Module 6 Flashcards
What kinds of point mutation are there?
Base substitution
Frameshift insertion
Frameshift deletion
What do nonsense mutations do?
Turn a base sequence from coding for a functional amino acid into coding for a ‘stop’ amino acid
What do mis-sense mutations do?
Change order of base sequence…
- conservative: maybe ‘silent’
- non-conservative: probably damaging
What kind of chromosome mutations are there?
Deletion
Translocation
Inversion
How are genes regulated?
Transcriptional (switching on/off)
Post-transcriptional (mRNA modification)
Translational (stop and start translation)
Post-translational (protein modification)
What is chromatin?
The tightly wound DNA-histone complex that is formed when DNA is condensed
What is heterochromatin?
Tightly wound DNA visible in cell division
What is euchromatin ?
Loosely wound DNA visible in interphase, which lets RNA polymerase access the DNA
What does acylation and phosphorylation do to chromatin?
Makes DNA coil less-tightly, allowing extra genes to be transcribed
What does methylation do to chromatin?
Makes DNA coil more-tightly, allowing fewer genes to be transcribed
What is an operon?
A group of genes under the control of the same mechanism
How does the Lac-operon work?
When lactose is present, it binds to the repressor protein and moves it out of the way of the operator, allowing RNA polymerase to bind to the promoter and transcribe LacZ, LacY and LacA
How does pre-mRNA become mature mRNA?
A cap is added to 5’ end and a tail to the 3’ end (nucleotides) and splicing occurs - removing the introns (non-coding DNA), the molecule can also be modified before translation - to make a variety of different polypeptides
What are protein kinases?
Enzymes that catalyse the addition of phosphate groups to proteins, thus changing the structure and function. This is often how enzymes are activated
What are Homeobox genes?
A group of regulatory genes which all contain a homeobox - a highly conserved 180bp code which produces a protein (with a part called a homeodomain) which switches genes on and off
What are Hox genes?
A group of homeobox genes only in mammals, found in clusters
What kinds of body symmetry can homeobox genes regulate?
Radial - like jellyfish
Bilateral - like humans
(Asymmetric - like a sea sponge)
What is morphogenic apoptosis?
Programmed cell death, acting like a ‘sculptor’ to form body shapes. Apoptic bodies ‘bleb’ and are consumed by phagocytes
What can effect the expression of regulatory genes?
Temperature, light intensity, and the effects of drugs (like Thalidomide)
What is meant by Homozygous?
Two identical alleles for a genotype
What is meant by Heterozygous?
Two different alleles for a genotype
What is continuous variation?
Variation that can take on any value in a range, generally polygene controlled
What is discontinuous variation?
Variation that can only take a discrete set of values, generally controlled by one or two genes
What is codominance, and how is it denoted?
When two different alleles of a genotype are equally dominant, and it is conventionally shown with a superscript letter to show the phenotype variant
What is the hereditary significance of sex-lined inheritance?
Any phenotype caused by a recessive allele on the X chromosome (C-23) will be more common in males, since there is not another X-locus allele to ‘out-dominate’ it. This gives rise to males being more susceptible to colour-blindness and haemophilia etc.
What is dihybrid inheritance?
Patterns of inheritance that depend on two genes which are not necessarily on the same homologous chromosome
What are the expected F1 phenotype ratios when two (F0 heterozygous) dihybrid alleles are crossed?
9:3:3:1
What is ‘linkage’ regarding dihybrid alleles?
When two dihybrid alleles yield phenotype ratios different to those expected because they are on the same chromosome - and less independent assortment occurred than expected / they tend to be inherited together
How is recombinant frequency calculated and interpreted?
number of recombinant offspring divided by total number of offspring. If the value is less than 50% the genes are considered linked, closer genes are even less likely to get separated!
How are degrees of freedom calculated for Chi-squared?
df = n - 1
What is epistasis?
Interaction of genes at different loci (often regulatory)
Regarding epistasis, define Hypostatic gene’ and ‘Epistatic gene’
The epistatic gene is the precursor / the one controlling the expression of the hypostatic gene (the one that might not be expressed)
What is the difference between dominant and recessive epistasis?
Dominant epistasis is controlled by dominant alleles (ORA)
What is gene flow?
