quorn ○ Soya Sauce • Production of drugs ○ Penicillin ○ Insulin • Production of enzymes ○ Pectinase ○ Calcium citrate ○ Bio-gas fuel production • Bioremediation of waste products ○ Waste water treatment
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Microorganisms to Make Food for Human Consumption
| Advantages
• Protein produced faster than animals/plants • Production easily increased or decreased according to demand ○ Easy to regulate speed of generation/growth • Protein contains no fat or cholesterol — health benefits • Requires small land surface area • Microorganisms easier to GM than animals or plants • Independent of seasons
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Microorganisms to Make Food for Human Consumption
| disAdvantages
Unappetising • Protein needs to be isolated from the growth substrate• Protein needs to be purified • Amino acid profile different from animal protein • Risk of infection of growth tank • Poor palatability
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Aseptic technique
Microorganisms grown on agar jelly in petri dishes • Hands always washed • Working area disinfected • Nearby bunsen burner warms air and causes airborne microbial contaminants to rise away from work area • Place neck of any open test tubes/containers over the bunsen burner to prevent bacteria in surrounding air from entering the vessel • Avoid removing petri dish lid entirely • Sterilise any equipment in the burner before making contact with the microorganism Growing microorganisms on agar plates consists of: Sterilisation Inoculation Incubation
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. Sterilisation
a. Agar and equipment must be sterile b. Achieved by using an autoclave — 121 degrees C — for 15 minutes c. All organisms are killed d. Keep lid on petri fish to maintain sterility
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. Inoculation a.
Microorganisms introduced to sterile medium b. Streaking — wire loop with microorganism on it is dragged across agar surface c. Seeding — pipette used to drop liquid medium on agar d. Spreading — glass spreader used to spread the drop across the agar
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3. Incubation
a. Petri dish placed in warm environment b. Place upside down to prevent condensation falling on the surface of the agar c. Do not open petri dish d. Observe culture growth after 24-48 h e. Wash petri dish after use
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Scaling-Up Growth
• Conducted in a fermenter • Culture bacteria in an aqueous environment • High pressure steam ○ Sterilizes environment • Sparger ○ Delivers oxygen • Waste products removed • Incoming air filtered • Outlet at the top • Respiration increase temperature ○ Lowered by a water jacket • pH may become more acidic ○ Alkali can be added to neutralize this
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Continuous Culture
• Useful and waste products continually removed • Some bacteria are removed • Useful for maintaining the culture in the log phase • Difficult to set up • More efficient as the fermenter operates continuously
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Batch Culture
• Closed environment • Competition for limited resources • Useful for maintaining culture in stationary phase • Must know the end of log phase and the end of stationary phase • Easy to set up and maintain • Less efficient as the fermenter is not in operation full time • Useful for producing secondary metabolites
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Microorganism in a Closed Culture
| Lag Phase
• Cells increase in size • Enzymes synthesized • No cell division • Gives time to ensure a stable environment • Cells taking in water • Population remains fairly constant
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Microorganism in a Closed CultureLog Phase
• Exponential growth due to high metabolic activity and reproduction • Cells are most vulnerable to anti-microbial during this period • Exponential growth
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Microorganism in a Closed CultureStationary Phase
Nutrient levels decrease • Toxic metabolites build up • Growth rate slows • Population stabilizes • Organisms die at the same rate at which new individuals are being produced
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Microorganism in a Closed Culture Death Phase
• Nutrient exhaustion • Increased levels of toxic metabolites • Microbial death exceeds numbers produced
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Primary Metabolites
• Substances produced by an organism as part of its normal growth • Vital for cell growth ○ Amino acids ○ Lipids ○ Vitamins • Produced during log phase
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Secondary Metabolites
• Substances produced that are not part of normal growth • Produced once the colony has reached its maximum sustainable size ○ Antibiotics ○ Penicillin • Produced during stationary phase
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Serial dilutions
repeated dilutions of a solution in order to reduce its concentration • Useful technique for identifying rate of growth of a colony • Original solution may contain high numbers of microorganisms • Need to dilute the broth in order to clearly see starting density of colonies and determine growth
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Immobilised enzyme
an enzyme that is fixed and unable to move freely throughout a solution.
