Ch. 8 Genomes, Transcriptomes, and Proteomes

Question 1

What is genomics?

Answer 1

the study of genomes (the genetic composition of a cell or organelle)

Question 2

What lab technique has become a routine approach to studying cells?

Answer 2

genome sequencing

Question 3

How were early attempts at sequencing human genomes carried out?

Answer 3

restriction enzyme digests of multiple donor genomes were performed and cloned into BACs or YACs

Question 4

What was done with the clones once they were made for sequencing?

Answer 4

The ~100 kb clones were sequenced using Sanger sequencing which could do about 600-750 bases at a time.

Question 5

How many times was each clone sequenced and why?

Answer 5

Each clone was sequenced four to six times to ensure accuracy (TOOK A LOT OF TIME)

Question 6

How were the many Sanger sequences put together into a complete genome generically?

Answer 6

Hybridization was used to find overlapping clones based on known sites (called STS’s) or known genes (called EST’s)

Question 7

What are contigs?

Answer 7

What overlapping pieces of cloned DNA were assembled into. Long continuous stretches of DNA.

Question 8

How were the many contigs assembled together?

Answer 8

Using a computer program that finds overlaps to produce the entire 3 B bp genome

Question 9

How is genome sequencing done now (modern day)?

Answer 9

Through next generation sequencing which makes cloning unnecessary.

Question 10

How are next gen. and sanger similar?

Answer 10

Both assemble fragments contigs and assemble the contigs into chromosomes using computer programs.

Question 11

What is genome annotation?

Answer 11

The assignment of location and function of genes and other functional sequences in a genome. (conversion of A,T,C,G into information a researcher can use)

Question 12

How can gene functions be determined (2)?

Answer 12

1. Computationally: computer database finds a match to a known gene
2. Experimentally: mutate a gene of unknown function to determine function

Question 13

What is phenotypic function?

Answer 13

Describes the genes effect on the organism

Question 14

What is cellular function?

Answer 14

Describes the genes effect on a cell

Question 15

What is molecular function?

Answer 15

Describes the biochemical activity of the gene

Question 16

What is comparative genomics?

Answer 16

Using sequenced genomes for comparisons between genomes

Question 17

What do sequence similarities imply and what are they called?

Answer 17

Sequence similarities (homologs) imply an evolutionary relationship between species.

Question 18

What are the two descriptors of genomes with sequence similarities?

Answer 18

Orthologs and paralogs

Question 19

What are orthologs?

Answer 19

Two sequences in DIFFERENT species that have similar sequence and function.

Question 20

What are paralogs?

Answer 20

Two similar sequences within a SINGLE genome that may have arisen through gene duplication (i.e. globin genes)

Question 21

What is synteny and how does it pertain to comparative genomics?

Answer 21

The organization of genes within a chromosome (patterns). It can also be compared.

Question 22

What kinds of life has genome sequencing benefited?

Answer 22

ALL types of life, not just humans. DNA is DNA so anything living can be sequenced.

Question 23

What are viral genomes useful for? (3)

Answer 23

Identification of viruses
Understanding evolution of viruses
Classification of viruses

Question 24

What are bacterial genomes useful for? (4)

Answer 24

Identification of bacteria
Evolution of bacteria
Classification of bacteria
Metagenomic analysis: studying whole community

Question 25

What are archaeal genomes useful for? (4)

Answer 25

Identification of archaea Evolution Relationship to bacteria and eukaryotes Adaptations for tolerating extreme conditions

Question 26

What are eukaryotic genomes useful for? (3)

Answer 26

Finding human disease related orthologs in other species Evolutionary relationships Gene function, etc.

Question 27

What are genes?

Answer 27

DNA sequences that code for a functional RNA or polypeptide

Question 28

What does "gene dense" genome mean?

Answer 28

Most of the sequence codes for functional products. Tend to be found in simpler species.

Question 29

How many genes does the human genome contain? How does it relate to other species?

Answer 29

~20,000 genes which is not much more than fruit flies, nematodes, and other "lower species". We are not special.

Question 30

What do human and other higher order species have in their genomes that make it more complex? Name examples (3).

Answer 30

The genomes of humans and other higher order species contain DNA not used for coding functional products. (introns, various repeated sequences, transposable elements)

Question 31

What do these non-coding DNA bases do?

