Lecture 2- Genomes and Evolution

Question 1

What are the two definitions of Genome?

Answer 1

1. ) An organisms entire DNA/RNA sequence.

2. ) All the organisms collection of genes.

Question 2

What are the units of both genetic maps and physical maps?

Answer 2

• Genetic maps have units in recombination frequency (Rf), centiMorgans (cM) and map units (m.u.)
• Physical maps have units in base pairs (b.p)

Question 3

Why does a genetic map come before a physical map?

Answer 3

• For genetic maps you only need to know the sequences for the two alleles that you are studying, so you can which traits the parents and offspring posses.
• For physical maps, you need to know the base sequences of the whole region.

Question 4

Do physical and genetic maps distances relate?

Answer 4

No, they do not.

Question 5

Where are recombination frequencies most common? (Where is Rf higher?)

Answer 5

• Recombination frequencies are less common near centromeres and more common near telomeres.

Question 6

Are recombination frequencies constant throughout each individual?

Answer 6

No, gender, ethnicity, and environmental factors all play a role in individual Rf.

Question 7

Describe genetic/DNA markers in a genetic map. What do blue markers mean?

Answer 7

• Genetic markers help determine the position of genes.
  Ex.) D1S440
• D = DNA, 1 = chromsome 1, S= single copy sequence (occurs once in the gene), # = location on the gene.
• Blue markers indicates known genes.

Question 8

How are physical maps created (positional cloning) and are they better are worse in displaying distances between genes?

Answer 8

• Physical maps are better at displaying gene distances. 1.)Enzymes cleave the DNA into fragments and are added to vectors to be cloned. ‘
  2.) Allow the enzyme to partially digest the DNA, so some fragments will overlap other fragments.
  3.) Computer fragments align the clones and put them in their proper order.
  Results:
  1.) If your clones overlap, then you know you have gap-free sequencing. Your clone overlaps with the end of one strand and at the beginning of another strand.
  2.) If you fail to capture a fragment in your vector and therefore don’t have that part of the sequence, then you will see a gap in your sequence where your clones don’t overlap.

Question 9

How can there be a discrepancy between a physical and genetic map?

Answer 9

• A sample size error (in a small population) can cause the genetic map to have a discrepancy in the location of its genes.
• This is because the small population study may have not included a representative of families which there was a recombination between two genes.

Question 10

Is genome size correlated with organism complexity? If not, what is?

Answer 10

• A large genome size does not mean you are a more complex organism.
• More protein diversity is what makes a more complex organism.
• More protein domains in more combination are the key.

Question 11

What are genes families? Describe them.

Answer 11

• Genes families are genes that come from a common ancestor but have had the time to diverge from one another through sequence changes that occurred after duplication.
• These genes can be mutated and not function anymore, have the same function, or even have a different function.

Question 12

What does homologous mean in genes? What are orthologs? What are paralogs?

Answer 12

• Homologous genes are genes that are related through evolution
• Orthologs are homologous genes that are found in different organisms but come from a common ancestor.
• Paralogs are homologous genes that are found in the same organism and arose from a past duplication.
  SEE PICTURE

Question 13

What are unique, moderately repetitive, and highly competitive sequences? Do repeated sequences usually contain genes? If so, which ones do and which ones don’t?

Answer 13

1. ) Unique sequences: only found once throughout the genome.
2. ) Highly repetitive sequences: about 5-300 base pairs long.
3. ) Moderately repetitive sequences: about 150-300 base pairs long.
   - Unique and highly repetitive sequences usually do not contain genes but moderately repetitive sequences contone histone protein genes and some rRNA and tRNA genes.

Question 14

What are the types of repetitive sequences?

Answer 14

1. ) Tandem repeats are sequences that are repetited back to back in a row.
2. ) Interspersed repeats are sequences found throughout the genome usually due to transposable elements.
   (a. ) Small Interspersed Elements (SINEs): Approx. 200-300 base pairs long.
   (b. ) Long Interspersed Elements (LINEs): Approx. thousands of base pairs long.

Question 15

What are polymorphic sequences? And how do they relate to individualism?

Answer 15

• Polymorphic sequences are different specific versions of sequences within a gene.
• The code for different alleles which leads to different phenotypic traits in individuals.
• Polymorphic sequences lead to different protein versions called isoforms which may have different activity in different individuals.

Question 16

What are the different types of polymorphic sequences?

Answer 16

1. ) Single nucleotide polymorphism: Different individuals may have a different base pair in a certain spot compared to others.
2. ) Insertion/deletion polymorphism: Some individuals may have a certain stretch of sequences while others may not have this stretch.
3. ) Copy number variations (CNVs): An individual may have a single copy or more than two copies of specific sequences.
   - These can give individual advantages or disadvantages.
   ex. ) More transcription, faster translation, may metabolize drugs faster, etc.

Question 17

What are transposable elements? What are they also known as and what are the two different kinds?