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Advantages of immobilising enzymes in biotechnology
• Enzymes don’t mix with product — lower purification cost • Enzymes can be re-used • Cells containing enzymes are replaced with immobilised enzymes, therefore no need to deal with cellular demand for nutrients or release of waste products • Enzymes are fixed within immobilising matrix which protects them from harsh environments ○ High temp/extreme pH more feasible
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Disadvantages of immobilising enzymes in biotechnology:
• Expensive to set up • Immobilised enzymes are less active than free enzymes so process is slower
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Methods of immobilising enzymes:
Adsorption • Covalent bonding Entrapment • Membrane barrier
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• Adsorption
○ Enzymes bound to e.g. clay surface by hydrophobic interactions and ionic links ○ Weak bonds — some enzymes break loose
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• Covalent bonding
○ Enzymes bound to e.g. clay surface by covalent bonds ○ Sharing electrons = strong bonds ○ Can be expensive and reduce enzyme action ○ But enzymes unlikely to break free into reaction mixture
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• Entrapment
○ Enzymes trapped in matrix ○ Enzymes fully active ○ Substrate diffuses into matrix ○ Product diffuses out of matrix ○ E.g. calcium alginate beads
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• Membrane barrier
○ Semi-permeable membrane around enzymes ○ Substrate small enough to pass through membrane to meet enzymes ○ Limits rate of reaction
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Example of use of immobilised enzymes:
• Lactase • Converted glucose to galactose ○ Hydrolysis reaction • Used to make lactose-free milk • Makes calcium-rich milk available to people who are lactose intolerant
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Ecosystem
dynamic system of interactions involving a community of living organisms and the abiotic factors of their environment. Ecosystems can range in size: • Large scale e.g. African grassland • Medium scale e.g. football field • Small scale e.g. a single tree
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Habitat =
the place where an organism lives
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Population =
a group of organisms of the same species who live in the same place at the same time and can breed
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Community =
all the populations of different species living in the same place at the same time
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Ecosystems are said to be dynamic: cuz
• Populations constantly rise and fall • This is because of interactions between living things and their ecosystem • Any small changes can have a large effect • Subject to change due to biotic and abiotic factors
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Abiotic
• Effects of non-living components • pH • Temperature • Soil type
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Biotic
• Effects of living components • Food supply • Predation • Disease
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Biomass
the combined total weight of a defined set of organisms. Biomass revolves around the idea that energy is created by producers in the food chain, which are then eaten. Energy and materials (such as amino acids and glucose) thereby travel up the food chain or trophic levels.
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Pyramid of Biomass • Indicates
• Indicates biomass at each trophic level • Area of bars is proportional to the dry mass of all organisms at that trophic level • Ecologists put organism in an oven, evaporating all of the water • In order to be less destructive, wet mass can be calculated, using previous data to calculate dry mass • However, these do not take the variation in energy released per unit into account
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Pyramid of Energy • This pyramid indicates
• This pyramid indicates the energy contained within the biomass of each trophic level • Organisms are burnt in a calorimeter • This calculates the energy released per gram • This is both time consuming and destructive, so is rarely used • However, these only take a ‘snapshot’ of the organisms and may provide a distorted view due to fluctuation in population
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Productivity
• Ecologists often look at the rate that energy passes through each trophic level • This gives an idea of how much energy is available to organism • It is measured in megajoules of energy per square meter per year • At the base of the food chain, productivity is called primary productivity • Gross primary productivity is the rate at which plants convert light energy into chemical energy • However, some energy is lost when the plant respires • Remaining energy is called net primary productivity
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Efficiency of Transfer
• At each level, some energy is lost • Less energy is therefore available for organisms at the next level • At each level organisms need energy to carry out life process • Respiration releases energy, some of which is converted to what • Energy remains stored in dead organisms and waste material, which is only available to decomposers • Waste material also includes parts that cannot be broken down and digested by consumers • Higher up in food chains, less energy is available to sustain living things so less tissue can be kept alive • This means that if organism are the same size, fewer can be sustained higher up the food chain
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Human manipulation of biomass transfer:
| Improving Primary Productivity
• Plants grown earlier or under light banks to maximise light exposure • Plants are irrigated to maximise water supply • Warmer temperatures, often in form of greenhouses, are used to increase speed of chemical reactions • Nutrient levels in soil are maintained • Pests are sprayed with pesticides to prevent loss of biomass from crops • Fungal diseases are limited through the use of fungicides • Herbicides used to kill weeds which provide the corps with unnecessary competition
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Human manipulation of biomass transfer:
| Improving Secondary Productivity
• Manipulation of energy transfer from producer to consumer • Animals harvested young, when most of their energy is used for growth • Steroid used to increase growth • Selective breeding used to produce breeds with higher growth rates • Animals treated with antibiotics to prevent loss of energy due to pathogens • Limiting movement reduces energy loss due to heat, maximising the mass
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Role of Decomposers
