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Question 1

Model of DNA prac

Answer 1

(Look up diagram of DNA)

Made that with modelling clay and carboard, twist to make double helix

Question 2

Secondary Sources: Outline current understanding of gene expression:

Answer 2

A gene is fully expressed when its polypeptide is synthesised, converted to a protein and the protein is fully functional.

In eukaryotic cells genes are turned on/off, only 5% on at a time average.

Epigenetics-The processes by which genes are expressed and the inheritance of the result of these processes

Factors controlling gene expression:

Transcription- promoter sequences initiate transcription and regulatory sequences control sections, rate and number of copies made. Editing also effects expression.

Translation- mRNA can be deactivated if its protein it codes for is no longer required

Protein Activation- can be deactivated and broken down if no longer required.

Question 3

Example of characteristics determined by multiple alleles in an organism other than humans.

Answer 3

Cat Coat Colour:

(T)a = Abyssinian (ticked coat)
T = Mackerel Pattern (striping, M on forehead)
(t)b=Blotched Pattern (swirls)

(T)a > T > (t)b

Genotypes:
Abyssinian- TaTa, TaT, Tatb
Mackerel- TT, Ttb
Blotched- tbtb

Question 4

Compare the inheritance of ABO anf Rhesus blood groups:

Answer 4

(I)A and (I)B are co-dominant
(i)o is recessive

Rhesus refers to D antigen only
Rh+ (DD or Dd)
Rh- (dd)

Question 5

Describe the processes involved in the transfer of info from DNA through RNA to produce a polypeptide:

Answer 5

Transcription:
Initiation- enzyme RNA polymerase binds with region of gene called promoter. Signals DNA to unwind so it can read one strand.
Elongation-addition of nucleotides to the mRNA strand.
Termination-mRNA strand is complete, detaches from DNA

Processing:
-occurs in nucleus
May include-
Splicing-removing introns. Introns are regions that do not code for proteins (exons do). 
Editing-changing some nucleotides.

mRNA then leaves nucleus through nuclear pores

Translation:
same as in blueprint for life except multiple ribosomes my attach at different sites for efficiency, ribosome bound with mRNA is called a polysome

-mRNA runs through ribosome at start point. tRNA with anti-codon to match front most codon bind, adding amino acid to the sequence.

Question 6

Polygenic Inheritance?

Example?

Answer 6

Polygenic Inheritance = multiple genes influence a greater number of possible phenotypes

Contols characteristics that show continuous variation i.e. A spectrum not A or B.

Example is human height- frequency of human heights within a population can be graphed on a bell curve

Question 7

Outline the use of highly variable genes for DNA fingerprinting of forensic samples, for paternity testing and for determining pedigree of animals:

How DNA fingerprinting works?

Answer 7

• All organisms which undergo sexual reproduction have a unique set of DNA.
• The non-coding regions of DNA (introns) are highly variable useful for genetically identifying individuals.
• recombinant DNA techniques like DNA hybridisation all DNA to be compared to samples

Used in:
forensic testing-blood and body fluids in crime scene compared to DNA of suspects.
Paternity testing-
Animal pedigrees-insight into the mating habit of certain species, selection of animals based on genotype not phenotype.

How DNA fingerprinting works:

1) sample of DNA collected
2) restriction enzymes used to cut DNA into fragments at certain sequences
3) Gel Electrophoresis:
- DNA placed in gel and electric current is applied.
- As DNA is negatively charged it moves towards the positive electrode.
- Smaller fragments move faster
4) strands in each DNA fragment are separated and a radioactively labelled gene probe added (like dna hybridisation) and place on cellulose paper membrane
5) membrane is then placed on an x-ray film by which the radioactive probe can be seen on the screen

Question 8

Diploid and haploid to describe somatic and gametic cells

Answer 8

Somatic(body) cells are diploid(2n)

Gametic(sex) cells are haploid(n)

Question 9

Dihybrid cross:

Answer 9

Same as punnet square but 4 factors on each axes

Gives ratio 9:3:3:1

Shows law of independent assortment- genes separate independently during meiosis in the formation of gametes (for factors that arent linked)

Question 10

Linked Genes?

Outcome of a dihybrid cross when both traits are inherited independently compared to when they are linked?