The movement of alleles between populations
What is genetic drift?
Genetic drift occurs in small populations and is the change in allele frequency due to the random nature of mutation
What is the difference between density dependant population limiting factors and density independent population limiting factors?
Density independent factors effect all population sizes (e.g. natural disaster)
Density dependent factors depend upon the population size (e.g. competition and predation)
What are the consequences of a genetic bottleneck?
Reduction in gene pool and new population is unlikely to be representative of the old one, the ‘Founder effect’ will probably occur - dramatically altering the future genome
Name the three main types of selection pressure
- Stabilising
- Directional
- Diversifying
What is allopatric speciation?
More common type of speciation, arises from a physical barrier, causes the founder effect
What is sympatric speciation?
Less common type of speciation, occurs when populations share the same habitat - results in inbreeding etc. and reproductive isolation (mainly plants)
What are the disadvantages of selective breeding?
Limits gene pool and genetic diversity
Increases susceptibility to disease
Decreases ‘genetic fitness’: most genetic diseases are on recessive alleles and inbreeding increases the chance of inheriting homozygous recessive genotypes
What is satellite DNA?
Short sequence repeated many times in the introns (non coding parts), telomeres and centromeres.
Mini-satellites ate repeated more than one thousand times and are sometimes called Variable Number Tandem Repeats (VNTRs), what are microsatellites sometimes called?
Short Tandem Repeats (STRs)
How are DNA satellites unique to each individual?
They always appear on the same place in the chromosome, but everyone has a different number of repeats. It is inherited (half) from each parent
How does the Polymerase Chain Reaction work?
1) at 95 degrees the strands of DNA separate
2) at 55 degrees, primers anneal (bind) to end of strands
3) at 72 degrees, taq-polymerase adds bases to the primer, and then builds up the rest of the strand
This is repeated millions of times (very quickly) in order to amplify a DNA sample
How do you obtain a DNA profile?
1) Polymerase chain reaction on sample
2 Digest sample with restriction endonucleases
3) Separate fragments by Gel Electrophoresis (agarose)
4) Hybridisation: Probes or pigments are added
5) Interpret results - compare bands etc. found
How do you obtain a DNA sequence?
DNA is mixed with primers, excess nucleotides and special ‘terminator’ nucleotides, and is put into a thermal cycler (PCR machine). Then the new strands are created, but the terminator bases stop the annealing process, so multiple strands of different lengths are created. Capillary sequencing can then isolate the difference chains and work out where the ‘overlaps’ are - to form a specific base-sequence
Define the terms…
- Bioinformatics
- Synthetic Biology
Bioinformatics is the organisation of raw biological data, synthetic biology is the use of such data to build models and simulations, and aid our understanding
How are genome-wide comparisons useful?
- Expose genetic weakness of pathogens
- Classification: DNA-barcoding by observing differences in the mitochondrial DNA (the cytochrome c oxidase genes)
What is proteomics?
The study of amino acid sequences (…of an entire organism usually)
What can spliceosomes do?
Reassemble pre-mRNA exons in different ways to make a wide range of different outcomes
How can you isolate a desired gene (concerning genetic engineering)?
- Use specific restriction endonucleases (ideally ones that make ‘sticky ends’)
- Isolate the active mRNA in cells that reflect the desired phenotype (e.g. Beta cells of pancreas will have a lot of Insulin mRNA kicking around), once isolated, reverse transcriptase can make it into a ‘proper’ double strand
What are the advantages of using a bacterial plasmid as a host?
Markers are present, such as antibiotic resistance genes (and more recently, pigment genes) to show if each plasmid is modified or not
How is DNA with sticky ends transferred into a plasmid?
The plasmid has the same restriction endonucleases applied to it, and then DNA ligase inserts the foreign code
State the ways in which the modified vector can be transferred into the host
Animal or Microorganism:
- Poration (hot calcium solution)
- Electroporation (small voltage same effect)
- Electrofusion (opens membrane of two cells and fuses them to form polyploid GMO), mainly used for MCAs (and plants)
Plants:
- Electrofusion (as above)
- Using a tumour-causing bacteria the host and infecting the plant, then harvesting cells from the callus to grow new plants from
What are the key ethical issues surrounding gene technology?
