Concurrent synthesis on the leading and lagging strands
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DNA replication occurs concurrently on the leading and lagging strands. The leading strand runs in the same direction as the replication fork and allows for continuous DNA synthesis. The lagging strand runs in the opposite direction and requires discontinuous DNA synthesis in fragments called Okazaki fragments. DNA polymerase III is the main polymerase in E. coli, consisting of a dimer core enzyme and accessory proteins that allow for high processivity of DNA synthesis on both strands concurrently.
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Denaturation and renaturation of dna
DNA is a double-helix molecule that carries genetic instructions. It is composed of two strands of polynucleotides made up of nucleotides, each containing a nitrogenous base, sugar, and phosphate. The strands are stabilized by hydrogen bonds between complementary bases and base-stacking interactions. DNA can be denatured into single strands by elevated temperature, extreme pH, low salt concentrations, or chemicals that disrupt hydrogen bonding between strands. Denaturation temperature depends on factors like base composition and length. Renaturation occurs when double-stranded DNA is cooled under conditions that allow the strands to re-form hydrogen bonds and complementary base pairing.
DNA replication
The document summarizes DNA replication. It describes that DNA replication produces two identical copies of DNA from one original molecule through a semi-conservative process. This involves unwinding of DNA at origins of replication by helicase to form replication forks that grow bidirectionally. DNA polymerase then synthesizes new strands using the original strands as templates. Replication occurs through initiation, elongation, and termination steps mediated by various proteins at the replication fork. The Meselson-Stahl experiment provided evidence that DNA replication is semi-conservative through density gradient centrifugation of parental and progeny DNA.
Replication in prokaryotes
The document summarizes the process of DNA replication in prokaryotes. It describes that replication initiates at the origin of replication (oriC) site and proceeds bidirectionally. There are three main steps - initiation, elongation, and termination. In initiation, proteins help unwind DNA at oriC. In elongation, primase synthesizes primers and DNA polymerase adds nucleotides to replicate both leading and lagging strands. In termination, RNA primers are removed and DNA ligase seals the replicated DNA, completing replication.
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The document discusses three models of DNA replication:
1) Asymmetric replication - the leading and lagging strands are replicated differently due to the 5' to 3' directionality of DNA polymerase. The leading strand replicates continuously while the lagging strand replicates discontinuously in short Okazaki fragments.
2) D-loop model - replication in mitochondria where one strand is displaced to form a D-loop and replicates first before the other strand.
3) Rolling circle model - used by plasmids and viruses where one strand is nicked and displaced to be used as a template, forming multiple copies linked together in a concatemer.
Translation
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3. The basic steps of translation include initiation of protein synthesis at the start codon, elongation through sequential addition of amino acids specified by mRNA codons, and termination when a stop codon is reached.
Homologous recombination
1. The document discusses models of homologous recombination including the Holliday model and the double-strand break repair model. It describes the key steps and proteins involved in each model.
2. Recombination involves the breakage and rejoining of DNA. In eukaryotes, the MRN/X complex processes DNA breaks. The Rad51 and Rad54 proteins then facilitate strand invasion and D-loop formation during homologous pairing.
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Tryptophan operon
The tryptophan operon regulates the biosynthesis of tryptophan in E. coli through transcriptional attenuation and repression. It contains five genes encoding the enzymes needed to synthesize tryptophan. When tryptophan levels are high, the tryptophan repressor binds to the operator site, preventing transcription. Additionally, a regulatory region can form a terminator stem-loop structure to halt transcription if tryptophan tRNA levels are high during translation of the leader mRNA sequence. However, if tryptophan levels are low, the terminator structure does not form and transcription of the operon proceeds.
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MODELS OF REPLICATION
The document discusses three models of DNA replication:
1) Asymmetric replication - the leading and lagging strands are replicated differently due to the 5' to 3' directionality of DNA polymerase. The leading strand replicates continuously while the lagging strand replicates discontinuously in short Okazaki fragments.
2) D-loop model - replication in mitochondria where one strand is displaced to form a D-loop and replicates first before the other strand.
3) Rolling circle model - used by plasmids and viruses where one strand is nicked and displaced to be used as a template, forming multiple copies linked together in a concatemer.
