Week 1 & 2 (History, Architecture, and DNA Review) Flashcards
Genomics Definition
a branch of biotechnology concerned with applying the technique of genetics and molecular biology to the genetic mapping and DNA sequencing of sets of genes or the complete genomes of selected organisms, with organizing the results in databases, and with applications of the data
genome mapping
the map outlines the sequence of the genome in order to understand where things are and to answer questions about them and make predictions
Genetics: 1871
Friedrich Miescher publishes his paper identifying the presence of “nuclein” (now knows as DNA) and associated proteins in the nucleus
In _________ Friedrich Miescher publishes his paper identifying the presence of “nuclein” (now knows as DNA) and associated proteins in the nucleus
1871
Genetics: 1952
The Hershey-Chase experiments (carried out by Alfred Hershey and Martha Chase) to demonstrate that DNA, rather than protein, carries our genetic information
In ________ The Hershey-Chase experiments (carried out by Alfred Hershey and Martha Chase) to demonstrate that DNA, rather than protein, carries our genetic information
1952
Genetics: 1953
discover the double helix structure of DNA
(Watson, Crick, Franklin, and Wilkins)
In ______ discover the double helix structure of DNA
(Watson, Crick, Franklin, and Wilkins)
1953
Sequencing/Mapping: 1977
Sanger develops a DNA sequencing technique used to sequence the first full genome (a virus)
In __________ Sanger develops a DNA sequencing technique used to sequence the first full genome (a virus)
1977
Sequencing/Mapping: 1983
The polymerase chain reaction (PCR) is developed (a technique used for amplifying DNA)
In _________ The polymerase chain reaction (PCR) is developed (a technique used for amplifying DNA)
1983
PCR
polymerase chain reaction (a technique used for amplifying DNA)
Sequencing/Mapping: 1990
human genome project is launched
why can we apply these techniques in different species?
because DNA is DNA is DNA
Complete Genomes: 2001
first DRAFT of the human genome sequence is released. 3 Gb (gigabase = billion)
Complete Genomes: 2003
Human genome project is completed and confirms humans have approximately 20,000 to 25,000 genes. The human genome is sequences to 99.99% accuracy (finished 2 years ahead of schedule)
what was the first agricultural genome done on?
chickens!
what project is launched in 2003 that aims to identify and characterize all the genes in the human genome?
ENCODE
What happened in 2007?
Solexa 1G sequencer available
Who/What is Solexa?
a company that came in in 2007 and said they could produce sequencers faster and cheaper
bp
base pair = 1
Kb
kilobase = 1,000
Mb
megabase = 1,000,000 (millions)
Gb
gigabase = billions
Tb
terabase = trillions
Pb
petabase = quadrillions
list bp, Pb, Kb, Mb, Tb, Gb in order from smallest to largest
bp < Kb < Mb < Gb < Tb < Pb
In the cost per human genome, we saw a huge drop in 2007 and it continues to decrease. Why did it drop so much in 2007?
solexa made sequencing faster and cheaper and from there more technology has become advanced
how many bases are in the public domain?
91 Quadrillion bases
Important date: 1871
Friedrich Maische identified the presence of ‘nuclein’
In _______ Friedrich Maische identified the presence of ‘nuclein’
1871
Important date: 1952
the Hershey-Chase experiments demonstrate that DNA, rather than protein, is the genetic material
In _______ the Hershey-Chase experiments demonstrate that DNA, rather than protein, is the genetic material
1952
Important date: 1953
Watson, Crick, Franklin, and Wilkins discover the double helix structure of DNA
In _______ Watson, Crick, Franklin, and Wilkins discover the double helix structure of DNA
1953
Important date: 1977
Sanger develops a DNA sequencing technique
In _____ Sanger develops a DNA sequencing technique
1977
Important date: 1983
Mullis develops polymerase chain reaction (PCR) - a technique used for amplifying DNA
In _______ Mullis develops polymerase chain reaction (PCR) - a technique used for amplifying DNA
1983
Important date: 1987
The term genomics first used in scientific literature
In ______ The term genomics first used in scientific literature
1987
Important date: 1990
the human genome project is launched
In ________ the human genome project is launched
1990
Important date: 2003
the human genome project is finished
In ______ the human genome project is finished
2003
Important date: 2007
Illumina “next generation” sequencer available
In ______ Illumina “next generation” sequencer available
2007
what is the human genome composed of?
(two major places where DNA is stored in the cell)
nuclear genome + mitochondria genome
(plants also have it in their chloroplast)
what is your favorite species and what is their karyotype?
DOGS! 78 karyotypes
Why do we get our mitochondrial DNA from maternal inheritance?
the female gamete has mitochondria, the male gametes mitochondria are in the tail of the sperm which breaks off during conception
What shape is mitochondrial DNA and DNA in chloroplasts in?
circular
heteropasmy and what can it cause
the presence of more than one type of mitochondrial DNA, this can form homoplasmic and heteroplastic cells during replicative segregation
homoplasmic cells
same type of mitochondria in a cell
heteroplastic cells
two types of mitochondria in a cell
what is a replication error?
an error that can occur when DNA is copied
size/length of the mammalian genome
(like if it were stretched out)
about 1 meter
chromatin
DNA with a protein scaffold (made up of histones/nucleosomes)
how many types of histones?