Answer 10

Linked genes = genes located on the same homologous chromosome that are usually inherited together. During meiosis genes wont independently split , but pass on to the gamete together.

Example:
Snapdragons-flower colour and pollen grain shape

Long and purple linked, round and red linked (written as LP/lp (but like a proper fraction)

1) cross breed pure breeding long purple with pure breeding round red. Get all long and purple offspring (F1)
2)cross breed F1 generation
Would expect 9:3:3:1 usually
Would expect 3:1 ratio if perfectly linked
Actually get neither (280,20,20,50)
Due to recombination.

During meiosis chromosomes join together in x-shaped regions called chiasmata. Two inner chromatids join to form chiasma (crossing over). The two pieces break off and recombine with the opposite strands. The result is gametes with the new allele combinations.

The Further apart on the chromosome linked genes are the more likely they are to get crossed over.

Question 11

Prac to model linkage:

Answer 11

Use plasticine to create a pair of chromosomes each a different colour. Small buts of the coloured plasticine represent the position of genes. Chromosomes duplicated to form 2 chromatids which are exact copies of each other. Chromosome pairs separate and then chromosomes separate, to form gametes. Two gametes then join and form a diploid cell. The genes on the chromosomes never changed positions between chromosomes, thus modelling linkage.

Question 12

Explain how cross breeding experiments can identify the relative position of linked genes:

Answer 12

The further apart linked genes are the more likely the recombination of the genes. Thus by cross breeding organisms within a species true breeding for different expressions of the gene being observed we can see how far apart the linked genes are relative to each by how often they recombine (% of offspring with recombinant = # of map units apart)

e.g. (AB/ab) when an AB is crossed with an ab would expect 100% AB or ab) any percentage of Ab or aB shows crossing over.

Question 13

Role of chromosome mapping in identifying relationships between species:

Answer 13

Chromosome maps developed for various species can be compared to determine their genetic closeness. Allows for the comparison of genotype (i.e basic chemical structure) rather than just phenotypic expression.

Been used to show chimpanzees and humans are even more related than previously thought.

Question 14

Discuss the benefits of the Human Genome Project:

-What is a genome?

Answer 14

A genome is a complete set of genetic material of an organism.

Benefits:

Greater Understanding Of Genetics:

• How genes are expressed, inherited
• effect of gene mutation
• how genes interact with each other
• uncover the function of genes thats function is still unknown

Understanding of Human Evolution:
-comparing human genome to genomes of other species will give insight into the pathways of evolution

Detection of Disease and Improvement in Health:

• faulty genes can be detected before the disease can develop +genetic counselling for carriers.
• Normal genes can be cloned and the product of these genes used to treat diseased individuals (e.g. Insulin for diabetics)
• makes gene therapy possible giving a normal gene to someone with a defective copy.

Medicine:

• improved drug design to minimise sound effects
• development of gene control and gene control

Risk assessment:
-affect of exposure to radiation and toxins in high and low doses can be assessed to reduce risk of inherited disease.

Question 15

Describe and Explain the limitations of data obtained from the Human Genome Project:

Answer 15

• position and coding of the genes do not explain the complex biochemistry of a cell
• Does not explain the function of genes nor the protein which it codes for, just the position of the base sequences that make up the genes
• only a small proportion of DNA actually codes for proteins.

Question 16

Limitations of Gene Linkage maps and chromosome mapping:

-why couldnt it be used to map the genome?

Answer 16

For Human Genome Project:

• only show relative position of genes, not actual position.
• do not provide the DNA base sequence of a gene
• only possible for genes which produce observable phenotypic traits.

Also:

• lethal combo of genes will not be present in offspring, unreliable
• only easily tests externally visible traits
• reliability of cross-breeding program: long gestation period is a problem
• only shows relative position not actual position

Question 17

Process of the Human Genome Project:

Answer 17

1) build chromosome maps that contain landmarks (easily identifiable sections of DNA) using linkage maps.
2) Thousands of sequence landmark maps stored in E.coli cells as bacterial artificial clones (BAC), Each BAC broken down into smaller segments and stored in phages (virus). BACs can be frozen indefinitely until needed, thawed at 37C and stirred to oxygenate causing the bacteria to multiply rapidly.