Translation
1. Translation is the process of converting the genetic code in mRNA into a protein by reading the mRNA codons in groups of three and adding the appropriate amino acids specified by tRNA.
2. There are 64 possible codons made up of combinations of the 4 bases in mRNA, with 3 codons serving as stop signals. tRNA contains anticodons that pair with mRNA codons and carry the corresponding amino acid.
3. The basic steps of translation include initiation of protein synthesis at the start codon, elongation through sequential addition of amino acids specified by mRNA codons, and termination when a stop codon is reached.
Homologous recombination
1. The document discusses models of homologous recombination including the Holliday model and the double-strand break repair model. It describes the key steps and proteins involved in each model.
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Tryptophan operon
The tryptophan operon regulates the biosynthesis of tryptophan in E. coli through transcriptional attenuation and repression. It contains five genes encoding the enzymes needed to synthesize tryptophan. When tryptophan levels are high, the tryptophan repressor binds to the operator site, preventing transcription. Additionally, a regulatory region can form a terminator stem-loop structure to halt transcription if tryptophan tRNA levels are high during translation of the leader mRNA sequence. However, if tryptophan levels are low, the terminator structure does not form and transcription of the operon proceeds.
Transcription in prokaryotes
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It also briefs about the conditions that would favor the transition from one form to the another
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This document summarizes DNA replication in prokaryotes. It begins by introducing DNA and its role in encoding genetic instructions. It then describes the general features of DNA replication, including that it is semi-conservative and bidirectional from the origin of replication. It discusses the various enzymes involved, including DNA polymerase, helicase, and ligase. It provides details on the three stages of replication in prokaryotes - initiation, elongation, and termination. Initiation begins at the origin of replication with unwinding, elongation involves continuous leading and discontinuous lagging strand synthesis, and termination occurs at terminus sequences.
Dna replication in prokaroytes and in eukaryotes
1. DNA replication is the process where parental DNA is used as a template to produce identical copies of DNA or daughter DNA. It ensures faithful transmission of genetic material to offspring.
2. Replication starts at specific origins of replication and involves initiation, elongation, and termination phases. Enzymes involved include DNA polymerases, helicases, primases, ligases and more.
3. Eukaryotic replication is more complex, with multiple polymerases and regulated initiation. Telomerase is required for end-replication and chromosome integrity.
4. DNA repair mechanisms include base excision, nucleotide excision, mismatch and double-strand break repair to fix errors and damage via pathways like non-homologous
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Eukaryotic translation is the process by which messenger RNA is translated into proteins. It involves three main phases: initiation, elongation, and termination. Initiation requires several eukaryotic initiation factors to form a pre-initiation complex and recruit the small ribosomal subunit to the 5' end of mRNA. Elongation then adds amino acids to the growing polypeptide chain via three elongation factors. Termination occurs when release factors recognize a stop codon and allow dissociation of the ribosome and release of the completed protein. The process is more complex in eukaryotes compared to prokaryotes due to the larger ribosome size and additional initiation factors required.
Wobble hypothesis
- Crick proposed the "wobble hypothesis" to explain how more than one codon can direct the synthesis of a single amino acid, given there are fewer tRNAs than codons.
- The hypothesis suggests the third nucleotide in a codon is not as important in binding to the tRNA anticodon. The first two nucleotides specify the amino acid.
- At the wobble position, the third nucleotide in the codon can bind in non-standard ways ("wobble") to the first nucleotide in the anticodon, allowing a single tRNA to bind to multiple codons and explain the degeneracy of the genetic code.
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1) Allosteric enzymes have additional sites called allosteric sites that are distinct from the active site. Binding of an effector molecule to these sites can induce a conformational change in the active site, increasing or decreasing the enzyme's activity.
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Prokaryotic DNA replication
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Dna replication in prokaroytes and in eukaryotes
1. DNA replication is the process where parental DNA is used as a template to produce identical copies of DNA or daughter DNA. It ensures faithful transmission of genetic material to offspring.
2. Replication starts at specific origins of replication and involves initiation, elongation, and termination phases. Enzymes involved include DNA polymerases, helicases, primases, ligases and more.
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- The hypothesis suggests the third nucleotide in a codon is not as important in binding to the tRNA anticodon. The first two nucleotides specify the amino acid.
