Biology F215

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  • Created by: molly
  • Created on: 26-05-15 14:28
What is a gene?
A length of DNA that codes for one or more polypeptides
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What is a polypeptide?
A polymer Consisting of a chain of amino acid residues joined by peptide bonds
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What is the genome of an organism?
The entire DNA sequence of that organism?
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What is the specific place a gene occupies on a chromosome called?
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What is the DNA in the chromosomes associated with?
Histone proteins
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What does degenerative mean?
All amino acids except Methione have more than one code
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Describe the genetic code?
Triplet code, widespread but not universal, some codes for STOP, 20 amino acids used, number of different triplet sequences is 64
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What are the four activated RNA nucleotides in transcription?
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How does the gene to be transcribed unwind and unzip?
Dips into the nucleolus, H-bonds break
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Enzyme involved in transcription?
RNA polymerase
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What do the two extra phosphoryl groups release?
Energy for bonding adjacent nucleotides
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What is the central dogma of molecular biology?
DNA directs its own replication and it's transcription to RNA.The RNA in directs translation to proteins
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What is the definition of translation?
The assembly of polypeptides at ribosomes
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What is the structure of a ribosome?
Two subunits, groove for mRNA to fit in to
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Why is the sequence of amino acids in a protein critical?
It determines the primary structure which determines the tertiary structure of s protein, if this is altered the protein can no longer function effectively
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What is the structure of tRNA?
Lengths of RNA, hairpin shape, three exposed bases at one end, three unpaired bases at the other end known as an anticodon
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What is the first exposed mRNA codon?
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What catalysises translation?
An enzyme in the small ribosomal subunit
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When does the polypeptide chain stop growing?
When a STOP codon is reached
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When does translation occur in prokaryotes?
As soon as some mRNA has been made
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What is a mutation?
A change in the amount of or arrangement of gentic material in a cell
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What is a chromosome mutation?
Involves changes to parts of or whole chromosomes
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What is a DNA mutation?
A change to genes due to changes in nucleotide base sequences
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What is a point mutation?
One base replaces another (substitutions)
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What type of mutation causes a frameshift?
Insertion/deletion mutations
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What are somatic mutations?
Associated with mitosis , not passed on
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What is CF the result of?
Deletion of a triplet of bases, deleting an amino acid
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What us Sickle Cell anaemia the result of?
Point mutation codon 6 of the gene for the B-polypeptide chains of haemoglobin, causes valine to be inserted in place of gluts mic acid.
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What do oncogenes promote?
Unregulated cell division
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What des Huntington disease result from?
Expanded triple nucleotide repeat - a stutter
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Symptoms of Huntington disease?
Dementia, loss of motor control - manifest later in life
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What is a silent mutation?
Has no effect on the protein
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What is a allele?
An alternative version of a gene
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What will happen if the mutation is in non- coding DNA region?
No change
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What is a neutral mutation?
Silent or gives no particular advantage or disadvantage to the organism
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Give an example of a neutral mutation?
Honeysuckle smelling, tongue rolling,ear lobes
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Give an example of an advantageous mutation?
Tasting post outs PTC
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What pigment is found in darker skin?
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What does Melanin result in?
Protection from harmful effects of UV light, less vitamin D synthesised
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Symptoms of a lack of vitamin D?
Rickets, narrow pelvis - childbirth difficulties
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What is epigenetic programming?
Stem cells became specialised as certain genes are turned off by methylation or association with Hisone proteins
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What does Z code for?
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What does Y code for?
Lactose permease
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What does the I region by the lac Operon do?
Regulator gene produces repress or protein
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What is the inducer?
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What is the function if lactose permease?
Takes up lactose from the medium into their cells
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What is the function of B-galactosidase?
Converts lactose to glucose and galactose for respiration
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What region does the Repressor protein bind to?
The operator
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What do Homeobox genes do?
Control the development of the body plan of an organism, including the polarity and positioning of the organs
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What do segmentation genes do?
Specifiy the polarity of each segment
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What are Homeotic selector genes?
Specify the identity of each segment and direct the development body segments - master genes in the control network of regulatory genes
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What are the two gene families?
The complext that regulates the development of thorax and abdomen segments, the complex that regulates the devlopment of head and thorax segments
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how many base pairs do homeobox genes contain?
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How many amino acids make up the polypeptides produced by Homeobox genes?
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what are transciption factors?
