Mira Molecular Biology Part1
Mira Molecular Biology Part1
Mira Molecular Biology Part1
(Part 1)
Ranim Mira
The nucleus contains the cell’s DNA (genome)
RNA is synthesized in the nucleus and exported
to the cytoplasm
Nucleus replication
Cytoplasm
DNA
transcription
RNA (mRNA)
translation
Proteins
1
DNA Replication
• Cell division involving mitosis produces 2 daughter cells that are genetically
identical to each other and genetically identical to the parent cell
• Remember that for this to happen, DNA in the parent cell must be replicated
(copied) before the cell divides – this process occurs during Interphase in the
cell cycle.
Storage of DNA
• In eukaryotic cells (animals, plants, fungi) DNA is stored in the nucleus, which is separated
from the rest of the cell by a semipermeable membrane
• The DNA is only organized into chromosomes during cell replication.
• Between replications, the DNA is stored in a compact ball called chromatin, and is wrapped
around proteins called histones to form nucleosomes
The Gene
• A gene is a unit of inheritance
• Carries the information for a: -polypeptide -structural RNA
molecule
• Genes contain most of the information necessary for
living cells to survive and reproduce.
• In most organisms, genes are made of DNA, where the
particular DNA sequence determines the function of the
gene.
• A gene is transcribed (copied) from DNA into RNA, which
can either be non-coding (ncRNA) with a direct function, or
an intermediate messenger (mRNA) that is then translated
into protein.
Gene Structure
• The structures of both eukaryotic and prokaryotic genes involve several nested
sequence elements.
• Each element has a specific function in the multi-step process of gene expression.
• The sequences and lengths of these elements vary, but the same general functions are
present in most genes.
• Regulatory sequences are located at the extremities of genes. These sequence regions
can either be next to the transcribed region (the promoter) or separated by many
kilobases (enhancers and silencers).
• The promoter is located at the 5' end of the gene and is composed of (a core
promoter sequence & a proximal promoter sequence). The core promoter marks
the start site for transcription by binding RNA polymerase while the proximal
promoter region binds transcription factors that modify the affinity of the core
promoter for RNA polymerase
• Enhancers and silencers may be distantly located from the gene. The binding of
different transcription factors, therefore, regulates the rate of transcription initiation at
different times and in different cells.
• The open reading frame (ORF) of a gene is therefore usually represented as an
arrow indicating the direction in which the sense strand is read. Only the region
between the start and stop codons encodes the final protein product.
• The untranslated regions (UTRs) contain further regulatory sequences. The 3' UTR
contains a terminator sequence, which marks the endpoint for transcription and
releases the RNA polymerase. The 5’ UTR binds the ribosome, which translates the
protein-coding region into a string of amino acids that fold to form the final protein
product. In the case of genes for non-coding RNAs, the RNA is not translated but
instead folds to be directly functional.
Gene Structure
• The structure of eukaryotic genes includes features not
found in prokaryotes. Most of these relate to post- Repressor proteins bound to the operator sequence
transcriptional modification of pre-mRNAs to physically obstructs the RNA polymerase enzyme,
produce mature mRNA ready for translation into protein preventing transcription.
which include: Riboswitches are another important regulatory sequence
transcripts are typically subdivided into exon & intron commonly present in prokaryotic UTRs.
regions. Exon regions are retained in the final mature
mRNA molecule, while intron regions are spliced out
(excised) during post-transcriptional processing
Eukaryotic post-transcriptional processing also adds a 5' cap
to the start of the mRNA and a poly-adenosine tail to the
end of the mRNA.
While
• The most obvious difference of the prokaryotic genes:
ORFs are often grouped into a polycistronic operon under
the control of a shared set of regulatory sequences.
The operator sequence next to the promoter is the main
regulatory element in prokaryotes.
Each ORF typically has its own ribosome binding site
(RBS) so that ribosomes simultaneously translate ORFs on
the same mRNA.
Gene Structure
Base-pairing: hydrogen bonds are relatively weak bonds compared to covalent bonds, it
can form between a pyrimidine and a purine.
Watson-Crick base-pairing rules
•A T
•G C
DNA
• The DNA model was developed by Watson
and Crick in 1953.
• They received a Nobel prize in 1962 for
their work.
• The model looks like a twisted ladder –
double helix.
• X-ray diffraction photograph of the DNA
double helix
Deoxyribonucleotides found in DNA
dA dG dT dC
Unusual structures of DNA
• There are major non-B-DNA structures have been described (Z-DNA, triplex DNA, G-
quadruplexes and cruciform DNA) which are stabilized by unconstrained negative supercoiling
and due to additional hydrogen bonds and can be formed under physiological conditions.