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3) Allosteric enzymes exhibit sigmoidal kinetics curves rather than traditional hyperbolic curves due to their cooperative binding behavior. Positive allosteric effectors increase enzyme activity while negative effectors decrease it.
mRNA This splicing
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mRNA processing
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DNA polymerases are a group of enzymes that are used to make copies of DNA templates, essentially used in DNA replication mechanisms. These enzymes make new copies of DNA from existing templates and also function by repairing the synthesized DNA to prevent mutations. DNA polymerase catalyzes the formation of the phosphodiester bond which makes up the backbone of DNA molecules. It uses a magnesium ion in catalytic activity to balance the charge from the phosphate group.
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This document discusses transcription in eukaryotes. It begins with definitions of transcription and describes the basic process of RNA being synthesized from a DNA template. It then covers the mechanisms of transcription, including initiation involving RNA polymerase and transcription factors, elongation, and termination. The key similarities between prokaryotic and eukaryotic transcription are that DNA acts as a template and RNA polymerase facilitates RNA synthesis. Key differences are that eukaryotic transcription occurs in the nucleus, is carried out by three classes of RNA polymerase, and RNAs are processed in the nucleus rather than the cytoplasm.
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DNA replication is fundamental process occurring in all living organism to copy their DNA. The process is called replication in sense that each strand of dsDNA serve as template for reproduction of complementary strand.
LEC#7 DNA Replication and Repair.pdf
DNA replication requires unwinding of the DNA double helix by helicases. Single-stranded DNA binding proteins prevent rewinding. DNA polymerases then synthesize new strands by adding nucleotides to the 3' end of the existing strand. In eukaryotes, the leading strand is continuously extended while the lagging strand is synthesized in fragments. Proofreading by exonuclease activity increases the fidelity of replication.
Rolling circle mechanism ppt
Rolling circle replication is a process that can rapidly synthesize multiple copies of circular DNA or RNA molecules. It involves the unidirectional replication of circular nucleic acids. The process begins with an initiator protein nicking one strand of the circular DNA. DNA polymerase then uses the 3' end of the nicked strand to initiate replication, displacing the 5' end. Replication continues around the circle to produce a long concatemer of copies. The concatemer is then cleaved and ligated to form multiple double-stranded circular DNA molecules. Rolling circle replication is used by some viruses and plasmids to replicate their genomes and can be harnessed for applications like signal amplification in biosensing.
Plasmid replication -methods & types
Plasmids are small, circular DNA structures that can replicate independently of the host chromosome. They are commonly found in bacteria and play important roles in processes like drug resistance. Plasmid replication involves the recognition of an origin of replication sequence by plasmid-encoded initiator proteins. This leads to unwinding of the DNA and assembly of a replisome complex. The replication then proceeds bidirectionally via a rolling circle mechanism, where the growing DNA strand displaces the parental strand. Replication terminates once the circular plasmid is completely duplicated.
Replication of DNA
DNA replication occurs through a semiconservative process where each parental DNA strand serves as a template for the synthesis of a new complementary strand. This results in two daughter molecules each composed of one original parental strand and one newly synthesized strand. In eukaryotes, replication occurs during S phase of the cell cycle. The major enzymes involved are DNA polymerases, helicases, and ligases which unwind, copy, and join the strands respectively. Errors are corrected by proofreading and repair mechanisms to maintain genomic integrity.
protein synthesis in prokaryotes.pptx
presentation covers basic structure of protein, its synthesis and regulation in prokaryotic organisms
4. The amino acid sequence of several leucine zipper proteins are ind.pdf
4. The amino acid sequence of several leucine zipper proteins are indicated in the figure below
The leucine zipper motif is comprised of a single a-helix. One portion of this ca-helix, termed the
leucine zipper domain, homodimerizes with another identical protein and becomes active as a
transcription factor. The other major domain is termed the DNA-binding domain, and as its name
suggests, this is the part of the cu-helix that interacts with negatively charged DNA. Proteins
with leucine zippers are often important transcription factors, or proteins that are involved in
stimulating transcription of genetic material into mRNA. Highlighted residues in the figure
below are conserved among different proteins and species. (a) Regulatory Source protein Amino
acid sequence Connector DNA-binding region Leucine zipper (6 Amino acids) C/EBP DKNS
NEY RVRR ERN NI A VRK SRD KA KQRN VET QQ K VLE TSDN DIR KRVE QLs
RELDT RG ELT Mamma Jun SQERIKA ERKIRMRN RIAA, SKCRK RKLERI A RILE E
KVKTLK AQN SELA STANMLTE QVAQLKQ Fos EERR RIRR IRR ERN KMA A AKCRN
RRREL TDTL QAETDQLEDK SALQTE IAN LKEKEK EF Yeast GCN4 PES SDPA AL
KRARNTEA AR RS IR ARK LQRMKQ LED K VE E LSKNYHLE NE VA RILK KLvGER
Solution
Answer:
a) every 3rd-4th residue after Leucine is a hydrophobic amino acid i.e alanine, valine, isoleucine,
phenylalanine, proline or glycine. other amino acids in this sequence are charged and polar.
