Chapter 1 : Nature and organisation of the genetic information Flashcards
Who discovered the hereditary factor ?
G. Mendel
Who’s the father of modern genetic ?
G Mendel
Who isolated the DNA ?
F. Miescher
What did F. Miescher ?
he isolated DNA
Who used the word “gene” for the first time ?
Johannson
What did Johannson ?
He used the word “gene” for the first time ?
Who showed that the chromosomes contains DNA ?
R. Feulgen
What did R.Feulgen discovered ?
That chromosomes contains DNA?
Who discovered the transforming factor ?
Griffith in 1928
What did Griffith ?
Made an experiment to show that there is a transforming factor in DNA and that it was the support of the genetic information
Who discovered the double helix structure of DNA?
Watson and Crick
What did Watson and Crick ?
They discovered the double helix structure of DNA
Who invented the DNA sequencing ?
Maxon and Gilbert
What did Maxon and Gilbert ?
They invented the DNA sequencing
What did Karry Muliss ?
He invented PCR
Who invented PCR ?
K. Muliss
What does the PCR ?
It emplifies some piece of DNA
What did Craig Venter ?
A massive sequencing of the human genome
Who had the idea to make the massive sequencing of the human genome ?
Craig Venter
What is DNA ?
The support of the genetic information
How the DNA was showed to be the support of genetic information ?
Thanks to the experiment of Griffith in 1928 and the demonstration of Avery in 1944
Explain the experiment of Griffith in a few words
same specy, 2 types of bacteria : smooth looking ones (capsid) = S = virulent rough looking bacteria = R = harmless Dead S (heat)+alive R = Dead mice bc of a TRANSFORMING FACTOR Used enzyme to know from where it was: DNAase (=alive mice, it's harmless again) and protease (=dead mice)
=> transforming principle in DNA
Explain the Chase and Hershey experiment in a few words
Some normal cell that stop growing at a certain point in a petri dish bc of contact inhibition, but some are modified = they keep growing
centrifugation and purification of the nucleus of modified cells, there are : prots, RNA and DNA that are added to normal cell, only the one with the DNA of modified cells became modified cells again
=> transforming principle in DNA
How to explain the transforming principle of DNA ?
S bacteria = G protein (=capsid) that S bacteria don’t have
When lysed, S bacteria released part of their DNA (one with the G protein gene), and R bacteria exchange their R gene with the S gene and can by then create a capsid too.
Only a few of them achieve this, but it’s enough to kill
What’s different between the horizontal gene exhange and the transfroming principle of DNA ?
transforming principle = same specy
horizontal transfer = different species
Define what’s a gene
It’s a nucleotide sequence used to program the synthesis of RNA and necessary to one function, i can also produce a protein but not always the case
How’s define the phenotype ?
By your DNA and your environment
What’s the DNA made of ?
Polymer of polynuclotides of 4 monomers (deoxynuleotides: A,C,G,T)=carbohydrates skeleton
What are the groupe attached to the extremity of the DNA molecule ?
5' = phosphate 3' = OH
How are bond nucleotides to each other ?
The phosphate (5') binds to the OH group (3') =phosphodiester bond
What are the 6 essential things to know about the DNA strand ?
- double strand
- helix structure
- complementary strands
- anti-parallel strands
- phosphodiester bonds btw nuclotides of a strand
- hydrogen bonds btw the nucleotides of the two strands
What happens when you put DNA at a high temperature ?
denaturation = the two strands separate themselves
What material is needed for DNA synthesis ?
- Template (single strand DNA)
- Primer (doube stranded RNA)
- Nucleotides
- DNA polymerase
What’s the template ?
A single strand DNA molecule which will be complementary to the newly synthetized one
What kind of bonds DNA Polymerase creates ?
Phosphodiester bonds
How hydrogenous bonds are created ?
“Naturally”
What are the different abreviation for nucleotides ?
The different dNTPS are :
- dATP
- dTTP
- dCTP
- dGTP
How does DNA polymerase reads and synthetizes it ?