Homeobox genes that bind to genes upstream and intiate transcription, so regulate the expression of other genes
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what are clusters that Homeobox genes are arranged in called?
Hox Clusters
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What is Apoptosis?
Programmed cell death that occurs in multicellular organisms , means 'falling off bones'
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What is the Hayflick consatnt?
Cells divide a limited number of times , cancer cells are immortal
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What is phagocytosis?
The endocytosis of large solid molecules into a cell
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Sequence of events of Apoptosis leaading up to phagocytosis
Enzymes break down the cell cytoskeleton, The cytoplasm becomes dense, with organelles tightly packed, the cell surface membrane changes and small bits called blebs form, Chromatin condenses and the nucleur envelope breaks, DNA breaks into fragment
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Cell signals that control Apoptosis?
Cytokines, hormones, growth factors, Nitric Oxide
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What is the role of Nitric Oxide in inducing apoptosis?
Making the inner mitochondrial membrane more permeable to hydrogen ions and dissipating the proton gradient, protiens are released into the cytosol which bind to apoptosis inhibitor proteins and allow process to take place
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What stage does the spindle form?
Prophase 1 and 2
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What stage does the nucleoulus disappear and the nucleaur envelope disintergrates?
Prophase 1 and 2
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At what stage do the Bivalents line up across the equator?
Metaphase 1
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At what stage does Random assortment occur?
Metaphase 1 and 11
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At what stage are the homologous chromosomes in each bivalent pulled by the spindle fibres to opposite poles?
Anaphase I
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What is the minimum number of gametes that can theoretically be produced by a human?
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What is the genotype?
The genetic makeup of an organism?
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What is a organism with two identical allels for a particular gene described as?
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Whats does Heterozygous mean?
Those with two different alleles for the same gene
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What does the mutation in CF do?
Disrupts the transport of chloride ions and water across the membranes of cells lining the airways, gut and reproductive tract. It changes the shape of the transmembrane chloride ions so that they can no longer function effectively.
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What is the charcteristics that are expressed in the organism known as?
The Phenotype
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What are Alleles called if they both contrubute to the phenotype?
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When is an allele said to be dominant?
If it is always expressed in the phenotype
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Defintion of Linkage?
Refers to two or more genes that are located on the same chromosome,normally inherited together
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What is Sex Linkage?
Where the gene that codes for a charcteristic is only found on one of the sex chromosomes
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What does Sickle-cell anaemia cause?
When abnoral haemoglobin is deoxygenated it is not soluble and becomes crstalline and aggregates into more linear and less globular structures, this deforms red blood cells making them inflexible and unable to sqeeze through the capillaries.
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what happends in sickle-cell anaemia?
After many cycles of oxygenation and deoxygenation, some cells become irreversibly sickled, some are destroyed , blood flow is impeded , organs can become damaged
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What is Epistasis?
The interaction of different gene loci so that one gene locus masks or supresses the expression of another gene locus
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How may the genes involved in Epistasis work?
Antagonistically or together in a complementary fashion
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What is hypostatic?
Where the alleles at the first locus are epistatic to the alleles at the second locus
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Is Epistasis inherited?
No, but it reduces phenotypic variation
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When does dominant epistasis occur?
when a dominant allele at one gene masks the expression of the alleles at a second gene locus
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What is the ration for recessive epistasis?
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What is the ratio for dominant epistasis?
12:3:1 or 13:3
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What is the ratio for epistasis by complementary action?
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how do you calculate the degrees of freedom?
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What does discontinuous variation describe?
qualitative differences between phenotypes, clear distinguishable categories, no intermediate categories
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What does continuous variation describe?
Quantitative differences between the phenoypes, no distinct categories, wide range of variation within the population
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What is monogenic?
When there is only one gene involed - discontinous variation
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Describe discontinuous varation?
Different alleles at a single gene locus have large effects on the phenotype, different gene loci have quite different effects on the phenotype, different gene loci have quite different effects on the phenotype
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Describe continous variation?
controlled by two or more genes, each gene provides an additive component to the phenotype,different alleles at each gene locus have a small effect on the phenotype, a large number of genes may have a combined effect on the phenotype - polygenes
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what is a polygenic characteristic?
One that is controlled by polygenes, genes are unlinked , they are on different chromosomes
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which traits, poygenic or monogenic, are influenced the most by the environment?
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What is a population?
All of the organisms of one species, who live in the same place at the same time, and who can breed together
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What is the gene pool?