3) Sequencing: requires-
-template DNA
-primers
-DNA polymerase
-bases (some with a dye attached, each letter having a different colour).
Primers attach to the template DNA to allow DNA polymerase to begin DNA replication as normal. When a base with dye attached is added to the sequence, coding stops.
The result being strands of different lengths with dye at one end and primer at the other.

4) Gel Electrophoresis:
-DNA placed in gel and electric current is applied.
-As DNA is negatively charged it moves towards the positive electrode.
-Smaller fragments move faster
-as they move through the gel, the dye on the end of each strand is read by a laser.
A computer then sequences the DNA strand and then maps the overlapping strands to produce a complete sequence.

Each time a sequence of 2000 bases is assembled it is published inline to allow labs all around the world to work on different sections.

Question 18

HAPMAP?

Answer 18

An international resource comparing the genomes of different populations, including those with and without certain diseases. A computer program compares the differences in the sequences in the hope of identifying a future solution.

Question 19

Recombinant DNA:
What is it?
Procedure to produce it?
Example?

Answer 19

Recombinant DNA- DNA including a section from another organism.

How:
‘Gene splicing’
1) Gene required is identified
2) Restriction enzyme is used to cut out the gene, leaving sticky ends which allow it to join with complementary sticky ends
3) The same restriction enzyme is used to split up the recipient DNA forming complementary sticky ends.
4 The gene is inserted into the recipient DNA and stabilised with DNA ligase.

Question 20

How can recombinant DNA technology be used to find the position of a gene on a chromosome

Answer 20

Using the appropriate restriction enzyme for that gene, the gene is cut out leaving the DNA in fragments. The fragments are then sorted via electrophoresis. The specific gene has thus been isolated and can be cloned many times. These are then tagged with fluorescent dye and used as probes to determine the position of the gene. This is done through dna hybridisation with an intact version of the chromosome (i.e. The dna from the gene is heated to denature it and the probe attaches to a single strand, due to complementary base pairs). The DNA probe can then be revealed via autoradiography.

Example: Human Insulin

1) gene cut from pancreas cell
2) circular piece of dna (plasmid) from E.coli cut open with same enzyme.
3) gene and plasmid mixed in same test tube, having both been cut by the same restrictive enzyme their sticky ends match and will stick together with help of ligase.
4) plasmid reinserted into the bacteria using calcium chloride (makes bacterial membranes porous)
5) bacterial cells reproduce, reproducing plasmid.
6) introduced gene will now be expressed by bacterial cells i.e. Make human insulin

Question 21

Gene therapy:
What is it?
Use for one identified disease?

Answer 21

Gene therapy- the treatment of disease by replacing, switching off or correcting faulty genes causing the disease
Steps:
1) Identify gene which causes the disease
2)locate the cells/tissues involved in the disease (symptoms)
3)creating multiple copies of the correct gene (gene splicing and recombinant dna into bacterial cells, usually E.coli)
4) inserting the correct gene to the affected cells by a satisfactory method

Gene therapy is still in the experimental stage, and while there had been some success using modified viruses as vectors there are problems:

• can cause immune response
• cannot penetrate past the outmost layer of cells, which are usually the first to be shed, cells behind unaffected

Example: Cystic Fibrosis
Caused by the deletion of 3 nucleotides from the CFTR gene on chromosome 7 which regulates the movement of Cl ions in and out of cells.

CF patients have a build up of Cl ions in their cells, affecting homeostasis, resulting in dehydrated mucous membranes with stickier thicker mucus.
Result-increased susceptibility to respiratory infections as barriers (cilia and mucous membranes) do not function effectively.
-incorrect functioning of liver and pancreas.

Question 22

Test cross:

Answer 22

Heterozygous with homozygous recessive

Gives 1:1 ratio if genes are linked

Question 23

Distinguish between mutations of chromosomes including

• rearrangements
• frameshift
• base substitution
• change in chromosome number

Answer 23

Rearrangements:

• duplication
• inversion
• translocation
• amplification

Frameshift: changes how the sequences is read

• deletion
• insertion

Base Substitution: self explanatory

Change in Chromosome number:

• Aneuploidy (n-1, n+1)
• polyploidy (2n, 3n)

Question 24

Describe the effect of a named genetic mutation on human health:

Answer 24

Down syndrome

Question 25

Outline the ability of DNA to repair itself:

Answer 25

DNA replication occurs regularly and damage to DNA is common. As such there are over 100 genes for DNA repair.

