Regulation of gene expression in eukaryotesAnna Purna
Presence of nucleus and complexity of eukaryotic organism demands a well controlled gene regulation in eukaryotic cell. Tissue specific gene expression is essential as they are multicellular organisms in which different cells perform different functions. This PPT deals with various control points for the gene regulation and expression within a cell.
Regulation of gene expression in eukaryotesAnna Purna
Presence of nucleus and complexity of eukaryotic organism demands a well controlled gene regulation in eukaryotic cell. Tissue specific gene expression is essential as they are multicellular organisms in which different cells perform different functions. This PPT deals with various control points for the gene regulation and expression within a cell.
Transcription in eukaryotes: A brief view
Transcription is the process by which single stranded RNA is synthesized by double stranded DNA. Transcription in eukaryotes and prokaryotes has many similarities while at the same time both showing their individual characteristics due to the differences in organization. RNA Polymerase (RNAP or RNA Pol) is different in prokaryotes and eukaryotes. Coupled transcription is seen in prokaryotes but not in Eukaryotes. In eukaryotes the pre-RNA should be spliced first to be translated.
In Eukaryotic transcription, synthesis of RNA occurs in the 3’→5’ direction. The 3’ end is more reactive due to the hydroxide group. 5’ end containing phosphate groups meanwhile, is not very reactive when it comes to adding new nucleotides. In Eukaryotes, the whole genome is not transcribed at once. Only a part of the genome is transcribed which also acts as the first, principle stage of genetic regulation.
Eukaryotes have five nuclear polymerases:
• RNA Polymerase I: This produces rRNA (23S, 5.8S, and 18S) which are the major components in a ribosome. This also produces pre-rRNA in yeasts.
• RNA Polymerase II: Helps in the production of mRNA (messenger RNA), snRNA (small, nuclear RNA), miRNA. This is the most studied type and requires several transcription factors for its binding
• RNA Polymerase III: This synthesizes tRNA (transfer RNA), 5S rRNA and other small RNAs required in the cytosol and nucleus.
• RNA Polymerase IV: Synthesizes siRNA (small interfering RNA) in plants.
• RNA Polymerase V: This is the least studied polymerase and synthesizes siRNA-directed heterochromatin in plants.
Eukaryotic transcription can be broadly divided into 4 stages:
• Pre-Initiation
• Initiation
• Elongation
• Termination
Transcription is an elaborate process which cells use to copy the genetic information stored in DNA into RNA. This pre-RNA is modified into mRNA before being transcribed to proteins. Transcription is the first step to utilizing the genetic information in a cell. Both Eukaryotes and Prokaryotes employ this process with the basic phases remaining the same. However eukaryotic transcription is more complex indicating the changes transcription has undergone towards perfection during evolution.
The flow of information in the cell starts at DNA, which replicates to form more DNA. Information is then ‘transcribed” into RNA, and then it is “translated” into protein.
Information does not flow in the other direction.
A few exceptions to the Central Dogma exist
some RNA viruses, called “retroviruses”.
SOS repair
a system that repairs severely damaged bases in DNA by base excision and replacement, even if there is no template to guide base selection. This process is a last resort for repair and is often the cause of mutations.
The delivery of newly synthesized protein to their proper cellular destination, usually referred to as protein targeting or sorting.
The mode of protein transport depends chiefly on the location in the cell cytoplasm of the polysomes involved in protein synthesis.
There are two modes of protein sorting:-
1) Co - translational Transportation.
2) Post - translational Transportation.
Protein targeting or protein sorting is the biological mechanism by which proteins are transported to their appropriate destinations in the cell or outside it. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, plasma membrane, or to exterior of the cell via secretion.
This presentation explains DNA transcription and RNA Processing.
It gives details about prokaryotic DNA transcription and eukaryotic DNA transcription. it also explains post-transcriptional modification both in prokaryotes and eukaryotes.
Transcription in eukaryotes: A brief view
Transcription is the process by which single stranded RNA is synthesized by double stranded DNA. Transcription in eukaryotes and prokaryotes has many similarities while at the same time both showing their individual characteristics due to the differences in organization. RNA Polymerase (RNAP or RNA Pol) is different in prokaryotes and eukaryotes. Coupled transcription is seen in prokaryotes but not in Eukaryotes. In eukaryotes the pre-RNA should be spliced first to be translated.
In Eukaryotic transcription, synthesis of RNA occurs in the 3’→5’ direction. The 3’ end is more reactive due to the hydroxide group. 5’ end containing phosphate groups meanwhile, is not very reactive when it comes to adding new nucleotides. In Eukaryotes, the whole genome is not transcribed at once. Only a part of the genome is transcribed which also acts as the first, principle stage of genetic regulation.
Eukaryotes have five nuclear polymerases:
• RNA Polymerase I: This produces rRNA (23S, 5.8S, and 18S) which are the major components in a ribosome. This also produces pre-rRNA in yeasts.