leucine occur every 7th position and hence followsa \'heptad\' kind of sequence.
b) The hydrogen bond in and alpha helix is between the negatively charged amino acid where the
N-H forms a hydrogen bond with a O=C at every 3-4 residues ahead in a protein sequence.
Therefore evry 3-4 residues will be oppositely charged to facilitate H-Bonding. Amphiphatic
helix is a type of helix having both hydrophobic and hydrophilic amino acids on two opposing
faces of an alpha helix, an organisation best suited for dimerization.
c) the leucine zipper actually works when two alpha helices form a coiled coil like structure
dimerizing with the aminoacid back bone. The basic DNA binding elements however still flank
from the helix and look like a partially opened zip. Something like this where ---- implies an
alpha helix.
\\--------
/--------
the side chains of the two helices pack in the holes provided by the hydrophobic amino acids at 3
position . the amino acids, arginine (N) and lysine (K) in the a.a chain have long side chains
which help in creating salt bridges between the two helices. since the cytosol is hydrophilic the
two alpha chains with hydrophobic side chains are drawn towards each other with nonpolar ends
inside the dimerization zone and the polar ends towards the cytosol to faciluate the energetically
favourable alignment and position.
d) The yellow region has a lot of positively charged amino acids which help in binding to the
negatively charged DNA sequence and hence help in DNA binding and sequence recognition
and help leucine zippers to function as transcription factors.
e) the z.
DNA & RNA
Genetic Codon The Three nucleotide base sequence in mRNA that act as code words for amino acids in protein constitute the genetic code or codons.
There are 64 different combinations of three base codons composed of Adenine (A), Guanine (G), Cytosine (C) and Uracil (U).
Written from the 5-’ end to 3’ end.
UAA,UAG & UGA do not code for amino acid. They are called as stop codon or non sense codon.
Characteristics of Genetic Code are:
University: same codon for same amino acid in all living organism.
Specificity: A particular codon will code for the same amino acid,highly specific or unambiguous.
Non overlapping : read from a fixed point as a continuous base sequence.
Degenerate: Most of the amino acids have more than one codon. 61 codons available to code for only 20 amino acids.
DNA :DNA stands for Deoxy Ribonucleic acid.
It’s the genetic code that determines all the characteristics of living organism.
DNA is a double stranded molecule, made up of two chains of nucleotides. Nucleotides consist of three subunits : a sugar, a phosphate group and a nitrogen base pair.
Sugar present is Deoxyribose and Nitrogen bases are :
Adenine (A)
Guanine (G)
Cytosine (C)
Thymine (T)
Structure of DNA : Double helical structure of DNA was proposed by James Watson and Francis Crick in 1953.
Features of model of DNA are:
DNA is a right handed double helix, have two polydeoxyribonucleotide chains twisted around each other on a common axis.
Two strands are antiparallel i.e., one strand runs in the 5’ to 3’ direction while the other in 3’ to 5’ direction.
The diameter of helix is 20 A° (2nm).
Each turn of the helix is 34 A° (3.4 nm) with 10 pairs of nucleotides, each pair placed at a distance of about 3.4 A°.
The two strands are held together by Hydrogen bonds formed by complementary base pairs. The A-T pair has 2 hydrogen bonds while G-C pair has 3 hydrogen bonds.
The complementary base pairing in DNA helix proves Chargaff’s rule. The content of adenine equals to that of thymine (A=T) and guanine equals to that of the cytosine (G≡C).
