1. 19. What is PCR? What advantage does this technique have over gene cloning?
PCR (Polymerase Chain Reaction) the amplification (large scale copying) of a segment of DNA; up to 100 billion copies in a few hours
BENEFITS
Faster than gene cloning
Only requires a small sample
DNA can be partially degraded

2. Briefly describe the process of PCR.
PCR animation
DNA sample is mixed with heat-stable DNA polymerase (taq polymerase), nucleotide monomers, and other ingredients
Exposure to heat denatures the DNA molecules
Primers hybridize target DNA
DNA polymerase attaches complimentary nucletoides
DNA is cooled to reanneal
Process repeats

3. 20. What is gel electrophoresis
20. What is gel electrophoresis? Why do the DNA fragments move through the gel? Why do the smaller fragments move farther? (12.10)
Gel electrophoresis acts as a molecular sieve to separate nucleic acids or proteins on the basis of charge and size
Fragments move because they are attracted to the positive pole (DNA is negatively charged due to phosphate groups)
Larger molecules get slowed down by fibers in the gel…have a harder time trying to navigate through the thick gel…smaller molecules make it further towards the + pole

4. 21. What is an STR and how are they used in a DNA profile?
Single Tandem Repeat (STR) : repetitive DNA sequences that lie in between genes and vary among individuals
used in DNA profiling
STR analysis: compares the length of STR sequences at 13 specific sites in genome

5. COmbined Dna Index System: database administered by FBI
22. What is CODIS? Name some famous cases where DNA profiling has been used.
COmbined Dna Index System: database administered by FBI
used all over world to search for DNA STR matches from crime scenes or suspects
OJ Simpson murder trial, Bill Clinton's indiscretions, used to exonerate 300 wrongfully convicted murderers, ID more than half of the victims of the WTC 911 attacks, paternity cases

6. 23. What are the chances that two non-related, randomly selected people would have the dame DNA profile?
Using the CODIS standard of 13 STR sites, chances are less than 1 in 10 billion.
ie; a standard DNA profile can provide a statistical match to a single individual

7. 24. Name some interesting uses of DNA profiling for non-human samples.
prove origin of imported food (ex: caviar)
provide origin of contraband animal products
show similarities between extinct and living species

8. 25. What is a SNP and its relationship to a RFLP
25. What is a SNP and its relationship to a RFLP? What can RFLP analysis be used for? Give an example
SNP (Single Nucleotide Polymorphism) = a single base pair variation in the genome
SNP's may alter a restriction site and thus change the length of restriction fragments formed by that enzyme
these sequence variations are called RFLP's (restriction fragment length polymorphisms)
RFLP's can be used to ID a mutant disease causing allele

9. RFLP animation
What are RFLPs? What two methods are used to do analysis of restriction fragments?
RFLP (Restriction Fragment Length Polymorphism) – when DNA is cut with restriction enzymes, size differences in homologous DNA sequences are reflected in the restriction fragments produced (depends on number of recognition sites)
(1) Gel Electrophoresis (separates strands based on length) and (2) DNA Probes (focus in on bands coming from sequences of interest)

10. What is a DNA Profile (fingerprint)?
DNA Fingerprint – a specific pattern of bands resulting from gel electrophoresis of RFLPs
Highly unlikely that two people will have the same fingerprint, HOWEVER, related individuals will share more banding patterns than unrelated individuals
Can be used to determine paternity or in criminal cases

11. Why are RFLPs useful in criminal cases?
Because everyone’s DNA is different, different fragment lengths will be produced for different people
Comparison of the gel electrophoresis from samples from the crime scene with samples from suspects can effectively rule people out or provide strong evidence of guilt
Fingerprint (12E) activity

12. 26. What is genomics and what can we learn from this branch of science?
the study of the complete set of genes (the genome) and their interactions
insight into evolutionary relationships and the genes shared amongst species.
insight into the function of a gene in one species compared to a similar gene in another species

13. to identify AND sequence all the human genes in the genome.
27. What was the goal of the HGP and how many years did it take to complete? Where is all this info stored?
to identify AND sequence all the human genes in the genome.
took 13 years
all info stored in a publicly available database called: GenBank

14. 28. What was the bigget surprise of the HGP? Explanations?
the small number of human genes - only about 21,000. Close to the number of genes in a microscopic worm. How do to account for our complexity with so few genes?
alt mRNA splicing

15. 98.5% of genome is non-coding DNA:
29 and 30. Name the locations of "junk" DNA and their possible functions. What are telomeres and transposons?
98.5% of genome is non-coding DNA:
introns, promoters, enhancer regions, microRNA's
"junk" DNA:
STR's
telomeric DNA at tips of chromosomes and and centromeric DNA at the centromere: provide chromosome structure
transposable elements (transposons: "jumping genes"): provide variability

16. Significant loss of telomere DNA  cell death!
What are telomeres? What is the relationship between telomeres and cell death? Telomeres and cancer?
Telomeres – repetitive sequences at chromosomal ends, possible involvement in protection of chromosomes
Significant loss of telomere DNA  cell death!
Stress has been proven to cause significant telomere shortening!!
“Too Much Stress May Give Genes Gray Hair”
Significant lengthening of the telomere can also lead to immortal cells (such as cancer) which evade normal cell aging

17. What are transposons? What do scientists think they are responsible for?
Transposons – “jumping genes,” DNA with long (100s of nucleotides) repeating segments that can move or be copied from one location to another on a single chromosome (or between chromosomes)
Along with disruption of gene function, believed to be responsible for the proliferation of dispersed repetitive DNA in the human genome

18. 31 and 32. Name some benefits of having the human genome mapped
31 and 32. Name some benefits of having the human genome mapped. Who was first to have genome mapped?
To identify all the genetic variations that affect human characteristics
Identify a genetic source to a number of human conditions and ailments
first human genome sequenced was a combination of individuals. This served as a reference standards
James Watson was first individual in 2007

19. 33. What is a proteome and what are the benefits of proteomics?
the full set of proteins encoded by a genome
humans have far more proteins (100,000) than genes (21,000)
benefits: we can see where and when certain proteins are made in different cells and how they interact with other proteins
gives a "whole system" understanding to the functioning of an organism

20. alternative RNA splicing 98.8% identical. Only 1.2% different
34. How do you explain the fact that humans have 5 times the number of proteins than the number of genes? 35. What % of human genome is identical from a chimp? What are some differences attributed to? 36. Significance of the FOXP2 gene in humans?
alternative RNA splicing
98.8% identical. Only 1.2% different
insertions or deletions of larger regions of the genome where repetitive DNA is located
gene implicated in speech and vocalization. This gene evolved more rapidly in humans than chimps

21. 37. Proof that H. neanderthalensis was a different species than H
37. Proof that H. neanderthalensis was a different species than H. sapien? Any genetic similarities?
H. neanderthalensis were human's closest relative in Europe and Asia
both species co-existed and co-mingled and probably interbreeded for a time
suddenly went extinct only 30,000 years ago
in 2009, a DNA analysis of 2 femur fossils from 2 Neanderthal females femurs was studied
Findings:
sapiens are more closely related to Neanderthals than chimps
Neanderthals had the same FOXP2 gene
another Neanderthal genome revealed a mutated allele for a pigment gene resulting in lighter skin color and red hair
analysis of lactase gene revealed that, just like many modern humans, H. neanderthalensis were lactose intolerant as adults