5 types
what charge do histones have and why is it important to the structure?
positive charge, thus it will bind to negatively charged DNA
Heterochromatin
“inactive” - plays a role in gene regulation and integrity
examples of heterochromatin
centromeres, telomeres
euchromatin
active (readily accessible for transcription)
the __________ is the fundamental repeating unit of chromatin
nucleosome
____ bases per turn of the helix
10
what is the purpose of histone tails?
makes chromatin have different marks on them so that antibodies can develop
constitutive heterochromatin
a highly condensed, static region of chromatin that remains compacted throughout the cell cycle (centromeres and telomeres)
centromeres
used by the cell during cell division to make sure that each daughter cell gets a copy of each chromosome
____________ sequence is the biggest problem in genomics
repetitive
centromeres have a highly ___________ sequence, which is one of the biggest problems in genomics
repetitive
telomeres location
located at the ends of the chromosomes, short tenderly repeated sequences further from the ends (many kilo bases in length)
what is the purpose of telomeres?
to assist with not losing DNA every time the cell divides
TTAGGG is repeated in the telomere in all _____________
vertebrates
what kind of repetitive DNA does telomeres and centromeres have?
tandem
tandem repetitive DNA
the repeats are close together, back to back
interspersed repetitive DNA
repeats present at different locations of the genome
segmental duplications
blocks that range from 1 to 400 Kb in length, occur at more than one site within the genome and typically share a high level of (>90%) sequence identity
how much of the human genome does segmental duplications make up?
about 5%
what is sequence identity?
how similar the sequence of DNA is to each other
SINES
short interspersed nuclear element (100-500 bp, 1 M copies)
LINES
long interspersed nuclear elements (5000 bases, 500,000 copies)
“jumping DNA”
transposon, sequence of DNA that is able to excise themselves and move somewhere else in the genomes
LINES are about _____% of the genome, and about ____Kb
17, 5-6
SINES are about ____% of the genome, and about ___bp
11, <500
mitochondria DNA is also know as _________ genome
cytoplasmic
genome = __________ (autosome/sex) + ___________ (mtDNA cpDNA)
Nuclear + Cytoplasmic
centromeres are ____ Kb to Mb
100’s
telomeres ___ Kb
10’s
what structure allows for genome compaction?
chromatin
there are __ copies of 4 histones
2
Dog: common names and genus and species name
- domestic dog
- canis
- canis familiaris
dog: haploid number and diploid number
- haploid: 39
- diploid: 78
dog: haploid genome size
2.4 billion base pairs (Gb)
What is the size of the human genome?
3 billion
3 parts of DNA and RNA
1) pentose sugar
2) nitrogenous base
3) phosphate group
what is the difference between a ribose sugar and deoxyribose sugar?
- deoxyribose has a hydrogen attached to the 2’ carbon
- ribose has a hydroxyl group attached to the 2’ carbon
DNA uses a ____________ (pentose sugar), while RNA uses a ____________ (pentose sugar)
deoxyribose, ribose
on the pentose sugar in DNA and RNA to 1’ carbon is attached to ______________, the 3’ carbon is attached to ____________, the 5’ carbon is attached to ______________
- 1’ = nitrogenous base
- 3’ = OH group that forms the phosphodiester bond
- 5’ = phosphate group
purines
- adenine
- guanine
pyrimidines
- cytosine
- thymine
- uracil
what is a nucleoside?
a base linked to sugar by 1’ carbon of pentose sugar
what is a nucleotide?
pentose sugar, nitrogenous base, and a phosphate group
nucleotide names for DNA and RNA?
- DNA = dGMP, dAMP, dCMP, dTMP
- RNA = GMP, AMP, CMP, UMP
what is a 5’–3’ linkage?
covalent bonds between phosphate group of one nucleotide and the 3’ carbon of the next nucleotide’s sugar, also called a phosphodiester bond
T/F: the two ends of the polynucleotide chain are not the same
- TRUE!
- the 5’ end has a phosphate group attached to the 5’ carbon of the pentose sugar
- the 3’ end has a OH group attached to the sugars 3’ carbon
.
does the nucleotide chain have polarity?
yes!
A - T has ____ hydrogen bonds
2
C - G has ____ hydrogen bonds
3
A - U has ___ hydrogen bonds
2
What was Watson and Crick’s key insight?
- DNA has a double helix
- the strands are antiparallel
- base complementarity
The strands of DNA are arranged helically, ____ base pairs between each turn of the helix
10
the _________ and ________ groove are important for binding of other molecules and the regulation of genes
major and minor
What is CPG methylation?
the nitrogenous base cytosine can be methylated by proteins which changed the chemical structure that may or may not allow transcription (regulates transcription without changing the DNA sequence)
what is epigenetics and what is an example?
- chemical modifications to DNA and RNA that can not be transmitted to the next generation
- modifications to the genetic code that are not inherited
TSS
- transcription start site
- where transcription begins
raw materials of DNA synthesis
- template (single stranded DNA)
- enzymes (DNA polymerase)
- raw materials (substrates - dNTs)
- Mg 2+ ions
what does dNTPs stand for?
deoxynucleotide triphosphate
____ ____________ catalyzes the formation of phosphodiester bonds
DNA polymerase
DNA is synthesized from ___ to ___
5’ to 3’
When does DNA replication occur?
occurs in the nucleus during S phase of the cell cycle
DNA replication is initiated by ____ primers
RNA
DNA replicates occurs in the ___’ to ___’ direction
5’ to 3’
DNA replication is _____conservative
semiconservative
why are there multiple origins of replication along the chromosome?
DNA is a very large molecule so having multiple origins speeds up the process
why does heterochromatin (inactive) replicate later than euchromatin (active)?
centromeres (heterochromatin) are there to ensure that daughter cells must have exactly each half of the chromosome, so it is the last thing that separates from the chromosome
gyrase
an enzyme that relieves tension when DNA is opened/unwinded
helicase
breaks the bonds in DNA so that it can open/unwind
__________ must first disassemble to allow DNA synthesis
histones
when histones disassemble, what happens to them?
old histones lie around and can be reused