• RNA Polymerase II: Helps in the production of mRNA (messenger RNA), snRNA (small, nuclear RNA), miRNA. This is the most studied type and requires several transcription factors for its binding
• RNA Polymerase III: This synthesizes tRNA (transfer RNA), 5S rRNA and other small RNAs required in the cytosol and nucleus.
• RNA Polymerase IV: Synthesizes siRNA (small interfering RNA) in plants.
• RNA Polymerase V: This is the least studied polymerase and synthesizes siRNA-directed heterochromatin in plants.
Eukaryotic transcription can be broadly divided into 4 stages:
• Pre-Initiation
• Initiation
• Elongation
• Termination
Transcription is an elaborate process which cells use to copy the genetic information stored in DNA into RNA. This pre-RNA is modified into mRNA before being transcribed to proteins. Transcription is the first step to utilizing the genetic information in a cell. Both Eukaryotes and Prokaryotes employ this process with the basic phases remaining the same. However eukaryotic transcription is more complex indicating the changes transcription has undergone towards perfection during evolution.
The flow of information in the cell starts at DNA, which replicates to form more DNA. Information is then ‘transcribed” into RNA, and then it is “translated” into protein.
Information does not flow in the other direction.
A few exceptions to the Central Dogma exist
some RNA viruses, called “retroviruses”.
SOS repair
a system that repairs severely damaged bases in DNA by base excision and replacement, even if there is no template to guide base selection. This process is a last resort for repair and is often the cause of mutations.
The delivery of newly synthesized protein to their proper cellular destination, usually referred to as protein targeting or sorting.
The mode of protein transport depends chiefly on the location in the cell cytoplasm of the polysomes involved in protein synthesis.
There are two modes of protein sorting:-
1) Co - translational Transportation.
2) Post - translational Transportation.
Protein targeting or protein sorting is the biological mechanism by which proteins are transported to their appropriate destinations in the cell or outside it. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, plasma membrane, or to exterior of the cell via secretion.
This presentation explains DNA transcription and RNA Processing.
It gives details about prokaryotic DNA transcription and eukaryotic DNA transcription. it also explains post-transcriptional modification both in prokaryotes and eukaryotes.
1.Definition
2.Transcription is selective
3.Transcription in Prokaryotes
•Initiation
•Elongation
•RNA polymerase vs DNA polymerase
•Termination
4.Transcription in Eukaryotes
•Initiation
•Elongation
•Termination
•Post transcriptional modifications
INTRODUCTION
HISTORY
MECHANISM OF PROTEIN SYNTHESIS
TRANSCRIPTION
TRANSLATION
TRANSCRIPTION
INITIATION
ELONGATION
TERMINATION
TRANSLATION
AMINOACYLATION OF tRNA
INITIATION OF POLYPEPTIDE CHAIN
ELONGATION
TERMINATION
CONCLUSION
REFERENCES
Copper- sources, daily requirement, absorption, transportation, storage, excretion, role in enzymatic action, role in iron metabolism, role in elastin maturation, role in bone formation, copper deficiency, copper toxicity, Wilson disease, Menkes disease.
Folic acid- Chemistry, One carbon metabolism and megaloblastic anemiaNamrata Chhabra
Folic acid- Structure, forms, absorption, transportation, storage, excretion, role in one-carbon metabolism, role in methionine synthesis, role in nucleotide biosynthesis, folate trap, folate antagonists, megaloblastic anemia
Sugar derivatives and reactions of monosaccharidesNamrata Chhabra
Reactions of monosaccharides, osazone formation, reduction, oxidation, reaction with acids and alkalies, ester formation and formation of amino sugars, amino sugar acids and deoxy sugars.
Definition of ELISA, Immunochemical principle of ELISA, Direct, Indirect, Sandwich and Competitive ELISA, applications of ELISA in the diagnostic field, and benefits/drawbacks of ELISA.
Molecular biology revision-Part 3 (Regulation of genes expression and Recombi...Namrata Chhabra
Regulation of gene expression in prokaryotes and eukaryotes, Recombinant DNA technology, Southern hybridization, Northern Hybridization, Western hybridization, cloning, PCR, Applications of RDT, Animal cloning, Multiple choice questions
Case studies, enzyme inhibition, factors affecting enzyme activity, regulation of enzyme activity, Isoenzymes, classification of enzymes, coenzyme and co-factors, the clinical significance of enzymes, and the mechanism of enzyme action
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
How to Make a Field invisible in Odoo 17Celine George
It is possible to hide or invisible some fields in odoo. Commonly using “invisible” attribute in the field definition to invisible the fields. This slide will show how to make a field invisible in odoo 17.
Macroeconomics- Movie Location
This will be used as part of your Personal Professional Portfolio once graded.
Objective:
Prepare a presentation or a paper using research, basic comparative analysis, data organization and application of economic information. You will make an informed assessment of an economic climate outside of the United States to accomplish an entertainment industry objective.
