mb part 2 Flashcards
While proposing the —- for DNA, Watson and Crick had immediately proposed a scheme
for—- .
double helical structure
replication of DNA
original statement of watson and crick is:
‘‘It has not escaped our notice that the—– we have postulated immediately suggests a
possible—- for the genetic material’’
(Watson and Crick,— ).
specific pairing, copying mechanism
1953
The scheme of watson and crick for replication suggested that the two strands would— and act as —- for the synthesis of —- .
separate, a template
complementary strands
After the completion of
replication, each DNA molecule would have one
— and — strand.
This scheme was termed as — DNA replication
parental and one newly synthesised strand.
semiconservative
It is now proven that DNA replicates—- , shown first in — and subsequently in—–
semiconservatively
Escherichia coli
higher organisms, such as plants and human cells.
— Meselson and—- Stahl performed the exp in — :
Matthew , Franklin
1958
MSE:
(i) They grew E. coli in a medium containing —- as the only nitrogen source for—- .
The result was that — was incorporated into newly synthesised DNA (as well as —-).
15NH4Cl (15N is the HEAVY
isotope of nitrogen)
many generations
15N
other nitrogen containing compounds
This heavy DNA molecule could be distinguished from the normal DNA by—– IN —-
centrifugation in a cesium chloride (CsCl) density gradient
15N is not a — isotope, and it can be separated from 14N only based on — .
radioactive
densities
Then they transferred the cells into a medium with normal— and took samples at —- as
the cells multiplied, and extracted the DNA that remained as —–.
The various samples were separated—- to measure the densities of DNA
14NH4Cl
various definite time intervals
double-stranded helices
independently on CsCl gradients
Can you recall what centrifugal force is, and think why a molecule with higher mass/density would sediment faster?
centrifugal force, angular velocity and mass are inversely proportional to each other. Thus a higher density molecule will sediment faster in centrifugation.
Thus, the DNA that was extracted from the culture one
generation after the transfer from 15N to 14N medium [that is
after —- ; E. coli divides in —-] had a hybrid or
—- density. DNA extracted from the culture after
another generation [that is after 40 minutes, II generation] was composed of —- of this hybrid DNA and of ‘light’
DNA.
20 minutes, 20 minutes
intermediate
equal amounts
Very similar experiments involving use of —- to
detect distribution of newly synthesised DNA in the — was
performed on —- faba (—-) by —– .
The experiments proved that the DNA in CHROMOSOMES also replicate
semiconservatively.
radioactive thymidine
chromosomes
Vicia
faba beans
Taylor and colleagues in 1958
In living cells, such as —-, the process of replication requires a set of —- (enzymes). The main enzyme is referred to as DNA-dependent
DNA polymerase since it uses a —- to catalyse the
—-.
E. coli, catalysts
DNA template
polymerisation of deoxynucleotides
DNA-dependent
DNA polymerase enzymes are —- enzymes as they have to catalyse polymerisation of a large number of —-
highly efficient
nucleotides in a very short time
. E. coli that has only 4.6 ×106 bp (compare
it with human whose diploid content is —), completes the
process of replication within —-; that means the — rate of polymerisation has to be approximately —–
6.6 × 10^ 9 bp
18 minutes
average
2000 bp per second.
Not only do these polymerases have to be — , but they also have to catalyse the reaction
with —.
Any mistake during replication would result
into —- .
fast, high degree of accuracy
mutations
Furthermore, — replication is a very expensive process.
energetically
—- serve dual purposes. In addition to acting as substrates, they provide energy for polymerisation
reaction (the two — in a deoxynucleoside triphosphates
are —-, same as in case of ATP).
Deoxyribonucleoside triphosphates
terminal phosphates
high-energy phosphates
In addition to DNA-dependent DNA polymerases, many additional enzymes are required to complete the process of replication with —-
high degree of accuracy.
For — DNA molecules, since the two strands of
DNA cannot be separated in its —- (due to very —-), the replication occur within a —- referred to as replication –
long
entire length
high energy requirement
small opening of the DNA helix,
fork
The DNA-dependent DNA
polymerases catalyse polymerisation only in one direction, that is —-
This creates some — at the replicating fork.
5 prime to 3 prime
additional complications
Consequently, on one strand (the template with polarity 3 to 5 prime), the
replication is —, while on the other (the template with polarity 5’ to 3’), it is —.
continuous, discontinuous
The —- fragments are later joined by the enzyme DNA ligase
discontinuously synthesised
The DNA polymerases on their own — the process of replication.
cannot initiate
Also the replication does not initiate randomly at any place in DNA. There is a definite region in —- DNA where the replication originates. Such regions are termed as —
E. coli
origin of replication
It is because of the requirement of the — that a piece of DNA if needed to be —- during recombinant DNA procedures, requires a vector.
origin of replication
propagated
The — provide the origin of replication during recombinant dna procedures
vectors
Further, not every detail of — is understood well.
replication
In —- , the replication of
DNA takes place at S-phase of the cell-cycle.
eukaryotes
The replication of DNA and cell division cycle should be —-.
highly coordinated
A failure in cell division after DNA replication results into — (a
—).
polyploidy
chromosomal anomaly
Def Transcription.