Usually operate during DNA replication but some operate continuously to repair spontaneous damage.

Example:

• enzyme removes damaged section
• DNA polymerase adds correct bases
• 3rd enzyme repairs break in DNA backbone

Sidenote: these methods of DNA repair are incredibly similar in all organisms. Relevant as high levels of radiation on early earth imply need to repair mutations in DNA was needed and thus indicates common ancestry.

Question 26

Describe the way transposable genetic elements operate and discuss their impact:

Answer 26

Transposons are sections of DNA which can move from one position on a chromosome to another position on the same chromosome.

Transposons operate by:
-inserting themselves into a gene causing a frameshift mutation
OR
-inserting themselves into flanking DNA (regulatory gene) turning a gene on or off

Impact on the Genome:
If a transposon inserts itself into a functional gene, it will probably damage it, the frameshift mutation altering the genes activity resulting in deregulation of the reading of genes (wont be functional), destabilisation of cells and changes in phenotypic characteristics.

However transposons can correct other mutations by inserting themselves in the site of the mutation and turning genes on or off and then removing themselves from the site.

E.g. When a retrotransposon moved into the DNA flanking the gene for pigment synthesis in grapes it produced white grapes from black-skinned ancestor.

Question 27

Germ Line vs Somatic mutations

In terms of effect on the species

Answer 27

Somatic mutations occur in body cells. Only effects the individual and is not inherited, thus does not affect a species.

Germ line mutations arise in gametic cells, in the ova or testis. The mutation will be passed onto offspring. This provides variation in the species upon which natural selection can occur, thus affecting the characteristics of a species.
-THIS IS HOW A NEW ALLELE IS CREATED

Question 28

Explain why selective breeding had been practised:

Example from agriculture?

Answer 28

Cross breeding combines favourable characteristics and produces breeds that are stronger and healthier (hybrid vigour). However if done indiscriminately can still result in a degradation of quality.

Selective breeding is the manipulation of the phenotype of the offspring to achieve desirable characteristics (via selective cross breeding) like resistance to disease, increased yield in crops and productivity in animals.

E.g. Belgian Blue Cow
Selectively bred for muscle mass for increased meat production, double the muscle mass of an average cow.

Question 29

History of the selective breeding of one species for agricultural purposes and describe the changes to the species as a result:

Answer 29

• Cereal crops first domesticated in 9000BC in the middle east, annuals including wheat
• new breeds formed by pollination with wild grass. Farmers select and replant the best seeds, over generations creating wheat unrecognisable from wild ancestors.

1788- farmers in australia can only grow wheat in areas of good rainfall and soil.

1890- steam rust becomes prevalent ruining crops

William Farrer noticed a few varieties of wheat with resistance to rust and began crossbreeding experiments.

1902- Farrer releases variety of wheat called ‘Federation’ which:

• matured early
• high yield
• resistance to rust

Soon over 80% of wheat grown in Australia was federation, became a net exporter of wheat.

Question 30

Gene Cloning?

Example?

Answer 30

Gene cloning: when a gene is located and and an identical copy created (cloned) out of DNA extracted from an organism.

This can be achieved through recombinant DNA technology, creating many copies of the gene and insert them into a plasmid.

E.g. Cloning of human insulin gene, human growth hormone

(Diagram in booklet)

Question 31

Distinguish between gene cloning and whole organism cloning:

Answer 31

Gene cloning- involves the production of identical single genes for specific purposes. This will transfer copies of single genes from one organism to another and result in many copies of the gene when those organisms reproduce.

• introduces new gene to a species
• used in gene therapy

Whole organism cloning- involves the transfer of the entire DNA in a somatic cell to a cloned organism. (Process examined earlier). The organism will therefore have its DNA entirely identical to the original cell (original organism).
-plants grown from cuttings will also be genetically identical

Question 32

Dolly the sheep:

Method-

Ways to verify animal produced is in fact a clone-

Answer 32

Method:
-entire DNA from an adult mammary cell (nucleus of a somatic cell) was taken and inserted into an enucleated egg cell from a sheep.