Answer 31

We don't really know. Their function is not well understood.

Question 32

What are SNPs?

Answer 32

Single nucleotide polymorphisms. They occur among individuals of a species and cause subtle phenotypic differences.

Question 33

How often do SNPs occur in humans?

Answer 33

~every 1000 human bp

Question 34

What is a halotype?

Answer 34

SNPs that are found/grouped together; the phenotypes occur together frequently.

Question 35

Why are halotypes useful?

Answer 35

They serve as markers of certain human populations and sequencing a genome allows us to identify halotypes present in an individual.

Question 36

How can we identify SNPs?

Answer 36

Sequence alignment can identify SNPs

Question 37

What happens after SNPs are identified? (2)

Answer 37

SNPs are grouped into a halotype and specific base differences in the halotype can be identified (tag SNP)

Question 38

How are tag SNPs used for halotype identification?

Answer 38

tag SNPs can be sequenced in an individual instead of a whole gene or genome to identify their halotype. (boils a ton of based down to a few tag SNPs)

Question 39

What are SNPs and halotypes used to study? (3)

Answer 39

Study human evolution migration genetic disorders, etc.

Question 40

What does comparative genomics identify?

Answer 40

Identifies differences between RELATED species

Question 41

Why do we want to identify differences between RELATED species?

Answer 41

Studying the differences and their effects may clarify major evolutionary events for humans or other species. (may not tell "why" or "when" it happened) examples include: duplications, transpositions, inversions, recombinations, etc.

Question 42

When should the product of a gene be produced?

Answer 42

only when needed.

Question 43

What is systems biology?

Answer 43

The study of cellular responses to events or environmental changes. The study of complex, interconnected processes. (big picture/holistic)

Question 44

Is genomics the only thing we can study?

Answer 44

No. Lots of -omes like trancriptomes, proteomes, etc.

Question 45

What is a transcriptome?

Answer 45

the RNA fragments produced in a cell

Question 46

Does the transcriptome change? What does this allow for the study of?

Answer 46

Yes. It changes in response to the environment, so cellular responses and the roles of genes involved in those responses can be studied.

Question 47

How were transcriptomes initially studied? Now?

Answer 47

initially studied with microarrays. Now we use next gen. techniques like RNA-Seq.

Question 48

How does RNA-Seq work? (5)

Answer 48

1. RNA harvested from cell 2. cDNA created using reverse transcriptase 3. cDNA sequenced 4. gene that each cDNA is derived from is identified 5. each sequence is counted and plotted to identify highly-expressed genes

Question 49

What are proteomes?

Answer 49

A snapshot of that polypeptides are produced in a specific condition/environment.

Question 50

Why study proteomes when we can look at transcriptomes and determine what they encode?

Answer 50

The presence of RNA DOESN'T guarantee it's being translated.

Question 51

How can proteomes be studied? (1)

Answer 51

2D-PAGE can be performed to separate cellular proteins into spots. The spots can be excised and identified with mass spec.

Question 52

How does 2D-PAGE work? (2)

Answer 52

It isolates by both isoelectric point (horizontal) and by size (vertical)

Question 53

What is phylogeny?

Answer 53

the evolutionary relationship among species

Question 54

How do genomes, transcriptomes, and proteomes effect phylogeny? (2)

Answer 54

Phylogeny has benefitted from the development of genome, transcriptome, and proteome technology. Results from these studies (DNA, RNA, P) have further supported that all cellular entities derive from a LUCA.

Question 55

What can genomes, transcriptomes, and proteomes be used to identify? Define it.

Answer 55

Minimal genome: the genes minimally required for life. (80-500 genes shared among ALL sequenced genomes)

Question 56

An artificial cell was created. How many genes and base pairs did it contain?

Answer 56

437 genes 531,000 bp

Question 57

How are phylogenies presented?

Answer 57

phylogenetic trees

Question 58

What do phylogenetic trees contain/do? (2)

Answer 58

Describe extant (currently present) taxa and HYPOTHETICAL common ancestors.

Question 59

What are phylogenetic relationships based on? (2)

Answer 59

Based on morphological and genetic features. (data sets)

Question 60

What are the implications of phylogenetic trees being hypotheses?

Answer 60

It is based on a data set, so adding or removing data can change the relationships/tree

Question 61

T/F Trees can be simple or complex.

Answer 61

true