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60 Cards in this Set

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Which company finished decoding the human genome first?
celera
draft: 2000
final publication: 2003
What is sequence annotation?
figuring out what a piece of a gene is and what it is useful for.
DNA probe:
denatured & watched radioactive probe complimentary break pairing.

- short sequence of DNA that is "unique" to that gene or other DNA segment. (x-ray film on top)
What is southern analysis (souther blotting)?
a method which combines gel electrophoresis and nucleic acid hybridization

- can detect just those bands that include parts of the beta-globin gene.

- the probe is a radioactive single-stranded DNA molecule that is complementary to the beta-globin gene.

- reveals not only whether a particular sequnce is present in a sample of DNA but also the size of the restriction fragments that contain the sequence.
What has changed molecular biology profoundly and forever?
the power of having genomic info. in a rapidly searchable database.
how has the power of having genomic info. in a rapidly searchable database changed molecular biology profoundly and forever?
1) it will change the world
2) with the power of computers and databases, what once took yrs, now can take only minutes.
3) It will help in finding therapies to genetically based diseases more rapidly.
4) it will help in finding cures for diseases that have a genetically determined host susceptibility profile (cancers, alzheimers..)
5) potential for abuse is enormous
How is genomics/proteomics done?
researchers now use a computer to do a search of a huge database of genome info. called Genbank with a search engine
Genbank is a searchable database for?
- genomes
- chromosomes
- cloned pieces of DNA
- viruses
- plasmids
- tRNA's, rRNA's, mRNA's, etc.
- cDNA's (DNA copies of mRNA's)
- EST's (expressed sequence tags)
- proteins
& much more.
Information from the HGP can be classified in what 3 basic categories?
1- comparative genomics
2- structural genomics
3- pharmacogenomics
what is comparative genomics?
compares the genomes of many different organisms, looking for the similarities and differences to find info. in evolution.

- req. the sequencing of the human genome and genomes of many other organisms

- mostly confirms what we know about living things

- huge computer databse are required to: store the sequence info., search the sequence info, compare the sequence info in a variety of ways.

- this tree of life is completely computer generated from genomic info.
What is structural genomics?
determines the 3D structures of proteins
what is pharmacogenomics?
analyze genes and proteins to identify targets for therapeutic drugs.
how densely packed are the genes on chromosomes?
it varies with the organism

- in general, the simpler the organism, the genes are more densely packed on the chromosomes.
are genes with similar functions grouped?
sometimes, often depends of whether the genes has the same evolutionary origin or not.
are genes that are used in the same metabolic pathway or developmental pathway grouped?
commonly but not always, for the same reason as that we find genes are often linked.
Are genes that are used in a metabolic pathway or developmental pathway coordinately controlled?
many are (organized as gene family), as this makes regulation more efficient.
Can genes on different chromosomes be coordinately controlled?
yes
have biologists been able to assign functions to all of the genes in the human genome?
as of dec. 2008 this has more or less been completed.
are all genes similar in terms of size?
no
size of genome of homo sapiens (man)?
3.2 billion bases
size of genome of drosophila melanogaster (fruit fly)?
165 million bases
size of genome of saccharomyces cerevisiae (brewer's yeast)?
12 million bases
size of genome of escherichia coli (gut bacteria)?
4.6 million bases
Are all genomes similar in terms of organization?
organisms that are closely related tend to have genomes that are organized similarly.

organisms that are not closely related have genomes that are organized differently.
how conserved are genomes?
in general, the more closely related, the more similar.
do the more complex organisms have more complex genomes than the simpler organisms?
yes
repetitive DNA:
DNA sequences that are repeated over and over at a locus in a chromosome

- often found at telomeres or centromeres

- indicates that tandem repeats have some function
tandem repeats, satellite DNA or simple sequence DNA:
short sequences that are usually exact copies

- are found at telomers of chromosomes (end of chromosomes) and has a normal function in chromosome replication

- during each division some of the repeats are lost

- when almost all of the repeats are lost, that seems to be a signal for apoptosis

- old, mistake-laden cells are eliminated this way.
Interspersed repetitive DNA:
DNA sequences that are repeated over and over at several loci in a chromosome