Answer 17

• Transposable elements can move from one place to another within a cells DNA.
• They are also called transposons
  (a. ) Nonreplicative transposons “cut and paste” themselves by moving from one spot and inserting themselves in another spot.
  (b. ) Replicative transposons “copy and paste” themselves by creating a copy of themselves which then inserts themselves within another spot of DNA.

Question 18

What is the purpose of a hybridization study and what is the process?

Answer 18

• A hybridization study is used to determine how similar two different organisms are to one another.
  Process:
  1.) Labeled organism DNA is cut into fragments and denatured.
  2.) The labeled fragments DNA is mixed with the denatured DNA fragments of another organism.
  3.) The denatured DNA fragments are able to anneal to anneal to one another.
  4.) The hybridized DNA is then collected in a column and data is collected. The more binding of hybridized DNA the more similar the two species are to one another.
  5.) The hybridized DNA is then heated slowly; the higher the melting temperature of the hybridized DNA, the more similar the species are also.

Question 19

If Chimpanzees are out closet relatives, then why are they not that similar to us in function?

Answer 19

• This is because it’s not about how much similar DNA is present between both organisms but rather similarity depends on the activity and expression of genes.

Question 20

How do polymorphic sequences allow scientists to trace human migrations?

Answer 20

• Since polymorphic sequences allow for individualism, scientists can trace these sequences back (certain alleles) and find in which populations they were present and find in which populations intermingling occurred.

Question 21

How does mitochondria DNA differ from nuclear DNA? And how is it used to trace back ancestors?

Answer 21

• Mitochondria DNA does not undergo recombination as nuclear DNA does.
• Since the same mitochondrial sequenced DNA comes from female relatives, you can trace back these relatives.
• The drawback is that you can only trace back your mothers side of ancestors.

Question 22

What is strange about the intermingling of humanoids and Neanderthals? How does this occur?

Answer 22

• There seems to be no Neanderthal mitochondria DNA contribution found in humans.
• This means that there were interminglings between Neanderthal men and humanoid women since mtDNA is passed down from female relatives only.

Question 23

How are all relative males related?

Answer 23

• All interrupted Relative males have the same Y chromosomal sequence.

Question 24

Why is the X chromosome known as “Smart and Sexy”

Answer 24

• X-chromosome has many more genes for brain development and cognition than any other gene in the human body.
• It also contains genes that deal with sperm count and motility.
• It was theorized back in the day that females picked there males by how smart they were (or if they were cuter round heads).
• Males with better X-chromosomes were smarter and better able to find food and survive. In addition, females were picking them as mates more often and since they head better sperm than this with a lesser X-chromosome, they produced more offspring. Or had a better chance in doing so.

Question 25

What has happened to chromosomes during evolution?

Answer 25

Chromosome rearrangements. Our chromosomes have genes that align with chimpanzees Gorillaz and other organisms.

Question 26

What is colinearity or synteny? How does this show?

Answer 26

• Named for the order of genes have been preserved between species.
• These can show the locations where chromosomal rearrangements occurred.

Question 27

What is the theory behind the splitting of humans and chimpanzees?

Answer 27

• It is thought that the high frequencies we now see in humans (larger brains, more complex cerebral cortexes, and other human individual characteristics) were outliers from the normal populations of chimpanzees.
• These outliers were better able to survive and function and started to mate to their own kind giving rise to the human species.

Question 28

As time and distance increase, what decreases and why?

Answer 28

• Diversity decreases because subsets of groups are being taken from a larger population pool. These subset groups then mate with one another resulting in less diversity.

Question 29

Describe the concept of the FADS gene?

Answer 29

• The FADS gene allowed humans to make polyunsaturated fats (that the brain needs) from plants and other food sources.
• Those who live by water did not have high activity FAD genes because they could get these polyunsaturated fats from fish.
• Those who live inland had a high frequency of these high activity FAD genes because they could not get the fish food source necessary for polyunsaturated fats.
• You do not see high activity FAD genes anymore because trade, agriculture, and technology has expanded.

Question 30

In what organ do genes express the most in the human body?

Answer 30

• Genes are expressed most in the brain compared to all other organs in the body.

Question 31

Can you see greater copies and activities in genes in different humans? If so, what are some examples?

Answer 31

1. ) Amylose gene:
   - See farmers and hunter gathers in dry climates have more copies of the amylase gene than those population which ea mostly meat or farm in the wet climate.
2. ) Parisite and Disease resistance/adaptability:
   - Sickle Cell anemia only found in African Americans.
3. ) Skin pigmentation:
   - Those who live in climates with higher UV rays have darker pigmented skin than those who do not.

Question 32

What is horizontal/lateral gene transfer? Who does it the most? Does this happen in humans?

Answer 32

• Lateral gene transfer is when one species requires genes from another species in the environment.
• Ex.) Plasmids in bacteria.
• Most common in bacteria and archaea but has happened in humans.
• IN vertebrates though, lateral gene transfer occurred a long time ago.