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
Embracing GenAI - A Strategic ImperativePeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
A Strategic Approach: GenAI in EducationPeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
1. Revision-Molecular Biology
PART-2
Professor (Dr.) NAMRATA CHHABRA
MHPE, MD, MBBS, FAIMER FELLOW
PRINCIPAL-IN-CHARGE, PROFESSOR & HEAD,
DEPARTMENT OF BIOCHEMISTRY
SSR MEDICAL COLLEGE, MAURITIUS
Transcription, Translation, Genetic code and Mutations
Case studies and Multiple-choice questions
3. DNA Transcription
•The synthesis of an RNA molecule from DNA is called Transcription.
• All eukaryotic cells have five major classes of RNA: ribosomal RNA
(rRNA), messenger RNA (mRNA), transfer RNA (tRNA), small nuclear RNA
and microRNA (snRNA and miRNA).
•The first three are involved in protein synthesis, while the small RNAs are
involved in mRNA splicing and regulation of gene expression.
4. Similarities between Replication and Transcription
The processes of DNA and RNA synthesis
are similar in that they involve-
(1) the general steps of initiation,
elongation, and termination with 5' to
3' polarity;
(2) large, multicomponent initiation
complexes; and
(3) adherence to Watson-Crick base-
pairing rules.
412-Jan-21 Our Biochemistry- Namrata Chhabra
5. Differences between Replication and Transcription
(1) Ribonucleotides are used in RNA synthesis rather than deoxy
ribonucleotides;
(2) U replaces T as the complementary base pair for A in RNA;
(3) A primer is not involved in RNA synthesis;
(4) Only a portion of the genome is transcribed or copied into RNA,
whereas the entire genome must be copied during DNA replication;
and
(5) There is no proofreading function during RNA transcription.
512-Jan-21 Our Biochemistry- Namrata Chhabra
6. Template strand
Except for T for U changes, coding strand corresponds exactly to the
sequence of the RNA primary transcript, which encodes the (protein)
product of the gene.
612-Jan-21 Our Biochemistry- Namrata Chhabra
8. Bacterial DNA-Dependent RNA Polymerase
The DNA-dependent RNA polymerase (RNAP) of
the bacterium Escherichia coli exists as an
approximately 400 kDa core complex consisting
of-
•two identical α subunits,
•similar but not identical β and β ' subunits, and
•an ω subunit and a
•A sigma subunit (σ)
•Beta is thought to be the catalytic subunit.
812-Jan-21 Our Biochemistry- Namrata Chhabra
9. Bacterial DNA-Dependent RNA Polymerase
• RNAP, a metalloenzyme, also contains two zinc molecules.
• The core RNA polymerase associates with a specific protein factor
(the sigma σ factor) that helps the core enzyme recognize and bind to
the specific deoxynucleotide sequence of the promoter region to
form the preinitiation complex (PIC)
• Bacteria contain multiple factors, each of which acts as a regulatory
protein.
912-Jan-21 Our Biochemistry- Namrata Chhabra
10. Mammalian DNA-Dependent RNA Polymerases
Mammalian cells possess three distinct nuclear DNA-Dependent RNA
Polymerases
• RNA polymerase I is for the synthesis of r RNA
• RNA polymerase II is for the synthesis of m RNA and miRNA
• RNA polymerase III is for the synthesis of tRNA/5S rRNA, snRNA
1012-Jan-21 Our Biochemistry- Namrata Chhabra
12. Termination of transcription (contd.)
•Beyond the hair pin, the RNA
transcript contains a strings of
Us, the bonding of Us to the
corresponding As is weak.
•This facilitates the dissociation
of the primary transcript from
DNA.
1212-Jan-21 Our Biochemistry- Namrata Chhabra
13. Modifications of primary transcript of mRNA in
prokaryotes
Transcription and translation are coupled in prokaryotic cells
1312-Jan-21 Our Biochemistry- Namrata Chhabra
14. Post Transcriptional modifications of
Ribosomal RNA (r- RNA)
• The 23S,16S, and 5S ribosomal RNAs of prokaryotes are produced form a single
RNA precursor molecule
• Cleavage and trimming are the mechanisms involved,
• Similar modifications are observed in the processing of eukaryotic r-RNA.
1412-Jan-21 Our Biochemistry- Namrata Chhabra
15. Post Transcriptional modifications of
Transfer RNA(t- RNA)
The extra nucleotides at both 5'
and 3' ends of t- RNA are
removed, an intron from the
anticodon arm is removed,
bases are modified and CCA
arm is attached to form the
mature functional t RNA.
1512-Jan-21 Our Biochemistry- Namrata Chhabra
16. Post Transcriptional modifications of
pre m- RNA
•The addition of the Guanosine
triphosphate (part of the cap is catalyzed
by the nuclear enzyme guanylyl
transferase.
•Methylation of the terminal guanine
occurs in the cytoplasm. and is catalyzed
by guanine-7-methyl transferase.
1612-Jan-21 Our Biochemistry- Namrata Chhabra
18. Post Transcriptional modifications of
Pre m RNA
Introns are removed from the primary transcript in the nucleus, exons
(coding sequences) are ligated to form the mRNA molecule
1812-Jan-21 Our Biochemistry- Namrata Chhabra
20. Clinical significance of Splicing
1) Antibodies against snRNPs
In systemic Lupus Erythematosus (SLE), an auto
immune disease, the antibodies are produced
against host proteins, including sn RNPs.