- longer sequences, usually not exact copies but close
Do repetitive DNA sequences map do anything significant?
not all of it, but tandem repeats do.
Cloning of tandem repeats/ satellite DNA ahs allowed the construction of what?
of artificial chromosomes that function similarly to natural chromosomes.
the size of...
a) ecoli
b)arabadopsis
c) H. sapiens
a) 6mbp
b) 100mbp (small for plants)
c) 3.2bbp
repetitive DNA of...
a) ecoli
b)arabadopsis
c) H. sapiens
a) little
b) moderate to lots (all plants)
c) lots
# of copies of a gene of...
a) ecoli
b)arabadopsis
c) H. sapiens
a) about 1
b) usually many
c) usually many
multigene families of...
a) ecoli
b)arabadopsis
c) H. sapiens
a) yes (but few isoforms)
b) yes (variable amounts of isoforms)
c) yes (and may isoforms)
ploidy of ...
a) ecoli
b)arabadopsis
c) H. sapiens
a) n
b) 2n (but other plants vary widely
c) 2n
# of chromosomes of...
a) ecoli
b)arabadopsis
c) H. sapiens
a) 1
b) 4
c) 46
introns of...
a) ecoli
b)arabadopsis
c) H. sapiens
a) no
b) yes
c) yes
RNA processing of...
a) ecoli
b)arabadopsis
c) H. sapiens
a) no
b) yes
c) yes
transposons of....
a) ecoli
b)arabadopsis
c) H. sapiens
a) yes variable amount
b) yes variable amount
c) human est. up to 45% of genome
# of genes of...
a) ecoli
b)arabadopsis
c) H. sapiens
a) about 4,100
b) about 26k, 15k unique
c) estimated at 22,000
% of coding DNA of...
a) ecoli
b)arabadopsis
c) H. sapiens
a) almost all
b) varies widely
c) about 1.5%
define interactome
the sum of all the proteins that interact with each other
(have some sort of regulatory effect)
what size is the human genome?
3.2 billion base pairs
how many genes consist the human genome?
22,000
what is the % of coding DNA?
1.5%
what is the % of introns, regulatoyr sequenes?
25%
What is the % of interspersed repeats (alu seq), transposons and retrovirus footprints? and what is it refered to, why?
25-45%

- sometime referred to as selfish DNA because it doesn't seem to do anything.
What % are tandem repeats, large segment repeats?
10-15%
What % is unique sequence but non-coding DNA (miRNA, siRNA)?
about 15%
Researchers have hypothesized that the difference between man and other primates is not in the genes but in what?
in fine tuning of regulation of the same genes by siRNA and miRNA's and in splicing of exons during RNA processing
what are transposons "jumping genes"?
- genetic elements that copy themselves and insert themselves into "random" places in the genome

- can add a functionality or destroy a functionality

- discovered by Barbra McClintock
sectoring:
an example of transposons making a phenotypic change by adding a functionality
What is a retrovirus footprint?
- retroviruses have RNA genomes that undergo reverse transcription to DNA

- the DNA then inserts into the genome

- sometime the retrovirus becomes mutated and is not longer functional = retrovirus footprint.
What was the first plant genome sequenced?
arabadopsis thaliana in 2000
plant genomes seem to be very _____?
plastic

- aneuploidy is common (2n+1)
- polyploidy is common (6n)
- genome size varies immensely due to polyplody.
transposons make up what % of some plant genomes?
90%
- maybe how some plant genomes expanded in size
How have plants (and other) genomes expanded?
- through transposons, retroviruses, polyploidy, aneuploidy.

- incorporation of DNA circles
------- certain cells during development make many copies of DNA circles with the rRNA/tRNA genes

------- DNA circles are necessary for rapid expression during development

------- rare mistakes are made and recombination with a chromosome occurs.
What is the ultimate goal of plant molecular biologists?
- make a virtual plant process

--- discover the function of all genes in arabadopsis

--- discover when and where these genes are expressed in the plant

--- with info. at hand, have an understanding of plant development at genetic level

--- then write a computer program to make a "virtual plant"

--- make it possible to experiment on the virtual plant w/o having to do the lab work.
Ethics: how can bioinformatics, genomics, and biology be abused?
- insurance/ employment discrimination

- unauthorized experimentation
--- use of someone else's data
--- human cloning
--- use of someone's cells to develop therapies