Function of DNA
RNA
DNA replication
Transcription
Translation
Dna replication 31
Replication begins at the origin of replication (oriC) and proceeds bidirectionally. It is semiconservative, meaning each parental DNA strand serves as a template for a new complementary strand. Specialized enzymes help unwind and copy the DNA, with DNA polymerase adding nucleotides to growing strands using DNA primers. DNA ligase then joins fragments together to complete replication. Errors are corrected through proofreading. Replication and repair mechanisms help preserve genetic information as cells divide.
structure of dna and transcription
1. The document provides an introduction to genetics and describes the structure and replication of DNA. It defines key genetic terms like gene, chromosome, DNA and explains the DNA double helix model proposed by Watson and Crick.
2. The summary describes the DNA double helix structure including that it consists of two anti-parallel polynucleotide chains held together by hydrogen bonds between complementary base pairs.
3. DNA replication is semi-conservative and involves unwinding of the DNA helix at the origin of replication to form a replication fork where new DNA strands are synthesized in the 5’-3’ direction.
molecular biology presentation.pptx
1. The Meselson-Stahl experiment provided evidence supporting the semiconservative model of DNA replication, where each parental DNA strand serves as a template for a new daughter strand.
2. DNA polymerase requires an RNA primer to initiate DNA synthesis. Polymerase I then replaces the RNA primer with DNA and seals the nick with DNA ligase.
3. DNA replication proceeds bidirectionally from an origin of replication. The leading strand is synthesized continuously while the lagging strand is made discontinuously in short Okazaki fragments.
Similar to Concurrent synthesis on the leading and lagging strands (20)
Bidirectional and rolling circular dna replication
Bidirectional and rolling circular dna replication
Dna chemistry structure,fuctions and its orgainization
Dna chemistry structure,fuctions and its orgainization
4. The amino acid sequence of several leucine zipper proteins are ind.pdf
4. The amino acid sequence of several leucine zipper proteins are ind.pdf
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ROOT CAP
Function
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3. Gleization
4. Calcification
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Plant systematics
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Plant systematics scientists
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Pits & plasmodesmata
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Minerals
Minerals are inorganic substances that occur naturally and are essential to life. Plants obtain minerals from soil and water, and animals and humans get minerals by eating plants or other animals. Minerals are important building blocks that support bones, teeth, blood, and metabolic processes in the body. Common dietary minerals include sodium, chloride, potassium, calcium, phosphorus, iron, magnesium, sulfur, zinc, chromium, cobalt, copper, fluoride, iodine, manganese, selenium, and molybdenum. While minerals are necessary for health, excessive intake of some can be toxic.
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This document discusses the medicinal uses of various spices. It provides information on the plant or herb, the part used (such as seeds, leaves, oil), and common ailments or conditions they have been used to treat. Some spices mentioned as having been used to treat digestive issues like gas, loss of appetite, and diarrhea, respiratory conditions like cough and bronchitis, and pain, inflammation and other musculoskeletal problems. The document serves as a reference for how spices have been used in traditional medicine.
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2. Sub fossil
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4. Macrofossil
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6. Trace fossil
7. Coprolites
8. Bioclast
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Concurrent synthesis on the leading and lagging strands
- 2. LEADINGAND LAGGING STRAND The parent strand that runs 5’-3’ in the reverse direction of fork movement is termed the leading strand ,and it serves as a template for the continuous DNA synthesis. The other parent strand that runs 5’-3’ in the direction of fork movement is termed the lagging strand , and it serves as a template for the discontinuous strand .
- 3. DNAPolymerase III It is a haloenzyme consist of a dimer containing 10 different polypeptide unit. This haloenzyme is main polymerase of E. coil. It is made up of three assemblies : • Clamp loading complex • B sliding clamp processivity factor • Core enzyme
- 4. Fig. showing the concurrent DNAsynthesis on the leading and the lagging strand
- 5. CONCLUSION • Concurrent DNA may be achieved on both the leading and lagging strand at a single replication fork . • The lagging template strand is “looped” in order to invert the physical direction of synthesis , but not the biochemical direction. • The enzyme functions as a dimer with each core enzyme achieving synthesis on one or the other strand.
- 6. THANKYOU