• The composite cell was fused with pulses of electric current, the result being genetically the equivalent to a zygote.
• electrical impulses stimulated cell division and the resulting embryo was implanted in a surrogate mother and gestate as normal.

Ways to verify animal produced was in fact a clone:

• DNA fingerprinting
• DNA hybridisation

Question 33

Discuss a use of cloning in animals or plants that is beneficial to humans:

Answer 33

BT Cotton:
-contains a gene for a protein from a bacterium that kills pest caterpillars but is harmless to humans and most animals.

-artificial gene containing the bacterial gene combined with a sequence from the plant gene (as bacteria use different regulatory sequences), is inserted into the cotton plant, cuttings (clones) of which are grown in tissue culture.

Limitations/problems: (pros are self-explanatory)
-constant exposure to a toxin creates evolutionary pressure for pests resistant to that toxin, creating a toxin-resistant population over time.

• expression of Bt gene can vary e.g. Lower toxin production in non-ideal temps.
• outcompetes normal cotton (both in terms of farm production and in the wild) therefore reducing genetic variability of the species over time, increasing their susceptibility to selective pressures.

Question 34

Describe the evidence which indicates the presence of ancestral vertebrate gene homologues in lower animal classes:

Answer 34

Gene homologues- sequences of DNA that are very similar and occur in different organisms.

Homologous structures like the pentadactyl limb provide evidence for evolution. Gene homologues do similarly on a molecular level.

Homeotic genes are highly conserved particularly a similar region of 180 bases they all share, the homeobox.

These genes are present in organisms vastly separated on the evolutionary scale. An example of a homologue is the gene cascade for the development of limbs, similar in rodents, molluscs, insects, humans, chickens etc.

A mouse homologue gene can regulate the corresponding gene in fruit flies.

Genes for repairing DNA is similar in all eukaryotes. Though to be because the high levels of radiation experienced on earth when life began meant mutation was common, thus repair necessary.

Biochemistry: Cells contain similar amino acids, nucleotides, sugars and fatty acids.
Chemical processes like protein synthesis are also similar.

Palaeontology and comparative embryology shows similar involving homologue genes in the development of bones, brain, limbs etc.

Question 35

How is it possible for different gene sequences to produce the same protein?

Answer 35

DNA sequence is made up of triplets (codons) that provide the info for specific amino acids. There is more than one codon that codes for a particular amino acid, so different codes can produce the same protein

Question 36

Gene glossary:

Answer 36

Two types of gene:

1) STRUCTURAL GENES- code for polypeptides that may produce structural proteins or enzymes.
2) REGULATORY GENES- control the expression of structural genes (can turn them on and off).

There are far more structural genes than regulatory genes meaning a small mutation in a regulatory gene can make a radical change in the expression of a whole string of structural genes

Homeotic Genes (both structural and regulatory): genes that control or regulate the the way in which organisms develop by producing proteins (transcription factors) which bind to DNA and switch genes on or off (according to position in the embryo, determined via morphogen gradients), important for differentiation of cells and 
to direct the development of a specific body part.

Homeobox: a sequence of 180 bases for regulating embryonic development found in all homeotic genes

Hox: a type of homeotic gene, set up the basic regional layout of an organism (eyes where the eyes should be etc)

Hedgehog Genes: hox genes that play a critical role in the patterning systems of limbs and spinal cord.

Homeotic genes are highly conserved so much so that a chicken can function perfectly well with a hox protein from a fly and vice versa.

DNA hybridisation found humans and chimpanzees are 98% genetically similar, indicating no more than 2% of our DNA is regulatory genes that differ us from chimps which are responsible for all phenotypic differences.

Question 37

Role of genes in embryonic development:

Answer 37

On fertilisation, zygote is formed containing all genes necessary to grow into a new individual.

As mitosis occurs, embryo grows into a mass of undifferentiated cells. As the embryo develops, cells differentiate and specialise according to the genes which regulate their developments, resulting in different genes switched on or off within the cell changing their metabolism and structure, becoming nerves, circulatory system etc.

The activities of genes are regulated by other genes to control, cell activities (the production of proteins and enzymes) at different times during development, turning on or off other genes according to their position, function and age of the embryo (determined via morphogen gradient).

