1. Frontiers of Biotechnology
Biology 1 Chapter 9

2. 9.1 Manipulating DNA Techniques used to manipulate DNA
Artificial nucleotides used to sequence genes
Artificial copies of genes used to study gene expression
Chemical mutagens used to change DNA sequences.

3. Computers analyze and organize data from genetics research.
Enzymes are used to cut and copy DNA.
Bacteria provides a mechanism to transfer genes between organisms.

4. It is easier to study genes if DNA can be broken down into smaller pieces.
Scientists use enzymes that act as molecular scissors that slice apart DNA.
The enzymes used come from different types of bacteria.
Bacteria produce enzymes that cut up the DNA of viruses.

5. A restriction enzyme or endonuclease is an enzyme that cuts DNA molecules when they identify a specific sequence.
Restriction enzymes cut DNA molecules in several places at once.
Any time the enzyme finds the exact DNA sequence, it cuts the DNA molecule.

6. The sequence of nucleotides that is cut by a restriction enzyme is called a restriction site.
Restriction enzymes are given this name because they restrict or decrease the effect of the virus.
There are hundreds of known restriction enzymes that cut DNA in different ways.

8. Some restriction enzymes make cuts that leave tails of free DNA bases.
These tails are called sticky ends.
If two pieces of DNA with sticky ends come close, the two segments may join.
These types of enzymes are often used in biotechnology.

10. Several things can be done with DNA that has been cut with restriction enzymes.
But before anything can be done, the DNA fragments have to be separated from one another.
Fragments are sorted by size by a technique called gel electrophoresis.

11. In gel electrophoresis, an electrical current is used to separate DNA fragments.
DNA has a negative charge so fragments move toward the positive end of the gel.
The gel also has small pores so molecules can move quickly. Larger molecules move slowly.

13. The length of a DNA fragment can be estimated by the distance it travels.
DNA fragments of different sizes appear as different bands on the gel.
The pattern of bands is like a map of the original strand of DNA.
This type of map is called a restriction map that shows lengths of DNA fragments.

14. Restriction maps can be used to study mutations.
Mutations may add or delete bases between restriction sites which would change the length of the DNA fragment.
Mutations can also change restriction sites.

15. Restriction maps are very useful in genetic engineering and diagnosing genetic diseases.
Comparisons can be made between two samples of DNA.
If restriction maps are different then it can be determined that a disease causing allele is present.

16. 9.2 Copying DNA
In order for scientists to get an amount of DNA that is large enough to be studied, they copy of segment of DNA.
Polymerase chain reaction (PCR) is a technique that produces millions of copies of a segment of DNA.
Polymerase enzymes that help copy DNA are used in this process.
Heat is used to separate DNA strands.

17. Steps of Polymerase Chain Reaction:
Separating of DNA segments by heat
Binding of primers to DNA strands once the DNA has cooled.
A primer is a short segment of DNA that acts as a starting point.
Copying by heating the DNA to temperature where polymerases work best.

18. 9.3 DNA Fingerprinting
A DNA fingerprint is a representation of parts of a person’s DNA that can be used to identify a person at the molecular level.

19. A DNA fingerprint is a type of restriction map.
A DNA is cut with restriction enzymes
The DNA fragments are run through a gel and a pattern of bands appears.
The pattern is analyzed.
DNA fingerprints can show family relationships.
DNA fingerprints of children are combinations of their parents.

21. DNA fingerprinting focuses on noncoding regions of DNA or sequences outside of genes.
Noncoding DNA sequences include stretches of nucleotides that repeat several times.
A DNA fingerprint shows differences in the number of repeats of DNA sequences.

22. When there are more repeats, a DNA fragment is larger.
The pattern of DNA fragments on a gel represents a person’s unique DNA.
DNA fingerprinting is used in identification:
Nucleotide sequence repeats are found in everyone
The number of repeat sequences can differ greatly, even among siblings.