• Dead and waste organic material is broken down by decomposers • Bacteria and fungi feed in a different way to other organisms, they are saprotrophs: ○ Secrete enzymes onto dead waste material ○ Enzymes digest material into small molecules ○ Molecules then absorbed into the body ○ Molecules are stored or respired to releases energy
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why Nitrogen Cycle
• Living things require nitrogen to make proteins and nucleic acids • Nitrogen is cycled between biotic and Abiotic components • Bacteria is involved in ammonification, nitrogen fixation, nitrification and denitrification
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Nitrogen Cycle
• Nitrogen Fixation Nitrification • Denitrification
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Nitrogen Fixation
○ Nitrogen is incredibly uncreative when in the atmosphere ○ Plants need a supply to be ‘fixed’ ○ Nitrogen fixation can occur when: – Lightning strikes – Haber process – Nitrogen fixing bacteria (Rhizobium) fixes it ○ Bacteria has a mutualistic relationship with the plant providing in with nitrogen and receiving carbon compounds in return
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• Nitrification
○ Chemotropic bacteria absorbs ammonium ions ○ Ammonium ions are released in putrefaction of proteins ○ Nitrosomonas bacteria oxidise ammonium to nitrates ○ Nitrobacteria oxidise nitrites to nitrates ○ As reaction requires oxygen, it only occurs in well aerated soil
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Denitrification
○ Bacteria can convert nitrates back to nitrogen gas ○ When bacteria involved are growing under anaerobic conditions, they can produce nitrogen gas and nitrous oxide
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primary succession
The development of communities from bare ground
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primary succession process
○ Pioneer community of algae and lichens grow on bare rock ○ Pioneer species = first species to colonise an abiotic area, which begin the process of succession ○ The rock is eroded and dead organisms build up ○ This produces soil for larger plants to grow. These plants succeeds the algae and lichens ○ Larger plants continue to succeed smaller plants until a final stable community is reached. This is the climax community ○ Deflected succession = when succession stops or is interfered with – E.g. when mowing grass
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Deflected succession
= when succession stops or is interfered with – E.g. when mowing grass
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Pioneer species
= first species to colonise an abiotic area, which begin the process of succession
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Climax Community
xFinal, stable community • Larger plants replace smaller plants in process of succession
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Secondary succession
is the sequential community changes that happen following deflection, when the environment is altered somehow
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how to Measure Distribution
SamplingQuadratsTransects
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Sampling
• Small portions of the habitat are studied • These are taken as representative for the larger habitat
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Quadrats
• Quadrats are used to enable sampling of a small space in the habitat • The square frame is used to define the sample area • Randomly place quadrats across the habitat • Or take samples at regular intervals across the habitat (systematic
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transects
• More systematic approach • Looking for changes in distribution or abundance • A line is taken along a habitat and sample are taken along this line • Line transect = regular intervals — record species making contact with the tape • Belt transect = regular intervals — place quadrat next to the line and study quadrat results
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Line transect =
regular intervals — record species making contact with the tape
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Belt transect
= regular intervals — place quadrat next to the line and study quadrat results
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A population cannot increase exponentially and infinitely. The size of a population naturally fluctuates but is usually within a certain range, which is determined by a few limiting factors.
○ Availability of resources ○ Nesting sites ○ Shelter ○ Predation ○ Parasites
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Carrying Capacity
The maximum population size that can be maintained over a period of time in that particular habitat The carrying capacity is the upper limit that these factors place on the population size
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Lag Phase of a Population
– Few individuals – Acclimatising to habitat – Reproduction and growth slow
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Log Phase of a Population
Resources plentiful – Reproduction fast
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○ Stationary Phase of a Population
– Population levels out at the carrying capacity – Habitat cannot support a large population – Rates of reproduction and mortality are equal – Population size stays stable
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Predator and Prey
Predators can act as a limiting factor on prey’s population size • When population gets bigger, more prey are eaten • Prey population shrinks, leaving less food available • Less food, so less predators survive and population size reduces • Fewer predators, fewer prey eaten, population size increases • More prey, so predator population rises again
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Competition
If resources are in short supply, competition will always exist • It occurs when resources are not present in adequate amounts to satisfy the needs of all individuals who depend on those resources
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○ Intraspecific Competition
Happens between individuals of the same species
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Interspecific Competition
– Happens between individuals of different species – Can affect both population size and distribution
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EXAM TIP
Consider which population limiting factors are dependent and independent of the size of the existing population. For example, cold temperatures can decrease the size of a population irrespective of its size. On the other hand, the availability of nesting sites for birds will only become a limiting factor when the population becomes dense enough
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Conservation =
Maintenance of existing biodiversity, including interspecies, genetic, intraspecies, habitat and ecosystem diversity. Often involves management and reclamation
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Preservation =
Maintenance of habitats and ecosystems in their present condition by minimising human impact.