The set of information carried by a population
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What does the Hardy-Weinberg principle measure?
The genetic diversity of alleles of an individual
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What did Darwin deduce?
That there is a competitve struggle for survival, there is varaition between individuals, those best adapted are more likely to survive and breed
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What is population genetics?
The study of gene pools and the allele and genotype frequencies of populations of organsims
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What is the Hardy-Weinberg principle?
The concept that both genotype frequencies and gene frequencies will stay consatnt from generation to generation, within a large interbreeding population where mating is random, there is no mutation , no selection or migration
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what assumptions does the Hardy-Weinberg principle make?
The population is very large(eliminates sampling error), mating is random, no selective advantage for any genotype, no mutation,migration or genetic drift
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what does p represent?
The frequency of the dominant allele
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what does q^2 represent?
the frequency of the recessive genotype
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What is a selection pressure?
An environmental factor that confers greater chances of survival to reproductive age on some members of the population
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What is the carrying capacity of a population?
The maximum population size that can be maintained over a period of time in a particular habitat
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What is environmental resistance?
The combined action of biotic and abiotic factors that limits the growth of a population
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What are abiotic factors?
non-living components of the environment
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What is stabilising selection?
A type of natural selection in which the allele and genotpye frequency within populations stays the same because organisms are well adapted to their environment
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What is directional selection?
leads to evolutionary change, where the selction pressure changes and a new charcterstic now gives organisms the selective advantage
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What are isolating mechanisms?
Geographic barriers, seasonal barriers (climate change), reproductive mechanisms
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What are reproductive mechanisms?
genitals incompatible, breeding seasons or courtship behaviours may vary
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What are fluctations or changes in allele frequency in a species called?
genetic drift
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What is the biological species concept?
a group of similar organisms that can interbreed and produce fertile offspring
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What is the phylogenetic species concept?
A group of organisms that have similar morphology(shape), physiology(biochemistry), embryology(stages of development) and behaviour and occupy the same niche
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Whats is a group that includes an ancestral organism and all its descendant species called?
A monophylectic group
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When is the biological species concept problematic?
When biologists want to classify living organisms that do not reproduce sexually, some members may look very different from each other
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Formula for % divergence(differences in base pair sequences)?
Number of substitutions/Number of base pairs analysed x100
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What are haplotypes?
specific base sequences
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What is a clade?
Any group of organisms with halotypes that are more similar to each other than those in any other group
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What is cladistics?
A method of classifying living organisms based on their evolutionary ancestry
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What a taxa?
A group of organisms used in hierarchical classification, e.g. Kingdom, Phylum, class
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How is cladistics different from taxonomic classification systems?
It focuses of evolution rather than on similarities between species, places greater importance on using objective and quantitative(molecular) analysis, it uses DNA and RNA sequencing, makes no distinction between extinct and extanct species
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How does cladistics use computer programming?
Uses this plus data obtained from nucleic acid sequencing to generate dendrograms or cladograms that represent the evolutionary tree of life.
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Why are mannual creations of diagrams not used in cladistics?
Because they would be extremely difficult to create when dealing with large numbers of species
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What does the term cladistics mean?
Comes from an ancient Greek word 'Klados' meaning branch
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What is a paraphyletic group?
One that includes the most recent ancestor but not all its descendants.It is a monophylectic group with one or more clades excluded, eg.g reptile and birds.
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What is the Linnaeon classification of organisms?
reflects evolutionary relationships, as well as monophyletic and paraphylectic groups as taxa.
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Why is cladistics significant?
sometimes led to organisms being reclassified, helped biologists understand evolutioanry relationships, confirmed Linnaean system of classification
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How do cow breeders practice artificial selection?
Each cow's milk yield is measured and recorded, progeny of bulls is tested to find out which bulls have produced daughters with high milk yields, semen from one bull collected and used to artificially inseminate cows,
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How do cow breeders practice selection 2?
Some elite cows are given hormones so they produce many eggs, the eggs are fertilised in vitro and embryos implanted into surrogate mothers, could be cloned or divided into more identical embryo
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What does the genus Triticum include?
Wild and domestic species of wheat
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What is the name of the genus that has contributed its genome to the modern bread wheat?
Aegilops/wild goat grass
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how many chromosomes do most wild wheat plants contain?
14 , n=7
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What is polyploidy?