• 2) Mutations at the splice site
• Mutations at the splice site can lead to improper
splicing and the production of aberrant proteins .
• For example, some cases of Beta thalassemia are as
a result of incorrect splicing of beta globin m- RNA
due to mutation at the splice site.
2012-Jan-21 Our Biochemistry- Namrata Chhabra
21. Biological significance of Splicing
Tissue specific proteins are produced from the same primary transcript by
alternative splicing 2112-Jan-21 Our Biochemistry- Namrata Chhabra
22. Inhibitors of Transcription
• Rifampicin- binds with Beta subunit of prokaryotic
RNA polymerase,
• It is an inhibitor of prokaryotic transcription initiation.
• It binds only to bacterial RNA polymerase but not to
eukaryotic RNA polymerases.
• Therefore, Rifampicin is a powerful drug for treatment
of bacterial infections.
• Used for the treatment of tuberculosis and leprosy
2212-Jan-21 Our Biochemistry- Namrata Chhabra
23. Mechanism of action of Actinomycin D
• Actinomycin D- Intercalates with DNA strands
• Actinomycins inhibit both DNA synthesis and RNA
synthesis by blocking chain elongation.
• They interact with G·C base pairs as they require
the 2-amino group of guanine for binding.
• Actinomycins are used as anticancer drugs
2312-Jan-21 Our Biochemistry- Namrata Chhabra
24. Mitomycin and Alpha amanitin
• Mitomycin- Intercalates with DNA strands
• blocks transcription,
• used as anticancer drug
• Alpha amanitin is a molecule made from the “death
cap” mushroom and is a known potent inhibitor RNA
polymerase.
• One single mushroom could very easily lead to a fast
death in 10 days.
• The mechanism of action is that alpha amanitin inhibits
RNA polymerase –II at both the initiation and
elongation states of transcription.
2412-Jan-21 Our Biochemistry- Namrata Chhabra
25. Question-1
A promoter site on DNA :
a) Transcribes repressor
b) Initiates transcription
c) Codes for RNA Polymerase
d) Regulates termination
e) Translates specific proteins
2512-Jan-21 Our Biochemistry- Namrata Chhabra
27. Question 2
The removal of introns and subsequent self-splicing of adjacent exons
occurs in some portions of primary ribosomal RNA transcripts. The
splicing of messenger RNA precursor is :
a) RNA catalyzed in the absence of proteins
b) Self-splicing
c) Carried out by spliceosomes
d) Controlled by RNA polymerase
e) Regulated by RNA helicase
2712-Jan-21 Our Biochemistry- Namrata Chhabra
29. Question 3
In bacterial RNA synthesis, the function of factor Rho is to :
a) Increase the rate of RNA synthesis
b) Allow accurate initiation of transcription
c) Participate in termination of transcription
d) Allow the binding of RNA polymerase to the promoter
2912-Jan-21 Our Biochemistry- Namrata Chhabra
30. Answer
c) Participate in termination of transcription
3012-Jan-21 Our Biochemistry- Namrata Chhabra
31. Question 4
Two couples present to the emergency room with severe nausea,
vomiting, and diarrhea. One of the patients admits that she served a
salad at a dinner party to which she had added a few mushrooms. With
this information, it is likely that their symptoms are as a result of
inhibition of:
a) RNA Polymerase II
b) RNA Polymerase I
c) RNA splicing
d) RNA Polyadenylation
e) RNA Polymerase III
3112-Jan-21 Our Biochemistry- Namrata Chhabra
33. Question 5
A second-year student isolates nucleic acids from the cell, and finds
that some of the nucleic acids are pseudouridine and ribothymidine.
Which type of nucleic acid might have been isolated?
a) t RNA
b) rRNA
c) m RNA
d) Sn RNA
e) Mi RNA
3312-Jan-21 Our Biochemistry- Namrata Chhabra
35. Question 6
A 35-year-old female develops fever, night sweats, weight loss, and a
blood-tinged cough. An infectious disease doctor prescribed
Rifampicin. Which of the following enzymes is inhibited by Rifampicin?
a) DNA-dependent DNA polymerase
b) DNA-dependent RNA polymerase
c) RNA-dependent DNA polymerase
d) RNA-dependent RNA polymerase
e) Reverse transcriptase
3512-Jan-21 Our Biochemistry- Namrata Chhabra
37. Question 6
Actinomycin D, is an inhibitor of transcription, which acts as by
inhibiting-
a) β- subunit of prokaryotic RNA polymerase
b) Movement of RNA polymerase along the DNA template
c) Sigma subunit of RNA polymerase
d) Prokaryotic Topoisomerase II
e) Prokaryotic helicase
3712-Jan-21 Our Biochemistry- Namrata Chhabra
38. Answer
b) Movement of RNA polymerase along the DNA template
3812-Jan-21 Our Biochemistry- Namrata Chhabra
39. Question 7
The initial RNA produced during the translation of DNA to RNA, which
contains both the coding exons and the non-coding introns, is known as
which of the following?
a) Amino acyl transfer RNA
b) m RNA
c) Ribosomal RNA
d) Heterogeneous nuclear RNA
e) Small nuclear RNA
3912-Jan-21 Our Biochemistry- Namrata Chhabra
41. Question 8
Which of the following processes is not involved in the post
transcriptional processing of t-RNA?