It reads the template from 3’ to 5’
and synthetizes the new strand from 5’ to 3’
What’s the semi conservative replication model ?
one parental strand, one new strand for each two daughter molecule
What’s the conservative replication model ?
one of the daughter molecule have the two parental strand, and the other daughter molecule have two new strand
What’s the dispersive replication model ?
the two strands of each daughter molecule have some parts of parental DNA and parts of newly synthetized DNA
What kind of replication model applies to DNA ?
The semi-conservative model
Explain in a few word how Caesium Chloride gradient works
Some DNA put in an environment with 15N (heavy nitrogen) => they only have 15N
then they’re put aside in an environment with 14N (light nitrogen
The 15N DNA is the parental one and the 14N DNA is the new one
The obtained DNA are put in the CsCl gradient and they migrate according to their density. As 15N is more dense, it goes down the gradient, and 14N less dense, it quite stays up. When it’s hydride DNA, it goes btw the two levels.
How do you call DNA with 14N ?
light DNA
How do you call DNA with 15N ?
heavy DNA
Where does the replication of DNA starts from ?
from the origin of replication (ORI)
The DNA replication is a uni or bidirectional mechanism ?
bidirectional (2 opposite directions)
How many ORi do you find in prokaryotes ?
Only one (one small circular chromosome)
How many ORI do you find in eukaryotes ?
many
1 chromosome = at least 1 ORI
How does the replication starts ?
By denaturating DNA = opening the heliw structure
What does the opened DNA structure form when replicating ?
Replication bubbles (looking like bubbles) with replication fork on each side of it
What’s the leading strand ?
The strand that needs only one RNA primer and synthetize DNA continuously
What’s the lagging strand ?
The strand that needs many RNA primers to synthetize a new strand
What are Okasakis fragments ?
They are on the lagging strand, each Okasaki fragment is made of one primer and the DNA synthetized after it, until the next primer
What’s the length of an Okasaki fragment in prokaryotes ?
~1000 bases (much longer than eukaryotes ones)
What’s the length of an Okasaki fragment in humans cell ?
~200 bases (much shorter than prokaryotes ones)
What’s the function of helicase ?
it’s an enzyme that opens the double helix structure
What’s the function of RNA polymerase in DNA replication ?
It’s an enzyme also called primase that synthetize RNA primers
What’s the double function of DNA Polymerase ?
- synthetize DNA from the primer
- rempace the RNA of the primer by DNA (degrade RNA=RNAase)
What’s the function of ligase ?
It binde the Okasaki’s fragments together to form a whole strand
Comment on the speed of replication in eukaryotes and prokaryotes
very fast in prokaryotes = 1500bp/sec
a bit slower in eukaryotes = 10 à 100 bp/sec (à cause processus de vérification)
The reading and synthesis of DNA is uni or bidirectional ?
Unidirectional
What happen to replication bubbles during DNA replication ?
they grow larger and larger until they meet themselves
What’s the function of SSBP enzyme ?
It avoid the two strands to reconnect themselves
What’s the difference btw synthetization of DNA in vitro and in vivo ?
in vivo = primases (=RNApol) that makes double stranded RNA primer for the synthetization to starts
What are the two functions of primers ?
- fixation of DNA polymeras
- synthetization of DNA
How many chromosome in the prokaryotes, and where is it situated ?
prokaryotes = 1 mb and it has no organelles so chromosome is directly in the cytoplasm
What do the prokaryotes’ genes code ?
- 90% are coding for proteins
- <1% non coding RNAs
+ regulatory regions
What do have prokaryotes that eukaryotes do not have ?
plasmids
What can you say about plasmid ?
- surnumerary
- selective advantage
- double strand DNA molecule
- self replicating
- multicopy
- daughter c has the same as its mother c
What does it mean when we say that plasmid is “self replicating” ?
it replicates at the same time as the bacteria genome
What does it mean when we say that plasmid is “multicopy” ?
there are many copies of the same plasmid in the cell
Are the plasmid under natural selection ?
yes obviously, cells only keep the one that are useful to it
What differenciates prokaryotes and eukaryotes when talking about the structure of the genome only ?