The process of copying genetic information from one strand of the DNA into RNA is termed as
transcription
In Transcription also, — governs the process of transcription, except the — complements now forms base pair with uracil instead of thymine.
complementarity
adenosine
However, unlike in the process of replication, which —, the — DNA of an organism gets duplicated, in transcription only a — of DNA and only — is copied into RNA.
This necessitates defining the — that would demarcate the region and the strand of DNA that
would be transcribed
once set in
total
segment, one of the strands
boundaries
Both the strands are not copied during transcription because:
- If both strands act as a—, they would code
for RNA molecule with —-(Remember complementarity
does not mean —-)
and in turn, if they code for proteins, the sequence of — in the proteins would be different. Hence, one segment of the DNA would be coding for two different proteins, and this would
——. - the two RNA molecules if produced simultaneously would be complementary to
each other, hence would form—- RNA.
This would prevent
—- and the exercise of transcription would become a — one.
template, different sequences
identical
amino acids
complicate the genetic information transfer machinery
a double stranded
RNA from being translated into protein
futile
A — unit in DNA is defined — by the three regions in
the DNA:
(i) A Promoter
(ii) The Structural —
(iii) A Terminator
transcription, primarily,
gene
There is a convention in defining the two strands of the DNA in the
— of a transcription unit.
structural gene
Since the two strands have — and the DNA-dependent — polymerase also catalyse the polymerisation in only one direction, that is, — the strand that has
the polarity 3’→5’ acts as a —-, and is also referred to as —-
opposite polarity
RNA
5’→3’,
template
template strand
The other strand of dna which has the polarity (5’→3’) and the — (except —-), is displaced during
transcription.
sequence same as RNA
thymine at the place of uracil
Strangely, this strand (5’ to 3’) (which —-) is referred to as coding strand.
does not code for anything
All the reference point while defining a
transcription unit is made with —-
coding strand
The promoter and terminator flank the — in a transcription unit.
structural gene
The promoter is said to be located towards 5’ -end (—-) of the structural gene (the reference is made with respect to
the —-).
upstream
polarity of coding strand
It is a — sequence that provides — for RNA polymerase, and it is the presence of a —- in a transcription unit that also — the template and coding strands.
DNA
binding site
promoter
defines
By switching promoters position with terminator: —–
the definition of coding and template strands could be reversed
The terminator is located towards 3’ -end (— ) of the coding strand and it —- of the process of transcription
downstream
usually defines the end
There are — sequences that may be present further upstream or downstream to the
—.
additional regulatory
promoter
A gene is defined as —
the FUNCTIONAL unit of inheritance.
Though there is no — that the genes are located on the —, it is difficult to literally define a gene in terms of —-
ambiguity
DNA
DNA sequence.
The DNA sequence coding for —- or — molecule also define a gene
tRNA or rRNA
However by defining a — as a segment of DNA coding for a —, the structural gene in a
transcription unit could be said as monocistronic (mostly in —) or polycistronic (mostly in —-).
cistron, polypeptide
eukaryotes
bacteria or prokaryotes
In eukaryotes, the
monocistronic — have — sequences; the genes in eukaryotes are —-
structural genes
interrupted coding
split
The coding sequences or —- are defined as —.
expressed sequences
Exons
Exons are said to be those sequence that appear in —- RNA.
mature or processed
The exons are interrupted by — .
introns
Introns or — do not appear in mature or
— RNA.
intervening sequences
processed
The —- further complicates the
definition of a gene in terms of a DNA segment
split-gene arrangement
Inheritance of a character is also affected by —- and —- sequences of a structural gene.
promoter and regulatory
Hence, sometime the regulatory sequences
are — as regulatory genes, even though these sequences —-
loosely defined
do not code for any RNA or protein.
In —, there are three major types of RNAs: —, —, —-.
bacteria
mRNA (messenger RNA),
tRNA (transfer RNA), and rRNA (ribosomal RNA)
— RNAs are needed to synthesise a protein in a cell.
All three
The mRNA provides the —, tRNA brings — and reads the —-, and rRNAs play — and — role during —-.
template
aminoacids, genetic code
structural and catalytic
translation
There is — DNA- dependent RNA polymerase that catalyses transcription of all types
of RNA in —.
single, bacteria
RNA polymerase binds to — and initiates
transcription (—-)
It uses nucleoside triphosphates as — and polymerises in a — fashion following the rule of —-.
promoter
Initiation
substrate
template depended
complementarity
RNA polymerase somehow also facilitates opening of the —- and —–.
helix and continues elongation
Only a short stretch of RNA remains —-.
bound to the enzyme (RNA pol)
Once the polymerases reaches the terminator region, the — falls off, so also the —-.