Where plants nuclei can contain more than one diploid set of chromosomes
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Describe modern wheat bread?
6n, 42 chromsomes in the nucleus of each cell, larger nuclei so bigger cells, three distinct genomes
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Where has the genome AuAu come from in bread wheat?
Whild wheat species such as T.urartu
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Where has the genome BB come fom in bread wheat?
Wild emmer wheat, Y.turgidum (4n species)
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Where has the genome DD come from in bread wheat?
Wild goat grass such as Ae.tauschii
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Difference between winter wheat and spring wheat?
Winter wheat -Uk, soft grains, low protein content, biscuits. Spring Wheat- Colder winters,North America, grains are harder, higher protein content, bread
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What characteristics are focused on when artifically selecting Triticum wheat?
Resistance to fungal infections, high protein content, straw(stem) stiffness, increased yield, resistance to lodging(stems bending over in wind and rain)
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Which concept has been used to classify T.aestivum and einkorn wheat?
The cladistic concept as they are different species but can interbreed to produce fertile offspring
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What is vegetative propagation?
The production of structures in an organism that can grow into new individual organisms, clones of the parent
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Definition of a clone?
Genes, cells, or whole organisms that carry identical genetic material because they are derived from the same orginal DNA
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How do bacteria divide asexually?
binary fission
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What are the advantages of asexual reproduction?
It is quick, allowing the organisms to produce rapidly and so take advantage of resources in the environment, it can be completed if sexual reproduction fails/is not possible, all offspring have the genetic information to survive in environment
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What are the disadvantages of asexual reproduction?
no genetic variety, so any genetic parental weakness will be in all the offspring, more susceptible to environmental changes
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How do elm trees produce asexually?
Basal sprouts(root suckers)
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Where and why do Basal sprouts grow from?
From the Meristem tissue in the trunk close to the ground , becasue least amount of damage is likely to have occured here
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What is a clonal patch?
A circle of new elms around the orginal elm tree trunk
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What are tubers, give an example of one?
Specialised underground stems that become swollen with nutrient molecules from which plants grow - Potato
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What is a bulb?
A condensed shoot with a very short stem and a fleshy leaf base , containg nutrients - buds develop at the side into new bulbs
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Give an example of a bulb?
Daffodil, Onion
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What are runners , give an example?
Specialised stems that grow along the ground from the parent plant;at the tips they form roots and shoots - Strawberry
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What does a tissue cultue refer to?
The separation of cells of any tissue type and their growth in or on a nutrient medium.
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Describe how you would clone a plant by taking cuttings?
A section of the stem is cut between leaf joints(nodes). The cut end of the stem is then often treated with plant hormones to encourage root growth, and planted.
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What is grafting?
Where a shoot section of a woody plany is joined to an already growing root or stem
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Why are tissue cultures useful?
You can clone a a large amount of a plant , very quickly from a small amount of plant material that is disease free
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What is an explant?
A small piece of tissue taken from the plant to be cloned (usually the shoot tip)
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What is a callus?
A mass of undifferentiated cells
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What does the water jacket inlet in a fermenter allow?
The circulation of water around the fermenter to regulate temperature
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What does the air inlet in a fermenter do?
Provides sterile air and so oxygen in aerobic fermenters
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What does the pressure vent in a fermenter do?
prevents any gas build up
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What do the electronic probes in a fermenter do?
Measure oxygen,pH and temperature levels
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Why are all inlets and outlets in a fermenter fitted with filters?
To prevent contamination
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What is a bactch culture?
Starter population , mixed with a specific quantity of nutrient solution, allowed to grow for a fixed period, prodcuts are removed and tank is emptied
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Give an example of a product produced in a batch culture?
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What is a continous culture?
where nutrients are added to the fermentation tank and products removed at regular intervals or continuously
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Give an exampe of a product produced in a continous culture?
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Which type of culture has the slowest growth rate?
Batch as nutrient levels decline over time
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Which type of culture is the easiest to set up and maintain?
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In which type of culture is contamination most severe?
Continous as huge volumes of product may be lost
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Which type of culture is the most efficient?
Continous as fermenter operates all the time
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Which type of culture is used to produce primary metabolites?
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What is a contaminant?
Any unwanted microrganism
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Why are unwanted microorganisms damaging?
They compete with culture of nutrients and space, reduce the yield of useful products, may cause spoilage, may produce toxic chemicals, may destroy the culture microorganism and their products
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What does the term aseptic technique refer to?