23. Identification with DNA fingerprinting depends on probability.
DNA fingerprinting compares at least 5 regions of the genome.
The more regions of DNA that are studied, the less likely that someone else would have the same fingerprint.
Fingerprinting is very reliable for identification.

24. DNA fingerprints are often used in legal cases.
PCR can be used to make large samples of DNA so evidence can come from a single drop of blood.
DNA fingerprints have been used against suspects but have also been used to prove someone’s innocence.

25. DNA fingerprints can prove family relationships such as paternity and kinship.
Bone fragments can be sequenced to identify victims of major catastrophes or settle historical debates.
This process has been used to identify the parents of lost children.

26. 9.4 Genetic Engineering
A clone is a genetically identical copy of a gene or organism.
The process of cloning is common in nature.
Identical twins are clones
Binary fission produces clones
Many plants naturally clone themselves
Some simple animals clone through regeneration.

27. Mammals cannot clone themselves
To clone a mammal, DNA is swapped between cells in a process called nuclear transfer.
An unfertilized egg is taken from an animal
The egg’s nucleus is removed
The nucleus of a cell from the animal that will be cloned is implanted into the egg.
If the egg begins to divide and forms an embryo, it will be transplanted into a female.

28. A clone does not always look exactly like the original and will probably not behave like the original.
This is because many factors such as the environment effect gene expression.

29. Scientists are now studying how to use organs from cloned mammals for transplant into humans.
Cloning could help save endangered species.
Cloning is controversial due to low success rates, premature aging, and ecological concerns such as reduced biodiversity.

30. Genetic research relies on the cloning of individual genes.
Scientists insert cloned genes from one organism into a different one.
The changing of an organism’s DNA to give the organism new traits is called genetic engineering.
Genetic engineering is possible because all organisms share the same genetic code.

31. Recombinant DNA is DNA that contains genes from more than one organism.
Recombinant DNA could be used in plants that make medicines and vitamins.
Scientists are also studying ways to use this technology in vaccines to protect against HIV.

32. Bacteria are commonly used in genetic engineering because they have tiny rings of DNA called plasmids.
Plasmids are closed loops of DNA that can replicate on their own.
Recombinant DNA is commonly found in bacteria because they naturally take DNA from other organisms and add it to their own DNA.

33. Scientists have been able to make artificial recombinant DNA:
Restriction enzymes are used to cut the desired gene from a strand of DNA.
Plasmids are cut with the same enzymes
The plasmid opens and the gene is added to the plasmid.
The sticky ends are bonded together by a process called ligation.

34. After a gene is added to a plasmid, the plasmid can be put into bacteria.
The bacteria become tiny gene factories that make several copies of the new gene.
The bacteria will express the new gene and make that gene’s product.

35. The bacteria with the recombinant plasmid are called transgenic.
A transgenic organism has one or more genes from another organism inserted into it’s genome.
Transgenic bacteria have been used to make human insulin that is used to treat people with diabetes.

36. Genetic engineering in plants
A gene is inserted into a plasmid and the plasmid is inserted into bacteria.
After the bacteria infect the plant, the new gene becomes parts of the plant’s DNA and is expressed.
This has allowed scientists to give new traits to plants such as natural pesticides.
This process has also increased crop yield.

37. Genetic engineering in animals
Transgenic animals are harder to produce than plants.
Animals are more resistant to genetic manipulation
To produce a transgenic animal, a researcher must first get a fertilized egg cell.

38. The foreign DNA is inserted into the nucleus.
The egg is implanted back into a female.
Only a small percentage of the eggs mature normally.
Only a portion of those that develop will be transgenic. Only a small number will have the foreign gene as part of their DNA.

39. Transgenic mice have been used to study cancer and anti-cancer drugs, diabetes, brain function and development, and sex determination.
Some mice have genes that have been turned off.
These mice are called gene knockout mice which are made by disrupting the function of a gene.