- Genome of eukaryotes is fragmented
- linear chromosomes in eukaryotes (circular in pro)
What’s the chromatin ?
DNA + proteins attached to it
How are called the extremities of chromosomes ?
telomers
How many copy of each chromosome do we have in our cell ?
excluding gametes, we have two copies of each chromosome (=diploidy)
What are chromosomes associated with, and what does it form ?
proteins, forming chromatin
How do you call the position of a gene on a chromosome ?
the locus
Is there a correlation btw the complexity of the genome and the complexity of the organism ?
absolutely not, it can have more chromosomes, a way longer genome, these two factors aren’t related
What are the two main family of DNA ?
Informative and non-informative DNA
What is informative DNA ?
DNA sequences that are transcripted as RNA (and then proteins or not)
What is non-informative DNA ?
DNA sequences that aren’t transcripted (as RNA nor as proteins)
What are the two types of informative DNA ?
coding genes and non-coding genes
Coding and non-coding genes belong to informative or non-informative DNA
informative DNA
What is the fucntion of coding DNA ?
- it codes proteins
- many exempaires/genome (++proteins)
Whats is the function of non-coding DNA ?
- it codes for RNA only !!
ex: genes for rRNA…
How important is informative DNA in the human genome ?
1,4%
What’s the function of non-informative DNA?
Structural/functional function
How’s consituted non-informative DNA ?
Of repeated sequences of DNA
What are the two types of non-informative DNA ?
- repeated in tandem (side by side)
- dispersed repetition
What percentage of DNA is constitute of non-informative DNA repeated in tandem ?
10%
What percentage of DNA is constitute of non-informative DNA have disperserd repetition ?
45%
Give an exemple of sequences in tandem
minisatellites
How many membrane does the nucleus have ?
2
How do you call the two membranes of the nucleus ? What do they form ?
inner layer + outer layer = an envelope
How to describe a nucleus that isn’t replicating ?
interphasic
How many nuclues per cell ?
One par cell (most of the time)
How are the chromosome when the nucleus is interphasic ?
they are all mixed together and can’t be dissociated from e/o
According to what the size and the form of the nucleus does change ?
according to the state of the cell
What are the two ultrastructures that the nucleus contains?
- chromatine (dna + prot)
- nucleolus
What is the nucleolus ?
a part of the nucleus that is way more dense
How do you call the inside of the nucleus ?
the nucleoplasm
How do you call the space between the inner and outer layer of the nucleus ?
perinuclear space
The envelope of the nucleus is a barrier btw what and what ?
btw the nucleoplasm and the cytoplaqm
What can we found in the nucleoplasm ?
The cellular matrix and the chromatin
With what is connected the outer layer of the nucleus ?
with the rough endoplasmic reticulum (in continuity, the lumens are connected)
Define the nuclear matrix
it’s a complex structure composed of lamina, proteins and RNA
=lamina+prots+RNA
what is the lamina ?
made of lamins, attached to the inner membrane
What’s the function of lamina ?
it maintains the envelope
Is the envelope of the nucleus completely waterproof ?
no, there are nuclear pores in the envelope
What are the nuclear pores ?
in the interruption of the nuclear envelope, are organized structure of ~50 proteins
(with cytoplasmic filaments and cytoplasmic particles)
What’s the function of the nuclear pores ?
they regulate cytonuclear exchange
What size can be a nuclear pore ?
80 to 100 nm
How do you call the proteins that form the nuclear pores ?
the nucleoporines
What’s NPC acronym for ?
Nuclear Pore Complex
How do the nuclear pores regulate the cytonuclear exchange ?
by modifying their diameter = regulation of molecules which enters the nucleus
What kind of transport go through the nuclear pores ?
passive AND active transport
What are the outputs of the nuclear envelope ?
the molecules made in the nucleus that have a function in the cytoplasm
What are the inputs of the nuclear envelope ?
the molecules made in the cytoplasm that have a fucntion in the nucleus
What are the two types of chromatin ?
eu chromatin and heterochromatin
How do you recognize euchromatin on a microscope image ?
it’s less dense so looks less dark
How do you recongize heterochromatin on a microscope image ?
it’s really dense so it looks very dark
How large can the diameter of nuclear pores can increase/decrease ?