Any measure taken at any point in a biotechnological process to ensure that unwanted microorganisms do not contaminate the culture that is being grown or the products that are being extracted
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What is the absence of unwanted microorganisms called?
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Describe the Aseptic techniques used at a laboratory and starter culture level?
All apparatus carrying microorganisms is sterilised before and after- heating in a flame until glowing, UV light, steam-sterlised at 121 degrees for 15 mins in an autoclave. Carry out work in fume cupboard or laminar flow cabinet,keep culture closed
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Describe Aseptic techniques and measures at large-scale culture level?
Washing,disinfecting and steam-cleaning the fermenter and associated pipes when not in use, surfaces made of polished stainless steel, sterilising all nutrient media before adding. fine filters on inlet and outlet
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Why is stainless steel used as an Aseptic technique?
to prevent microbes and medium sticking to the surfaces
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What is the immobilisation of enzymes?
Any technique where enzyme molecules are held, separated from the reaction mixture. Substrate molecules can bind to the enzyme molecules and the products formed go back into the reaction mixture leaving the enzyme molecules in place
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What is adsorption?
Where enzyme molecules are mixed with the immoblising support and bind to it due to a combination of hydrophobic interactions and ionic links, Agents include clay, resin, glass beads, porous carbon
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What is the extraction of enzyme from fermentation mixture known as?
Downstream processing
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What are the advantages of immobilising enzymes?
Purification costs are low, available immediately for reuse, more stable because of the matrix, less affected by temperature
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What are the disadvantages of immobilising enzymes?
additional time and equipment needed, so is more expensive to set up, can be less active as not mixed freely, contamination is costly
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Are the bonds in adsorption strong?
No, so enzymes can become detached (leakage)
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What is covalent bonding?
Molecules are covalently bonded to a support and to each other - e.g. clay particles using a cross linking agent like gluteraldehyde or sepharose
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Advantages and disadvantages of covalent bonding?
Does not immbobilise a large quantity of enzymes but binding is very strong so there is little leakage
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What is entrapment?
Enzymes may be trapped, for example in a gel bead or a network of cellulose fibres, trapped in natural state so active site not affected.
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Disadvantages of entrapment?
Reaction rates can be reduced because substrate molecules need to get through the trapping barrier, so active site is less easily available
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What is membrane separation?
Enzymes may be physically separated from the substrate mixture by a partially permeable membrane- enzyme solution held on one side whilst substrate solution passes along the other- can pass through
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what enzyme is used to convert penicillin into amino penicillanic acid on a large scale?
Acyclase - held in alginate beads
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What is genomics?
The study of whole set of genetic information in the form of DNA base sequences that occur in the cells of organisms of a particular species, placed in a public access data base
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What is DNA profiling (genetic fingerprinting) used in?
Crime scene analysis and paternity and maternity testing
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What are the process's used to research into the function of genes and regulatory DNA sequences called?
Genomic sequencing and comparative genome mapping
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What is genetic engineering used in?
the production of pharmaceutical chemicals, genetically modified organisms and Xenotransplantation
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What is gene therapy used for?
to treat conditions such as cystic fibrosis
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What is the function of non-coding DNA?
regulatory functions
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How many base pairs can a sequencing reaction operate on?
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why are overlapping fragments of DNA used in sequencing used?
to ensure greater accuracy
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What are microsatellites?
Short runs of repetitive sequences of 3-4 base airs found in several thousand locations on the genome
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What are microsatellites used for?
To map genomes to identify which part of the genome they have come from
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What is the 'shotgun' approach?
Where samples of the genome are sheared into smaller sections of around 100,000 base pairs
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What are clone libaries?
Many copies of the sections of the genome produced in culture
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How would you sequence a BAC section?
Cells containing specific BACs are taken and cultured, DNA is extracted and restriction enzymes are used to create smaller fragments, electrophoresis, automated process, computer programmes compare overlapping regions
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What is comparative gene mapping?
The comparison of DNA sequences coding for the production of proteins/polypeptides and regulatory sequences in the genomes of different organisms of different species
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What is the value of comparative gene mapping?
gives clues to the relative importance of genes to life, evolutionary relationships, effects of mutation, comparing pathogenic and non-pathogenic organisms, DNA of individuals can be analysed to identify mutant alleles
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What is electrophoresis used for?
To seperate DNA fragments based on their size
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Why is DNA negatively charged?
because of the many phosphoryl groups
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What is southern blotting?