A) Attachment of poly A tail
B) Trimming
C) Splicing
D) Attachment of CCA arm
E) Base modification
4112-Jan-21 Our Biochemistry- Namrata Chhabra
44. Genetic Code
Genetic code is a dictionary that corresponds with sequence of
nucleotides and sequence of Amino Acids.
Words in dictionary are in the form of codons
Each codon is a triplet of nucleotides
64 codons in total and three out of these are Non Sense
codons.
61 codons for 20 amino acids
4412-Jan-21 Our Biochemistry- Namrata Chhabra
46. Genetic Code-Characteristics
Specificity- Genetic code is specific (Unambiguous)
A specific codon always codes for the same amino acid.
e.g., UUU codes for Phenyl Alanine, it can not code for any other
amino acid.
4612-Jan-21 Our Biochemistry- Namrata Chhabra
47. Genetic Code-Universal
Universal- In all living organism Genetic code is the same.
The exception to universality is found in mitochondrial codons
where AUA codes for methionine and UGA for tryptophan,
instead of isoleucine and termination codon respectively of
cytoplasmic protein synthesizing machinery.
AGA and AGG code for Arginine in cytoplasm but in
mitochondria they are termination codons.
4712-Jan-21 Our Biochemistry- Namrata Chhabra
48. Genetic Code-Redundant
Redundant- Genetic code is
Redundant, also called
Degenerate.
Although each codon
corresponds to a single amino
acid, but a single amino acid
can have multiple codons.
Except Tryptophan and
Methionine each amino acid
has multiple codons.
4812-Jan-21 Our Biochemistry- Namrata Chhabra
49. Genetic Code- Non-Overlapping and Non-
Punctuated
All codons are independent sets of 3 bases.
There is no overlapping ,
Codon is read from a fixed starting point as a continuous
sequence of bases, taken three at a time.
The starting point is extremely important, and this is called
Reading frame.
4912-Jan-21 Our Biochemistry- Namrata Chhabra
50. Non-Sense Codons
There are 3 codons out of 64 in
genetic code which do not encode
for any Amino Acid.
These are called termination
codons or stop codons or
nonsense codons. The stop
codons are UAA, UAG, and
UGA. They encode no amino
acid. The ribosome pauses and
falls off the mRNA.
5012-Jan-21 Our Biochemistry- Namrata Chhabra
51. Initiator codon
AUG is the initiator codon in majority of proteins-
In a few cases GUG may be the initiator codon
Methionine is the only amino acid specified by just one codon,
AUG.
5112-Jan-21 Our Biochemistry- Namrata Chhabra
52. Wobbling phenomenon
The rules of base pairing are relaxed
at the third position, so that a base can
pair with more than one
complementary base.
Some tRNA anticodons
have Inosine at the third position.
Inosine can pair with U, C, or A. This
means that we don't need 61 different
tRNA molecules, only half as many
are required.
52
t RNA (first
base)
m RNA
(Third base)
Base pairing
C G Traditional
A U Traditional
U A Traditional
U G Nontraditio
nal
G C Traditional
G U Nontraditio
nal
I U Nontraditio
nal
I C Nontraditio
nal
I A Nontraditio
nal
12-Jan-21 Our Biochemistry- Namrata Chhabra
53. Question 9
The following are all characteristics of genetic code except:
a. Universal
b. Degenerate
c. Non-overlapping
d. Ambiguous
5312-Jan-21 Our Biochemistry- Namrata Chhabra
57. Question 10
Which statement about genetic code is most accurate?
a) Information is stored as sets of dinucleotide repeats called codons
b) The code is degenerate (more than one codon may exist for a single
amino acid)
c) Information is stored as sets of trinucleotide repeats called codons.
d) There are 64 codons, all of which code for amino acids.
e) The sequence of the codons that make up a gene exhibits an exact
linear correspondence to the sequence of amino acids in the
translated protein.
5712-Jan-21 Our Biochemistry- Namrata Chhabra
58. Answer
e) The sequence of the codons that make up a gene exhibits an exact
linear correspondence to the sequence of amino acids in the translated
protein.
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60. Translation
• The pathway of protein synthesis is called Translation
because the ‘language’ of the nucleotide sequence on the
mRNA is translated into the language of the amino acid
sequence.
• The mRNA is translated from its 5’end to its 3’end , producing
a protein synthesized from its amino terminal end to its
carboxyl terminal end.
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61. Components required for Translation
• Amino acids
• Transfer RNA
• Messenger RNA
• Aminoacyl t RNA synthetase
• Functionally competent ribosomes
• Protein factors
• ATP and GTP as a source of energy
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62. Steps of Protein Synthesis
The process of protein
synthesis is divided into 3
stages-
- Initiation
- Elongation
- Termination
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64. The small subunit/IF3 complex binds to the mRNA.