40. Knockout mice are very useful:
Gene function can be studied
Genetic diseases can be studied
Changes in gene expression and traits can be observed

41. Concerns about genetic engineering
Possible effects of genetically engineered organisms on human health and the environment.
Is genetic engineering ethical?
Not enough research has been done and some added genes to crops might cause allergic reactions or other side effects.

42. Possible effects of genetically modified plants on the environment and biodiversity.
Effects on insects that pollinate plants
Unknown effects of interbreeding
Decreased genetic diversity.

43. 9.5 Genomics and Bioinformatics
A genome is all of an organism’s genetic information.
Genomics is the study of genomes and includes sequencing all of an organism’s DNA.
Scientists compare genomes to find similarities and differences.

44. Comparing DNA helps researchers find genes that cause disease and understand how medications work.
Comparing DNA can also help scientists study relationships between species and interactions among genes in an organism.

45. Steps of gene sequencing:
Gene sequencing is determining the order of DNA nucleotides in genes or a genome.
Steps of gene sequencing:
A radioactive primer is added to a single strand of DNA
Polymerase builds a short segment of a new DNA strand.

46. The lengths of the new strand are controlled so they can be separated by gel electrophoresis.
Based on the pattern of DNA fragments on the gel, the DNA sequence of the original strand can be put together.

47. Humans do not have the largest genome.
There are somewhere between 30,000 and 40,000 genes in the human genome.
The human genome has at least 3 billion base pairs.
This gives an average of about 1 gene in each sequence of 100,000 base pairs.

48. The human genome project has 2 goals:
Map and sequence all of the DNA base pairs of the human chromosomes.
Identify all of the genes within the sequence.
HapMap is a project used to study how DNA sequences vary among people and how this may play a part in diseases.

49. Most biological processes and physical traits are the result of interactions among many different genes.
Bioinformatics is the use of computer data bases to organize and analyze biological data.

50. Bioinformatics can be used to:
Store, share, and find data
Predict and model the functions of genes and proteins
Find genes that code for known proteins
Find the genetic basis of diseases and causes of diseases.

51. DNA microarrays are tools that allow scientists to study many genes and expression at once.
It is a small chip that is dotted with all of the genes being studied. One chip can hold thousands of genes.
The genes are laid out in a grid pattern

52. Complementary DNA (cDNA) is labeled with a fluorescent dye and is added to the microarray.
cDNA is made from an mRNA molecule.
The cDNA is identical to a gene’s DNA sequence.

53. A glowing dot on the computer program shows a match.
This allows scientists to determine which genes are expressed and how much they are expressed.

55. Proteomics is the study and comparison of all the proteins that result from the genome.
Proteomics includes the study of the functions and interactions of proteins.
Proteomics has benefits in studying comparisons among organisms, and the causes and treatments of diseases.

56. 9.6 Genetic Screening and Gene Therapy
Genetic screening is a process of testing DNA to determine a person’s risk of having or passing on a genetic disorder.
Genetic screening is used to look for specific genes or proteins that indicate a disorder.

57. There are tests for about 900 genetic disorders.
While genetic screening can help save lives it also leads to some difficult choices.
Is the information helpful or harmful?
Should screening be required?

58. Gene therapy is the replacement of a defective or missing gene, or the addition of a new gene.
For gene therapy to work, the new gene must get into the correct cells of a patients body.
Once in the body, the gene has to become part of the cell’s DNA.

59. One method of gene therapy involves taking a sample of bone marrow stem cells and infecting it with a genetically engineered viruses.
The stem cells are put back into the patient’s bone marrow.

60. Much of gene therapy is still experimental.
Researchers are studying methods to treat cancer.
Genes that stimulate the immune system to attack cancer cells
Suicide genes in cancer cells

61. Challenges of gene therapy
Correct gene has to be added to correct cells
Gene expression has to be regulated
Will the new gene affect other genes
Few long lasting positive results have been observed in trials