Module 6 Flashcards
Substitution
= a nucleotide base is replaced with another
Insertion =
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
Deletion
= the absence of a nucleotide, causing ‘frameshift’ where all the subsequent bases are shifted back 1 place relative to the twin DNA strand
gene mutations can be
Neutral Harmful Beneficial
gene mutations Neutral
○ 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
gene mutations Harmful
○ May result in change in final protein shape where protein and active site is deformed and therefore cannot fulfil function
gene mutations Beneficial
○ 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
Point mutation
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
Silent mutation
○ No change in amino acid sequence of polypeptide
Missense mutation
○ The mutation changes the code for 1 amino acid ○ 1 amino acid in the sequence is changes
nonsense mutation
○ 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
Lac system genes
• 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
Lac operon in the absence of lactose
• 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
Lac operon in the presence of lactose:
• 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
Homeobox Genes
• 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
Apoptosis •
Programmed cell death • Occurs in multicellular organisms
Sequence of events Apoptosis •
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
control Apoptosis
Controlled by a diverse range of cell signals • Nitric oxide can induce apoptosis
Development
• 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
Transcription factors
• 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
Introns mn Exons
• 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
• Homeobox genes
are found across all multicellular organisms
• Hox genes
are a sub-type of Homeobox gene which are only found in animals
Genotype =
genetic makeup of an individual
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.
mutagenic agents
– X-rays – Benzopyrene found in tobacco smoke – Viruses – Gamma rays
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)
○ Aneuploidy
chromosome number is not a multiple of the haploid number for that organism
Polyploidy
diploid gamete fertilised by a haploid gamete ○ Resulting zygote is triploid (3n chromosomes)
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
gemertic variable can be caused by
Genetic variation caused by mutations ○ Caused by mutagenic agents ○ Caused by chromosomal mutations ○ Aneuploidy ○ Polyploidy
Phenotypic factors
Variation caused by the environment alone ○ E.g. losing a limb in an accident
Variation caused by the environment alone ○
E.g. losing a limb in an accident
• 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)
epigenetics
○ Environmental conditions can affect the expression of some genes
Monohybrid
investigations that examine the inheritance of a single characteristic:
Dihybrid
investigations that examine the inheritance of two characteristics:
why are Linked genes more likely to be passed on together
since their loci are close together on the chromosome.
Linkage
when two or more genes are located on the same chromosome
Autosomal linkage
linked genes which are on non-sex chromosomes
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
Epistasis
interaction of non-linked genes where one masks the expression of the other
Recessive epistasis •
Homozygous recessive alleles mask expression of another allele at different locus
Codominance =
when both alleles present in the genotype contribute to the phenotype wg bloodtype and cow coat colour
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
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
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
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
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
polygenic
, it is determined by the interactions of several genes and the alleles at those loci — in that one individual.
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
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
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
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
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
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.
Hardy-Weinberg Principle predicts.
the ongoing frequencies of alleles and genotypes within a closed, freely and randomly breeding population
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
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
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
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
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
Natural selection =
selection of genes which adapt a species to surviva
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
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
DNA can be manipulated in several ways:
• DNA profiling • Genomic sequencing • Genetic engineering • Gene therapy
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
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
High throughput sequencing =
methods of rapid, inexpensive gene sequencing developed in 21st century
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
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
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
Synthetic biology
= designing useful biological devices and systems • E.g. biomedicine, food production
Applications of DNA Sequencing
Comparisons between species Comparisons between individuals Predicting amino acid sequences synthetic biology
DNA profiling
g refers to the practice of DNA analysis that confirms the identity of an individual.
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
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
DNA profiling in analysis of disease
• Protein electrophoresis can identify type of Hb produced by an individual • Diagnose sickle cell anaemia
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.
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.
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