E.g. During embryonic development the genes for cellular respiration are active in all cells. Hence the genes are switched on, expressed, in all cells.

Hox genes act to switch on the development of major body parts. The transcription factors they produce switch on a sequence of genes called a gene cascade to build a complex body part like a limb. If the wrong hox gene is stimulated the body part will grow in the wrong place in the embryo.

Question 37

Role of gene cascades determining limb formation in birds and mammals:

Answer 37

Gene cascade: a gene regulated sequence of development that occurs in embryos involving the turning on or off of genes in a particular order.

The development of limbs requires many genes to be switched on or off in the appropriate sequence to form muscles, bones, blood vessels, nerves, etc in the correct arrangement in the limb.

In mammals and birds the limb develops from anterior to posterior. The base of the limb developed before the end.

It is Hox genes that specify the anterior-posterior axis by producing the transcription factors that switch on the other genes, triggering the gene cascade. Other homeotic genes turned on then release more transcription factors and continue the cascade.

A major feature of the cascade is morphogen gradients, chemicals that diffuse across the cell tissues. Thus the gradient acts as a positioning system that tells a cell where in the body it is by the concentration present, allowing the cell to know where it is and thus what how to specialise. This ensures the genes are switched on in the right sequence in the right places to form the limb.
These gradients also turn on other homeotic genes for the cascade.

E.g. Failure of homeotic genes in the formation of a chicken wing or arm of a human can result in the radius and ulna not being formed

Humans still have the genes for the monkey-like tail and when occasionally gene regulation fails a human is born with a tail.

Gene cascade to produce ribs required morphogen gradient to switch on or off Hox6 (promotes rip production) and Hox10 (stops it)

Question 37

Evidence available from current research about the evolution of genes and their actions:

Answer 37

The result of HGP and increasing number of animal sequencing projects provide a powerful tool for investigating evolutionary relationships.

The presence of homeotic genes in almost all multicellular animals implies these genes evolved from a common ancestor. Similar in structure and function (control the pattern of body formation in embryonic development by encoding for transcription factors, important for cell differentiation) in all cases.
E.g. Gene at the top of the cascade that produces eyes in mice so similar it can be replaced with the equivalent gene in insects and vice versa.

Genes for repairing DNA is similar in all eukaryotes. Though to be because the high levels of radiation experienced on earth when life began meant mutation was common, thus repair necessary.

However research has also shown evolution in genes:

• shows an increase in homeotic genes over time via gene duplication i.e. Animals appearing earlier in geological history show a smaller number of homeotic genes.

-research indicates that the gene coding for haemoglobin evolved from that of myoglobin. Both are oxygen carrying proteins, myoglobin is made of one polypeptide and coded for by one gene, carrying limited oxygen while haemoglobin is 4 polypeptides thus coded for by 4 genes and carries more oxygen.
This indicates evolutionary progress as the genes for haemoglobin give an advantage.

Discovery of homeotic genes supports theory of evolution and punctuated equilibrium by showing that small mutations of these genes can result in large changes to morphology

(e.g. Human tail thing)

Question 38

Secondary sources: available evidence to assess the evidence analysis of genes provides for evolutionary relationships:

Answer 38

Because genetic information is passed through reproduction, analysing genes is invaluable to determining evolutionary relationships between organisms. Closely related=similar genes.

DNA hybridisation shows humans and chimpanzees 98% genetically similar, greater than previously thought.

Can also disprove previous evolutionary trees. Through dna hybridisation and DNA sequencing shown that closest living relative to the flamingo is not the long legged, graceful waddling bird but the squat grebe. Thus demonstrating that physical similarity does not necessarily mean genetic similarity (due to convergent evolution)

Question 39

Diploid number?

Answer 39

Number of chromosomes present in a bodies diploid cell

Question 40

Restriction Mapping:

Answer 40

Maps can be produced by cutting DNA with restriction enzymes and separating the fragments generated by electrophoresis. By comparing the size and number of fragments, one can look for the greatest number if similarities to find the most clearly related species.

Question 41

Gene expression:

Answer 41

Gene code is synthesised (via

Transcription and translation) into a function protein. That protein is put to use.

Question 42

What is the human genome project?

Answer 42

An international project to determine the position of every gene on each of the chromosomes of humans and the base sequence of each of these genes.