This results in termination of —
nascent RNA, RNA polymerase
transcription
An intriguing question is that how is the RNA polymerases able
to catalyse all the three steps, which are —, — and —.
initiation, elongation and
termination
The RNA polymerase is ONLY capable of catalysing the process of —-.
elongation
RNA pol associates — with initiation-factor —-
and termination-factor —to initiate and terminate the transcription,
respectively.
Association with these factors alter the — of the RNA polymerase to either initiate or terminate
transiently
(σ), (ρ)
specificity
In bacteria, since the — does not require any processing to become
active, and also since transcription and translation take place in the — (there is no separation of — in bacteria), many times the translation can begin —
mRNA
same compartment
cytosol and nucleus
much before the mRNA is fully transcribed.
Consequently, the transcription and translation can be — in bacteria.
coupled
In eukaryotes, there are two additional complexities –
(i) There are — RNA polymerases in the — (in addition to the RNA polymerase found in the —).
AT LEAST three
nucleus
organelles
There is a clear cut — of RNA polymerase in eukaryotes.
division of labour
The RNA polymerase – transcribes rRNAs
(—)
I- 28S, 18S, and 5.8S
RNA polymerase III is responsible for transcription of —-,— and —-.
tRNA, 5srRNA, and snRNAs (small nuclear
RNAs)
The RNA polymerase II transcribes —-, the —-
precursor of mRNA-
heterogeneous nuclear RNA (hnRNA).
The second complexity in eukaryotic transcription is that the —- contain both
the exons and the introns and are —
primary transcripts
non-functional
Hence, Primary transcript is subjected to a process called – where the — are removed and exons —.
splicing, introns
are joined in a defined order
— undergoes
additional processing called as capping and tailing.
hnRNA
In capping an — (–) is added to the — end of —
unusual nucleotide (methyl guanosine triphosphate)
5’-end of hnRNA.
In tailing, —- (—) are
added at — end in a template — manner.
adenylate residues (200-300)
3’-end
independent
It is the fully processed –, now called mRNA, that is transported out of the
nucleus for —
hnRNA
translation
The —- of such complexities in eukaryotic transcription is now beginning to be
understood.
significance
The — represent probably an ancient
feature of the genome.
split-gene arrangements
The presence of introns is —-, and the process of splicing represents the —-.
reminiscent of antiquity
dominance of RNA-world
In recent times, the understanding of —- and —- in the living system have assumed more importance.
RNA and RNA-dependent processes
During replication and transcription a — was copied to form another —. Hence, these processes are easy to conceptualise
on the basis of —.
nucleic acid, nucleic acid
complementarity
The process of translation requires transfer of genetic information from a —- to synthesise —-.
polymer of nucleotides to synthesise a polymer of amino acids
Neither does any complementarity exist between — and —, nor could any be drawn theoretically.
nucleotides and amino acids
There existed —, though, to support the notion that change in — (–) were responsible for change in amino acids in proteins.
ample evidences
nucleic acids (genetic material)
This led to the proposition of a — that could direct the sequence of amino acids during synthesis of —.
genetic code
proteins
If determining the — of genetic material and the
structure of DNA was very exciting, the proposition and — were most —.
biochemical nature
deciphering of
genetic code
challenging
In a very true sense, Proposition of genetic code required
involvement of scientists from several disciplines – —-,—-,—-,—-.
physicists, organic
chemists, biochemists and geneticists
It was —, a —,
who argued that since there are only 4 bases and if they have to code for 20 amino acids, the code should constitute a —-.
George Gamow
physicist
combination of bases
George gamow suggested that in order to code for all the 20 amino acids, the code should be made up of —.
This was a very —proposition, because
a permutation combination of 4^3
(4 × 4 × 4) would generate —–;
generating —-.
three nucleotides
bold
64 codons, many more codons than required
Providing proof that the —– was a ,more daunting task
code was triplet
The —- method developed by —- was instrumental in synthesising RNA molecules with defined combinations of bases (— and —-).
chemical
Har Gobind Khorana
homopolymers and copolymers
—- and —-, — system for protein synthesis finally helped the code to be deciphered.
Marshall Nirenberg’s cell-free
—- enzyme (—) was also helpful in polymerising RNA with defined sequences in a template independent manner (—-).
Severo Ochoa
polynucleotide phosphorylase
enzymatic synthesis of RNA
(i) The codon is —-.
— codons code for amino acids and —codons do
not code for any amino acids, hence they function as —-
triplet
61, 3- stop codons.
(ii) Some — are coded by —-, hence the code is —-.
amino acids
more than one codon
degenerate
(iii) The codon is read in —in a — fashion. There are
no punctuations.
mRNA , contiguous
(iv) The code is — : for example, from bacteria to human UUU would code for —-
NEARLY universal
Phenylalanine (phe).
Some exceptions to this
rule of universality of code have been found in — codons, and in some —.
mitochondrial, protozoans
(v) — has dual functions. It codes for — , and it
also act as — codon.
AUG
Methionine (met), initiator
(vi) UAA, UAG, UGA are —- codons
stop terminator