• The four-stranded nucleic acid structures called G-quadruplexes (G4s) and possess a high
degree of plasticity compared to the double-stranded canonical arrangement. Unique properties
include polymorphism, robustness and fast folding. These translate into biological functions of
importance to disease and ageing – G4s are abundant in the telomere as well as oncogenes and
may be important in virus life cycles.
• Bent DNA: Adenine base is rigid and when replaced by other bases due to photochemical
damage, anti-tumor drugs or mispairing of bases.
DNA Replication
• DNA Helix: In general, DNA is double-
stranded (ds), it takes the form of a right-
handed helix with approximately 10 base
pairs per turn of the helix.
• Two strands of the DNA double helix are
antiparallel & complementary to each
other.
• A nucleic acid polymer has a free 5’-
phosphate group at one end and a free 3’-OH
group at the other end
• The sequence is read from the free 5’-end
using the letters of the bases
• This example reads
5’—A—C—G—T—3’
Nucleases
• Nucleases are enzymes that are known to cleave
phosphodiester bonds in nucleic acids. They are
an important tool in DNA repair & molecular
cloning. On the basis of the locus (Site) of their
activity, nucleases are divided into
endonucleases and exonucleases.
• Endonuclease is found only in prokaryotes
while exonuclease is found in both eukaryotes
and prokaryotes. It is found only in prokaryotes. It is found in both eukaryotes
and prokaryotes.
Nucleases
Restriction Enzymes: are specific endonucleases, which recognize specific short sequences of DNA and
cleave the DNA at or near the recognition sequence. Recognition sequences: usually 4 or 6 bases but there
are some that are 5, 8, or longer
• Recognition sequences are palindromes
Palindrome: sequence of DNA that is the same when one strand is read from left to right or the other strand
is read from right to left– consists of adjacent inverted repeats.
• Example of a palindrome:
GAATTC
CTTAAG
Restriction enzymes are isolated from bacteria, derive names from the bacteria.
Genus- first letter capitalized
Species- second and third letters (small case)
Additional letters from “strains”
Example: EcoRI
• E Escherichia
• Co coli
• R R strain
• I Roman number, first enzyme discovered from Escherichia coli R
Hybridization vs Denaturation
• Nucleic acid hybridization (Annealing) is the formation of a duplex between two
complementary sequences using hydrogen bonds.
• Intermolecular hybridization: between two polynucleotide chains which have complementary
bases
• DNA-DNA
• DNA-RNA
• RNA-RNA
While,
DNA denaturation is a process of separating
dsDNA into single strands by either physical or
chemical agents like: Heat, UV light, high pressure,
sonication and surface action. Acids, alkalis, heavy
metals, DMSO, NaOH, guanidine detergents,
And urea.
DNA Replication
Purpose: cells need to make a copy of DNA before dividing so each
daughter cell has a complete copy of genetic information
3 proposed Models of Replication
DNA Replication
Meselson and Stahl Experiment
Replication of DNA
Semi-Conservative Model
• base pairing allows each strand to
serve as a template for a new strand
• new strand is 1/2 parent template &
1/2 new DNA
DNA Replication
DNA Replication
Large team of enzymes coordinates replication which needs the participation of more
than 20 enzymes & proteins called DNA replicase system or replisomes.
DNA Synthesis (Replication)
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DNA Synthesis (Replication)
DNA Synthesis (Replication)
DNA Synthesis (Replication)
.
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DNA Synthesis (Replication)
.
DNA polymerases
. DNA
lagging strand
DNA polymerase III
polymerase I
3’
ligase primase
Okazaki 5’
5’ fragments
3’ 5’ SSB
3’
helicase
DNA
polymerase III
5’
leading strand
3’
3 5
3
5
3 5 5
3
Lagging strand
ligase
growing 3
replication fork
5
Leading strand
Lagging strand
3
5
3
DNA polymerase III
Okazaki fragments
joined by ligase Leading strand
“spot welder” enzyme continuous synthesis
DNA Synthesis (Replication)
RNA primer is added
built by primase
serves as starter sequence for DNA polymerase III
5
3 5 3
5
3
3 5
growing 3 primase
replication fork DNA polymerase III
5
RNA 5
3
DNA Synthesis (Replication)
PROOFREAD:
DNA Polymerase I proofreads new
strands and backtracks to correct errors
3
3
5 ligase
growing 3
replication fork
5
RNA 5
3
• 3. DNA replication is
• 8. Association of histones H1 with nucleosome shows
• (a) conservative (b) conservative and discontinuous
• (a) the occurrence of transcription (b) the occurrence of replication
• (c) semi-conservative and discontinuous (d) semi-conservative and semi-
discontinuous • (c) exposed DNA double helix (d) the condensation of DNA into chromatin fibre
• 9. The 3’ – 5’ phosphodiester linkage joins
• 4. Which of the following is used in DNA replication studies? • (a) two DNA strands (b) two nucleotides
• (a) Neurospora crassa (b) Drosophila melanogaster • (c) a nitrogenous base with pentose sugar (d) two nucleosides
• 5. Which of the following helps in opening of DNA double helix in front of replication fork? • (a) Endonuclease (b) DNA polymerase
• 12. Which of the following is true about DNA polymerase? • a) Ligase b) Helicase
• b) It can synthesize DNA in the 3’ to 5’ direction • 17. Which of the following enzymes is the principal replication enzyme in E. coli?