9 to 26 nm
How many protein complexes form the nuclear pores ?
8 complexes = nuclear pore
Tell some exemples of molecules getting out of the nucleus by the nuclear pores
mRNA, rRNA, tRNA
Tell some exemples of molecules getting in the nucleus by the nuclear pores
- proteins (for chromatin and lamina)
- transcription factor
- ribosomal proteins
What is the state of the chromosomes in euchromatin ?
decompacted, they are active (bc more accessible to the cell)
What’s the DNA structure in euchromatin ?
Pearl necklace structure
What is the state of the chromosome in heterochromatin ?
well more compacted, they are inactive (bc less accessible to the cell)
Where do you mainly find heterochromatin ?
new to the inner membrane
Can DNA be a free molecule ?
no, even isolated it keeps its pearl necklace structure
What’s the DNA structure in heterochromatin ?
solenoid structure (fibers piles)
What’s the protein used for the structuration of DNA ?
histones
what are the 5 different types of histones ?
H1? H2A, H2B, H3, H4
Are histones basic or acid ? from what amino acids are they mainly made ?
they are basic
basic aa : lysine and arginine
=binds to acid DNA
What is pearl necklace structure made of ?
fibers made of sequences of nucleosomes
What is a nucleosome ?
Core particle :
- core of 8 histones
- Fragment of DNA wrapped around
+ DNA linker internucleosomal
How many bp are wrapped around the histone core ?
140/200 bp
How many bp do we found in DNA linker ?
60 bp
What is the histone core of nucleosome made of ?
2xH2A; 2xH2B; 2xH3; 2xH4
What’s the first level of organisation of DNA ?
the nucleosomes of the pearl neacklace structure in euchromatin
From which proteins are solenoids tructures made of ?
histone H1
What’s the second level of organisation of DNA ?
solenoids structures in heterochromatin
What’s the third level of organisation of DNA ?
the condensed chromosome during the division of the cell
Are chromosome randomly placed in the nucleus ?
no, each of them occupy a specific chromosome territory
Are the chromosomes territories the same for all eukaryotes ?
no, it depends on the type of the cell
Why do the chromosome territories different btw the different cell of an organism ?
bc it depends on which part of the DNA the cell need to use
What is the nucleolus ?
NOT A COMPARTIMENT
but a specific area in the cell where chromosomes with the rRNA-45S Gene reunites
How many nucleolus per cell ?
Usually 1, but sometimes more and sometimes none
What can you deduce from the number/size of nucleolus ?
we can deduce the metabolic activity of the cell, the more it has the more active it is
What are the two functions of the nucleolus ?
- rRNA synthesis
- formation of ribosomal subunits (only the subunits, not the whole ribosome)
Do ribosomes exist as a free form ?
no bc the two subunits onky assembly themselves when replicating
What are the two subunits that constitutes the ribosome ?
the small subunit
the large subunit
With which RNA is the small ribosomal unit made of ?
RNA 18S
With which RNAs is the large ribosomal unit made of ?
RNA 28S, 5S and 5.8S
Where are produced the RNA28S, 18S and 5.8S ?
in the nucleolus
Is RNA5S produced in the nucleolus ?
no, it’s only RNA28S,18S and 5.8S
Which gene code for RNA 28S, 18S and 5.8S ?
rRNA 45S gene (found in the nucleolus)
Is rRNA-45S a coding or non-coding gene ?
non-coding -> no proteins but RNA
rRNA-45S gene can be found many times in our genome, are the repetitions in tandem or dispersed ?
the repetitions of rRNA-45S gene are dispersed in the genome
What are the different chromosome that has rRNA-45S genes ?
the chromosomes :
- 13,14,15
- 21, 22
What is abundantly synthetized in the nucleolus ?
ribosomal RNA
Where is rRNA 5S produced ?
in the nucleus but not in the nucleolus so it has to move