Specifically, it binds to the sequence AGGAGG, known as the
Shine-Delgarno sequence, which is found in all prokaryotic
mRNAs.
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65. Meanwhile, the fmet tRNA binds to Initiation Factor 2 (IF2), which
promotes binding of the tRNA to the start codon.
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66. The small subunit/IF3 complex scans along the mRNA until it
encounters the start codon. The tRNA/IF2 complex also binds
to the start codon. This complex of the small ribosomal
subunit, IF3, initiator tRNA, and IF2 is called the initiation
complex.
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67. At this point, the large ribosomal subunit joins in. A molecule of
GTP is hydrolyzed, and the initiation factors are released. The
ribosomal complex is now ready for protein synthesis.
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68. When the ribosome is assembled, two tRNA binding sites are created;
these are designated 'P' and 'A' (P stands for peptidyl, A stands for
amino acyl). The initiator tRNA is in the P site, and the A site will be
filled by the tRNA with the anticodon that is complementary to the
codon next to the start. (In this case, it is the tRNA that binds proline.)
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69. When the second tRNA base pairs with the appropriate codon in the mRNA,
an enzyme called peptidyl transferase catalyzes the formation of a peptide
bond between the two amino acids present (while breaking the bond
between fmet and its tRNA).This activity is intrinsic to the 23S r RNA found in
the large subunit. Since the r RNA catalyzes this process , it is referred to as
the Ribozyme
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70. Elongation
At this point, the whole ribosome shifts over one codon. This shift
requires several elongation factors (not shown) and energy from the
hydrolysis of GTP. The result of the shift is that the uncharged tRNA that
was in the P site is ejected, and the tRNA that was in the A site is now in
the P site. The A site is free to accept the tRNA molecule with the
appropriate anticodon for the next codon in the mRNA.
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71. The next tRNA base pairs with the next codon, and peptidyl transferase
catalyzes the formation of a peptide bond between the new amino acid
and the growing peptide chain.
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72. Termination
When a termination codon enters the A site, translation halts. This is because there
is no tRNA with an anti codon that is complementary to any of the stop codons.
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73. Inhibitors of protein synthesis
• The tetracyclines (tetracycline, doxycycline, demeclocycline,
minocycline, etc.) block bacterial translation by binding reversibly to
the 30S subunit and distorting it in such a way that the anticodons of
the charged tRNAs cannot align properly with the codons of the
mRNA.
• Puromycin structurally binds to the amino acyl t RNA and becomes
incorporated into the growing peptide chain thus causing inhibition of
the further elongation.
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74. Inhibitors of protein synthesis
• Chloramphenicol inhibits prokaryotic peptidyl transferase
• Clindamycin and Erythromycin bind irreversibly to a site on
the 50 s subunit of the bacterial ribosome thus inhibit
translocation.
• Diphtheria toxin inactivates the eukaryotic elongation
factors thus prevent translocation.
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75. Post Translational Modifications
The newly synthesized protein is modified to become functionally
active. The various post translational modifications are as follows-
-Trimming
-Covalent Alterations
a)Phosphorylation
b) Glycosylation
c) Hydroxylation
d) Gamma carboxylation
e) Isoprenylation
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76. Post Translational Modifications
Trimming removes excess amino acids.
Phosphorylation may activate or inactivate the protein
Glycosylation targets a protein to become a part of the plasma
membrane or lysosomes or be secreted out of the cell
Hydroxylation such as seen in collagen is required for acquiring the
three-dimensional structure and for imparting strength
Defective proteins or destined for turn over are marked for destruction
by attachment of a Ubiquitin protein. Proteins marked in this way are
degraded by a cellular component known as the Proteasome.
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77. Question 11
The initiation of translation in eukaryotes requires which of the
following:
a. Initiation factor (IF-2)
b. Elongation factor (EF)-2
c. A 40-S ribosomal subunit
d. Methionyl-tRNA (f Met).
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78. Answer
c) A 40-S ribosomal subunit
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79. Question 12
Which of the following statements about prokaryotic translation is
incorrect?
a. Transcription and translation are simultaneous
b. Initiation takes place with the help of Methionyl-tRNA (f Met)
c. 20 S and 60 S subunits together form a ribosome of 80 S
d. Chloramphenicol inhibits prokaryotic translation.
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80. Answer
c. 20 S and 60 S subunits together form a ribosome of 80 S
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81. Question 13
Which of the following components is required in prokaryotic protein
synthesis?
a. Aminoacyl t RNA synthetase
b. Helicase
c. Topoisomerase
d. Primase.
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83. Question 14
A 34-year-old female develops a nonproductive cough and a low-grade
fever. The attending physician suspects Mycoplasma pneumonia and
starts empirically with Erythromycin.
Which of the following describes the mechanism of action of
Erythromycin?
a) Inhibits the 50S ribosomal subunit.
b) Inhibits the initiation factor- 1(IF-1).
c) Binds to shine Dalgarno sequence.
d) Inhibits the incoming aminoacyl tRNA.