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Reasons for conservation
• Ethical • Economic Social
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• Economic Reasons for conservation
○ Many plant and animal species are rich food source ○ Genetic diversity in wild strains needed for hybrid vigour○ Natural predators can drive out pests ○ Conservation of wild/rare species can boost local tourism
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• Social Reasons for conservation
Microorganisms and plants can be a source of medicinal drugs
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Methods of conservation
• Protected areas like National Parks • Ex situ protection e.g. zoos, botanical gardens • Increase habitat carrying capacity by increasing available food • Control predators and poachers • Vaccinate individuals against disease • Preserve habitats by reducing waste/pollution
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Small-scale Timber Production
Coppicing involves cutting a tree trunk close to the ground to encourage growth • It is a traditional supply to obtaining a sustainable supply of wood • Once cut, new shoots grow from the stems • Woodland managers divide trees into 3 sections, cutting one section a year until all the trees have been cut ○ This is rotational coppicing • In each section some trees are left un-cut • These standards supply larger pieces of timber • Rotational coppicing is very good for biodiversity • It allows different habitats to thrive and presents succession
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Large-scale timber production
• Often involves clear-felling of trees • If done altogether, this can destroy areas of woodland • Leaving each section to mature for 50-100 years allows biodiversity to increase • Felled trees are replaced • Selective cutting involves felling only the largest and most valuable trees, which has little impact on the ecosystem • In order to sustainably manage the forest, foresters must:○ Control pests and pathogens ○ Only plant plants that will grow well ○ Position trees an optimal distance apart
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Fish Farming
• Fishing takes place in a way that allows it to be continued indefinitely • Stocks are not depleted • Over-fishing therefore not possible • Ecosystem structure, production and function is preserved
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Habitat Disturbance
• Increase in population size has placed huge demands on water, energy and sanitation services • Demand for oil has increased • Conversion or land for agriculture has resulted in the fragmentation of habitats ○ Forests of scalesia trees and shrubs have almost been eradicated to make way for agricultural land
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Terai Region
• Southern Nepal • Over-exploited for the past 10 years by agricultural pressures • Forests provide source of fuel for local people • WWF and Nepalese government focused on conservation of the area • Local people could exploit the forest but had responsibility to look after it • Developing waterholes, forest corridors to enable animal migrations • Tiger population are using forest corridors ○ Population is growing
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Maasai Mara
Savannah region in Kenya • Surrounding communities suffer poverty and rely heavily on tourism for wildlife watching • Conservation maintains biodiversity of the region whilst helping local people financially • In 1986 the security of the land was threatened and Maasai people claimed parts of it for themselves • Land use became progressively more agricultural • Mobility of livestock was reduced • Density of wildlife dropped 65% over last 30 years • In 2005, some land-owners unionised and turned their land into conservancies to generate tourism income • Conservancies are now paid by tourism operators for land set aside for conservation • However the the landowners must move their livestock out of the designated conservancies during tourism season • There are constraints on how they can use the land
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Over-exploitation of resources on the Galapagos Islands
Giant tortoises historically taken on ships as a food source • 200,000 taken in less than half a century • Depletion of sea cucumber populations • The shark fin market has led to the deaths of 150,000 sharks each year • 14 species are listed as endangered
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Human Activity on the Galapagos Islands
| Introduced Species
• Alien species deliberately brought to the islands • These have eradicated native species • The goat has been one of the most damaging species ○ Eats Galapagos rock purslane ○ Outcompetes giant tortoise in grazing • Cats hunt a number of species including the lava lizard and young iguanas • The Charles Darwin Research Station has introduced many measures to prevent and limit this: ○ Quarantine system ○ Culling of dominant alien species ○ 36% of coastal areas designated as ‘no take’ zones • It is essential to find a balance between the environmental, social and economic concerns