A nylon or nitrocellulose sheet is placed over the gel, covered in paper towels, pressed and left overnight, the DNA fragments are transferred to the sheet
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How would you make DNA fragments visible on the sheet?
Label DNA with a radioactive marker before samples are run and place photographic film over sheet
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When can a radioactive probe be used?
If one particular fragment or sequence of DNA is being searched for
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What is a DNA probe?
A short single-stranded piece of DNA (around 50-80 nucleotides long) that is complementary to a section of the DNA being investigated
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How is a probe labelled?
Using a radioactive marker, usually by using 32P in the phosphoryl groups forming the strand so that the location can be revealed with film or by using a fluorescent marker that emits a colour on exposure to UV light
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What is the binding by complementary base pairing known as?
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How is a DNA microarray used?
It is a fixed surface with DNA probes on it, used to reveal faulty or mutated alleles
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What type of bonding is responsible for annealing?
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What are primers?
Short,single-stranded sequences of DNA, around 10-20 bases in length
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What does PCR rely on regarding the structure of DNA?
Antiparallel backbone strands, made up of strands with a 3' and a 5' end, grows only from the 3' end, complementary base pairing rules
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How is PCR different from natural DNA replication?
Can only replicate short sequences ( a few hundred base pairs), primers are required, heating and cooling used instead of DNA helicase
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What temperature is the mixture first heated to in PCR and why?
95 degrees, to break the hydrogen bonds
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Why are primers needed in PCR?
because DNA polymerase cannot bind directly to single stranded DNA fragments
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What is the temperature reduced to in PCR and why?
55 degrees, to allow primers to anneal at either end
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What is the temperature raised to the second time in PCR and why?
72 degrees as this is the optimum temp for DNA polymerase
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Why is DNA polymerase described as thermophilic?
because it is not denatured by extreme temperatures
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What happens in automated DNA sequencing if a modified nucleotide is added?
The polymerase enzyme is thrown off
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What does the laser read in automated DNA sequencing?
The colour sequence
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`What does transgenic mean?
When an organism contains DNA that has been added to its cells as a result of genetic engineering
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What is recombinant DNA technology?
processes that involve combining DNA from different organisms or from different sources in a single organism
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In GE where can the gene be obtained from?
the mRNA produced from transcription can be obtained in the cells where the gene is expressed, can be synthesised using an automated poly nucleotide sequencer, DNA probe can be used to locate gene and restriction enzymes used to cut it
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What vectors can be used in GE?
Can be sealed into a bacterial plasmid using ligase, sealed into a virus or yeast cell chromosomes
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Why do vectors often contain regulatory sequences of DNA?
To ensure that the inserted gene is transcribed in the host cell
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Why is it difficult to get a gene in a vector in a cell?
Because it can form quite a large molecule that does not easily cross the membrane to enter the recipient cell
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What methods are used to get the vector into the cell?
Electroporation- a high-voltage pulse is applied to disrupt the membrane, Microinjection- DNA is injected into host nucleus using a fine micropipette, viral transfer, Ti plasmids, Liposomes- DNA is wrapped in lipid molecules, fat soluble so diffuse
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How are Ti plasmids used as vectors?
They can be inserted into the soil bacterium, which infects the plant and inserts the plasmid DNA into the plans genome
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What is a sticky end?
A short run of unpaired exposed bases seen at the end of the cut section
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Another word for restriction enzymes?
Restriction endonucleases
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How do restriction enzymes work?
Enzyme catalyses a hydrolysis reaction which breaks th phospate-sugar backbones of the DNA double helix in different places
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What are the two main reasons for carrying out genetic engineering?
To improve a feature of the recipient organism, to engineer organisms that can synthesis useful products
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What do plasmids often carry?
Genes that code for resistance to antibiotic chemicals
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How is the rate increased at which plasmids are taken up by bacterial cells?
The addition of calcium salts and 'heat shock' - where the temperature of the culture is lowered to around freezing and then quickly raised to 40 degrees
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What are transformed bacteria?
bacteria that take up a modified plasmid
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What is a polypeptide?


A polymer Consisting of a chain of amino acid residues joined by peptide bonds

Card 3


What is the genome of an organism?


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Card 4


What is the specific place a gene occupies on a chromosome called?


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Card 5


What is the DNA in the chromosomes associated with?


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