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84. Answer
a) Inhibits the 50S ribosomal subunit
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85. Question 15
A -4-year-old girl has been brought to the Pediatric OPD with fever and
cough that sounds like a “whoop”. The pediatrician learns that the child
has not been properly immunized and has yet to receive Pertussis
vaccination.
The mechanism by which the pertussis toxin causes cell death is
through the inhibition of:
a. Translocase
b. Peptidyl transferase
c. Elongation factor (EF)-2
d. Aminoacyl t-RNA synthetase.
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87. Question 16
An 18-year-old girl has been advised to start with Tetracycline for the
treatment for her acne. Which of the following statements best
describes the mechanism of action of Tetracycline?
Tetracycline:
a. binds reversibly to the 30S subunit and distorts it.
b. inhibits prokaryotic Peptidyl Transferase
c. inactivates the prokaryotic elongation factors
d. structurally binds to the aminoacyl t RNA.
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88. Answer
a. binds reversibly to the 30S subunit and distorts it.
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89. Question 17
A 34-year-old has reported to the Medical OPD with a high -grade fever,
dry cough, headache, loss of appetite, and pain abdomen lasting from
the past seven days. She has been diagnosed with typhoid fever, for
which she has been started with Chloramphenicol.
The drug acts by inhibiting prokaryotic :
a. Translocase
b. Peptidyl transferase
c. Initiation factor (IF)-2
d. Aminoacyl t-RNA synthetase.
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91. Question 18
Immunoglobulins, hemoglobin, and collagen are modified post-
translationally by the process of:
a) Hydroxylation
b) Subunit aggregation
c) Methylation
d) Trimming.
e) Carboxylation
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94. INTRODUCTION
● A mutation is a permanent change in the
nucleotide sequence of a gene.
● Mutations may be either gross, so that
large areas of chromosome are changed,
● or may be subtle with a change in one or a
few nucleotides.
Mutations
Large scale
Point
mutations
94
101. Mutagens
● Chemicals
o Nitroso compounds
o Hydroxylamine NH2OH
o Base analogs
o Simple chemicals (e.g. acids)
○ Alkylating & methylating agents (e.g. N-
ethyl-N-nitrosourea (ENU)
101
102. Mutagens
● Chemicals
o Polycyclic aromatic hydrocarbons e.g. benzopyrenes
o DNA intercalating agents (e.g. ethidium bromide)
o DNA cross linker (e.g. platinum)
o Oxidative damage caused by oxygen(O)radicals
102
103. Mutagens
❖ Radiations
● Ultraviolet radiation (non-ionizing radiation) - excites electrons to a higher
energy level. DNA absorbs ultraviolet light. Two nucleotide bases in DNA -
cytosine and thymine-are most vulnerable to excitation that can change base-
pairing properties. UV light can induce adjacent thymine bases in a DNA strand
to pair with each other, as a bulky dimer.
● Ionizing radiation
103
107. Insertional
mutagenesis
● Insertions in the coding
region of a gene may
alter splicing of the
mRNA (splice site
mutation), or
● cause a shift in the
reading frame (frame
shift), both of which can
significantly alter the
gene product.
107
108. A) Point mutations
iii) Deletions remove one
nucleotide from the DNA.
Like insertions, these
mutations can alter the
reading frame of the gene.
108
109. B) Large-scale mutations
B) Large-scale mutations in chromosomal structure, including:
Amplifications (or gene duplications) leading to multiple copies of all
chromosomal regions, increasing the dosage of the genes located within
them.
109
111. B) Large-scale mutations
c) Chromosomal Mutations:
○ Chromosomal translocations: interchange of genetic parts from
nonhomologous chromosomes.
○ Interstitial deletions: an intra-chromosomal deletion that removes a
segment of DNA from a single chromosome, thereby apposing
previously distant genes.
○ Chromosomal inversions: reversing the orientation of a
chromosomal segment.
111
112. Effects of point mutations
Single-base changes in the mRNA molecules may have one of several effects
when translated into protein:
1. Silent mutations-There may be no detectable effect because of the
degeneracy of the code.
2. This would be more likely if the changed base in the mRNA molecule
were to be at the third nucleotide of a codon.
112
113. Effects of point mutations
(2) A missense effect will occur when a different amino acid is incorporated
at the corresponding site in the protein molecule. This mistaken amino
acid—or missense, depending upon its location in the specific protein—
might be acceptable, partially acceptable, or unacceptable to the function
of that protein molecule.
Most single-base changes would result in the replacement of one amino acid
by another with rather similar functional groups. This is an effective
mechanism to avoid drastic change in the physical properties of a protein
molecule.
113
114. a) Acceptable Missense mutations
● The sequencing of a large number of hemoglobin mRNAs and genes from many
individuals has shown that the codon for valine at position 67 of the chain of
hemoglobin is not identical in all persons who possess a normally functional chain of
hemoglobin.
● The codon changes by point mutation from GUU (of valine) to GAU of Aspartic acid
in Hb Bristol.
● Similarly in Hb Sydney the codon changes from GUU to GCU for Alanine.