- Warfare implications
- Crops (monocultures, disease etc.)
- Animal/ Human implications (economic imbalances and designer babies)
What is natural cloning?
Asexual reproduction (bacteria, some plant mechanisms such as runners etc.)
How can plants be artificially cloned?
Micro-propagation
How can animals be artificially cloned?
Artificial twinning
Somatic Cell Nuclear Transfer (SCNT)
What is bioremediation?
When biological organisms are used to break down organic material (in soil or water etc.)
What are the different phases of a bacterial colony growth?
Lag phase
Log / exponential phase
Stationary phase
Decline / death phase
What are secondary metabolites?
Products of microbial metabolism which are not essential for normal growth, but are still used (e.g. an antibiotic)
When is batch fermentation stopped?
Before death phase
What are impellers and what is a sparger (in a bioreactor)?
Impellers are the stirring ‘pedals’ and the sparger supplies necessary gases
State an advantage of using isolated enzymes?
Less downstream processing (product is pure)
How can isolated enzymes be immobilised?
- Adsorption to inorganic carrier
- Entrapment in a matrix
- Bonded to a carrier
- Encapsulated
What is an ecosystem?
The sum of all the living organisms that interact with physical attributes in a defined area
What abiotic factors are organisms in an ecosystem subject to?
Light intensity Temperature Water availability Oxygen availability Edaphic Factors (how loamy the soil is basically)
What are trophic levels?
Stages in a food chain, including the producers
How is energy lost between trophic levels?
As heat, in respiration and lost to decomposition/detritivores (from both excretion and death)
What do decomposers do?
Turn organic molecules into inorganic ones, they are mainly fungi and bacteria and are known as saprotrophs
What are detritivores?
Organism that speed up decay, by breaking down large organic molecule into smaller units, they perform internal digestion e.g. woodlouse
State the role (and give examples) of nitrogen fixing bacteria
Turn atmospheric nitrogen into ammonia. Azotobacter and Rhizobium (often found in legume root nodules)
State the role (and give examples) of nitrifying bacteria
Convert ammonium compounds into NO3-. Nitrosomonas and Nitrobacter
State the role of denitrifying bacteria
Convert nitrates back into atmospheric nitrogen under anaerobic conditions
What abiotic factors can fix nitrogen?
Lightning strikes and the haber process
Why is atmospheric carbon dioxide concentration slightly higher at night, and in the winter
Less photosynthesis is occurring at these times
What is primary succession?
brand new colonisation, pioneer species (often onto bare rock)
What is secondary succession?
recolonization, often onto bare-earth after an environmental event (such as a forest fire)
State the main seral stages
Pioneer community
Intermediate community
Climax community
What is it called when human activities deflect succession and prevent the formation of a climax community (e.g. by intense agriculture etc.)?
Plagioclimax
What is a population’s carrying capacity?
How many organisms of that species the local system can sustain - showed by the ‘stable state’ on a growth curve
What is the difference between interspecific competition and intraspecific competition?
Intraspecific competition is between members of the same species
What general trend is shown in a predator-prey graph?
The peaks in predator population mirror the peaks in prey population
Define conservation
Maintaining biodiversity through human action
Define preservation
Protecting an area by restricting or banning human influence
Why is conservation important?
Economic reasons (resources) Social reasons (aesthetics) Ethical reasons (moral responsibility)
What are the aims of sustainability?
Preserve the environment
Ensure availability of resources
Allow societies to live prosperously
Enhance LEDCs and create financial ‘balance’ / equality
What is coppicing?
Cutting trees near the roots, so that they may regrow the next season
How is the ecosystem of the Masai Mara managed?
Limits on grazing
Relying on ecotourism for economy
Research is going into poaching and conservation
Striking a balance between under/over hunting etc.
How is the ecosystem of the Terai region in Nepal managed?
Recent improvements in soil and water quality
Stopping further deforestation
Promoting diverse crop agriculture
Fertilisation techniques
How is the ecosystem of Peat bogs in the UK managed?
Loss of ecosystem from overexploitation - conservation of the bogs is paramount
Seedling trees are being removed
Controlled grazing on the wetland keeps it how it should be
Give three examples of sensitive ecosystems?
Galapagos
Antarctica
UK National Parks (Snowdonia and Lake District)