• d) It can synthesize mRNA in the 5’ to 3’ direction • c) DNA polymerase III d) None of the mentioned
• 13. What is the reaction in DNA replication catalyzed by DNA ligase? • 18. Which of the following form is predominantly expressed in cells?
• c) Formation of a phosphodiester bond between the 3’-OH of one Okazaki fragment • 19. The Chargaff rules state that the number of purines and pyrimidines are equal
and the 5’-phosphate of the next on the lagging strand (A+G = T + C) in any double-stranded DNA molecule. Watson and Crick later solved
the structure of DNA and nitrogen base pairings.
• d) Base pairing of the template and the newly formed DNA strand
• Which of the following base-pairing rule is true?
• 14. Which of the following reactions is required for proofreading during DNA
replication by DNA polymerase III? • a) Adenine pairs with Guanine and Thymine pairs with Cytosine
• a) 5’ to 3’ exonuclease activity • b) Adenine pairs with Thymine and Guanine pairs with Cytosine
• b) 3’ to 5’ exonuclease activity • c) Adenine pairs with Cytosine and Guanine pairs with Thymine
• d) 5’ to 3’ endonuclease activity
Test your understanding
• 20. The DNA replication occurs in a semi-conservative manner which means: • 24. As the two strands of the double helix are separated, the positive supercoiling
a) Two daughter cells with one consisting of double-helical parent DNA, others have newly interferes with the further unwinding of DNA.
synthesized DNA.
• Which of the following enzyme makes a break in a strand of DNA to release the
• b) Two daughter cells each consisting of one parental strand and one newly supercoiling and facilitate the replication to occur?
synthesized DNA. a) DnaA protein b) Single-strand binding protein
c) Two daughters cells each consisting of one-half parental and another half newly c) DNA polymerase d) Topoisomerase
synthesized DNA resulting from the crossover.
d) None of the above 25. Which of the following enzyme has a unique ability to introduce positive and
negative supercoiling of the DNA and it is the target for antibacterial agents such as
• 21. Which of the following are the characteristic feature of DNA replication? ciprofloxacin/quinolones?
a) DnaA protein b) DNA helicase
• a) DNA replication is template-directed c) DNA gyrase d) DNA polymerase
• b) DNA replication requires short RNA primers • 26. DNA replication is bidirectional and anti-parallel. Which of the statement is
FALSE regarding DNA replication?
• c) DNA replication is a highly accurate process
• a) The DNA synthesis i.e. addition of nucleotide occurs from 5'-3' position
• d) All of the Above
• b) The DNA synthesis is semi-continuous with continuous leading strand and discontinuous
lagging strand.
• 22. In prokaryotes, DNA replication begins at a single site that is rich in AT nucleotide • c) The synthesis of leading and lagging strands occurs simultaneously
sequence, where two strands unwind and separate.
• d) None of the Above
• This ATP dependent process is catalyzed by a protein known as..................................?
• a) DnaA protein b) Single-strand binding protein
• 27. The DNA polymerase is a template-directed enzyme that synthesizes a new
• c) DNA polymerase d) Topoisomerase complementary strand from a parent strand, but it requires the existing short
nucleotide sequence for its elongation.
• 23. The short strand of .......................... primer is required for the replication of DNA: Which of the following enzyme is required for the synthesis of this primer?
1. Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York:
Garland Science; 2002. DNA Replication Mechanisms. Available from:
https://www.ncbi.nlm.nih.gov/books/NBK26850.
2. Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer
Associates; 2000. DNA Replication. Available from:
https://www.ncbi.nlm.nih.gov/books/NBK9940/.
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