● Both Hb Bristol and Hb Sydney are normal Hb variants with normal oxygen carrying
capacity.
● Thus these are acceptable mutations.
114
115. Partially acceptable Missense mutations
● Clearly, this missense mutation hinders normal function and
results in sickle cell anemia when the mutant gene is present in
the homozygous state.
● The glutamate-to-valine change may be considered to be
partially acceptable because hemoglobin S does bind and
release oxygen, although abnormally.
115
116. c) Unacceptable Missense Mutations
● The hemoglobin M mutations generate molecules that allow the Fe2+ of the heme
moiety to be oxidized to Fe3+, producing methemoglobin.
● Here the single nucleotide change alters the properties of a protein to such an extent
that it becomes non- functional.
● Hb M results from histidine to tyrosine substitution.
● Distal Histidine of alpha chain of Globin is replaced by Tyrosine.
● The codon CAU is changed to UAU with the resultant incorporation of Tyrosine and
formation of MetHb.
● Met hemoglobin cannot transport oxygen.
116
117. (3) A nonsense mutation
A nonsense codon may appear that would then result in the premature
termination of a peptide chain and the production of only a fragment of the
intended protein molecule.
The probability is high that a prematurely terminated protein molecule or
peptide fragment will not function in its assigned role.
117
118. (3) A nonsense mutation
● The codon UAC for Tyrosine may be mutated to UAA or UAG, both are stop
codons. Beta Thalassemia is an example of nonsense mutation.
● In certain conditions as a result of mutational event the stop codon may be
changed to normal codon (UAA to CAA) .
● This results in the elongation of protein to produce “Run on polypeptides”.
The resultant protein is a functionally abnormal protein.
118
119. Frameshift Mutations
● A frame shift mutation is a mutation caused by inserts or deletes of a number of
nucleotides from a DNA sequence.
● Due to the triplet nature of gene expression by codons, the insertion or deletion
can disrupt the reading frame, or the grouping of the codons, resulting in a
completely different translation from the original.
● The earlier in the sequence the deletion or insertion occurs, the more altered
the protein produced is.
119
120. Triplet deletion
A triplet deletion removes exactly
one amino acid from the
polypeptide ,the most common
mutation in cystic fibrosis is Delta
F508 (i.e. deletion of amino acid
number 508 (a phenylalanine, F).
120
121. Trinucleotide expansion
● The commonest inherited cause of mental retardation is a
syndrome originally known as Martin-Bell syndrome.
● Patients are most usually male, have a characteristic
elongated face and numerous other abnormalities
including greatly enlarged testes.
● In 1969 the name of the syndrome was changed to the
fragile X syndrome.
121
122. Trinucleotide expansion
● The mutation was tracked down to a trinucleotide expansion in
the gene now named FMR1 (Fragile site with Mental
Retardation).
● A number of diseases have now been ascribed to trinucleotide
expansions.
● These include Huntington's disease and Myotonic dystrophy.
122
123. Gene deletions
● Alpha Thalassemia is an
example of Gene
deletion.
● The clinical
manifestations are as per
the number of genes
deleted.
123
124. Consequences of Mutations
Harmful mutations
● Changes in DNA caused by mutation can cause errors in protein
sequence, creating partially or completely non-functional proteins.
● To function correctly, each cell depends on thousands of proteins to
function in the right places at the right times.
● When a mutation alters a protein that plays a critical role in the body, a
medical condition can result.
● A condition caused by mutations in one or more genes is called a genetic
disorder.
124
125. Consequences of Mutations
● If a mutation is present in a germ cell, it can give rise to
offspring that carries the mutation in all of its cells.
● This is the case in hereditary diseases.
● On the other hand, a mutation can occur in a somatic cell of an
organism.
● Such mutations will be present in all descendants of this cell,
and certain mutations can cause the cell to become malignant,
and thus cause cancer.
125
126. Consequences of Mutations
Beneficial mutations
● A very small percentage of all mutations actually have a positive effect.
● These mutations lead to new versions of proteins that help an organism
and its future generations better adapt to changes in their environment.
● For example, a specific 32 base pair deletion in human CCR5 (CCR5-Δ32)
confers HIV resistance to homozygotes and delays AIDS onset in
heterozygotes.
● The CCR5 mutation is more common in those of European descent.
126
127. Question 19
Triple repeat sequence disease occurs in:
a) Alzheimer’s disease
b) Cystic fibrosis
c) Ataxia telangiectasia
d) Huntington’s chorea
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129. Question 20
Which of the following changes in mRNA (resulting form point
mutation) would result in the synthesis of a protein identical to the
normal protein?
a. UCA – UAA
b. UCA- CCA
c. UCA- UCU
d. UCA- ACA
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131. Question 21
A-58-year-old male has recently been diagnosed with
hemochromatosis. He presents with bronze discoloration of the skin
and is found to have elevated plasma glucose and ferritin levels. The
physician finds that he is carrying a mutation where tyrosine is
substituted for Cysteine of the HFE gene. This disease results from
which of the following mutations?
a. Silent
b. Nonsense
c. Missense
d. Frameshift.
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