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Transcription and Translation

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Topic Overview

Transcription and Translation

Ribonucleic Acid (RNA)

 

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  • RNA is a single-stranded polynucleotide composed of ribose sugar, phosphate, and nitrogenous bases.

  • Nitrogenous bases: Adenine, Guanine, Cytosine, Uracil (uracil replaces thymine).

  • Sugar is β-D-ribose with a free 2′-OH group, making RNA chemically less stable than DNA.

  • RNA synthesis occurs in the 5′ → 3′ direction.

  • Types of RNA:

    • mRNA → codes for proteins.

    • tRNA → transports amino acids.

    • rRNA → structural and catalytic component of ribosome.

    • snRNA, snoRNA → involved in RNA processing.


Messenger RNA (mRNA)

 

https://www.researchgate.net/publication/280392530/figure/fig2/AS%3A284582667669516%401444861203880/RNA-processing-begins-with-the-addition-of-a-5-cap-and-a-3-polyrA-tail-to-the.png

 

https://www.shaalaa.com/images/_4%3Aabe5490185de49969a5540ef5a0c6acb.png

 

https://www.researchgate.net/publication/361955257/figure/fig3/AS%3A11431281254237712%401719091385503/Main-aspects-of-polycistronic-and-monocistronic-gene-expression-A-Monocistronic-coding.tif

  • mRNA carries genetic information from DNA to ribosome.

  • In eukaryotes, initially synthesized as heterogeneous nuclear RNA (hnRNA).

  • Structural components of eukaryotic mRNA:

    • 5′ cap (7-methyl guanosine) → prevents degradation and helps ribosome binding.

    • Coding region (exons) → translated into protein.

    • 3′ poly-A tail (200–250 A residues) → stability and nuclear export.

  • Prokaryotic mRNA:

    • Usually polycistronic.

    • Lacks 5′ cap and poly-A tail.


RNA Polymerase

 

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https://ww2.uthscsa.edu/learning-modules/biochem/04-rna-transcription/RNApolymerases.png

 

https://media.springernature.com/lw685/springer-static/image/art%3A10.1007%2Fs00253-020-10577-0/MediaObjects/253_2020_10577_Fig1_HTML.png

  • RNA polymerase catalyzes synthesis of RNA using DNA as template.

  • Forms phosphodiester bonds between ribonucleotides.

  • Does not require a primer.

  • Types of RNA polymerase in eukaryotes:

    • RNA polymerase I → rRNA (28S, 18S, 5.8S).

    • RNA polymerase II → mRNA and snRNA.

    • RNA polymerase III → tRNA and 5S rRNA.

  • Prokaryotes possess a single RNA polymerase; specificity provided by sigma (σ) factor.


Transcription

 

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https://www.genome.gov/sites/default/files/media/images/tg/Antisense.jpg

 

https://upload.wikimedia.org/wikipedia/commons/5/5b/Transcription_Bubble_image.jpg

  • Transcription is the synthesis of RNA from DNA template.

  • Occurs in:

    • Nucleus → eukaryotes.

    • Cytoplasm → prokaryotes.

  • Template strand is the antisense strand.

  • Base pairing rules:

    • A pairs with U.

    • G pairs with C.

  • Three stages:

    • Initiation

    • Elongation

    • Termination


Transcription Signals

 

https://upload.wikimedia.org/wikipedia/commons/thumb/5/5a/TATA_box_mechanism.png/500px-TATA_box_mechanism.png

 

https://media.springernature.com/m685/springer-static/image/art%3A10.1038%2Fs41588-020-0620-7/MediaObjects/41588_2020_620_Fig1_HTML.png

 

https://cdn.kastatic.org/ka-perseus-images/49c2b6fa9744d75f1fe75ee3ff5b7ffc879ef806.png

  • DNA sequences that regulate transcription.

  • Promoter:

    • Located upstream of transcription start site.

    • Contains TATA box (Pribnow box in prokaryotes).

  • Enhancers:

    • Increase transcription efficiency.

    • Can act at a distance and in either orientation.

  • Terminator sequences:

    • Signal the end of transcription.


Initiation of Transcription

 

https://upload.wikimedia.org/wikipedia/commons/8/82/Figure_16_04_01.jpg

 

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https://www.cell.com/cms/attachment/604063/4782425/gr1.jpg

  • RNA polymerase binds to promoter region.

  • Prokaryotes:

    • Sigma factor recognizes promoter.

    • RNA polymerase holoenzyme initiates transcription.

  • Eukaryotes:

    • Requires general transcription factors (TFIIA, TFIIB, TFIID).

    • TFIID contains TATA-binding protein (TBP).

  • DNA strands unwind forming transcription bubble.

  • First ribonucleotide is added without primer.


Elongation of Transcription

 

https://cdn.kastatic.org/ka-perseus-images/1da89713b9aa8067742244d916749e72561bb3cc.png

 

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  • RNA polymerase moves along template strand.

  • RNA chain grows in 5′ → 3′ direction.

  • Energy derived from hydrolysis of NTPs.

  • DNA unwinds ahead and rewinds behind the enzyme.

  • Newly synthesized RNA remains temporarily hybridized with DNA.


Termination of Transcription

 

https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41467-019-09146-5/MediaObjects/41467_2019_9146_Fig1_HTML.png

 

https://img.sparknotes.com/figures/5/531c62f0d28ea4ccc5bf20ebe5828d16/rhoindept.gif

 

https://ars.els-cdn.com/content/image/1-s2.0-S1097276515004475-fx1.jpg

  • Termination marks the end of RNA synthesis.

  • Prokaryotes:

    • Rho-dependent termination → rho protein required.

    • Rho-independent termination → GC-rich hairpin loop followed by poly-U.

  • Eukaryotes:

    • Termination occurs after poly-A signal (AAUAAA).

    • RNA is cleaved downstream of signal.


Post-Transcriptional Processing

 

https://www.frontiersin.org/files/Articles/403882/fnmol-11-00304-HTML/image_m/fnmol-11-00304-g001.jpg

 

https://www.researchgate.net/publication/280392530/figure/fig2/AS%3A284582667669516%401444861203880/RNA-processing-begins-with-the-addition-of-a-5-cap-and-a-3-polyrA-tail-to-the.png

 

https://www.shaalaa.com/images/_4%3A6864bbd6abea481c80a06df355aa36da.png

  • Occurs only in eukaryotes.

  • Converts hnRNA into mature mRNA.

  • Steps:

    • 5′ capping → protection and ribosome recognition.

    • 3′ polyadenylation → stability and transport.

    • Splicing → removal of introns.

  • Essential for proper gene expression.


Spliceosomes

 

https://upload.wikimedia.org/wikipedia/commons/3/30/Spliceosome_ball_cycle_new2.jpg

 

https://ars.els-cdn.com/content/image/3-s2.0-B978012401667500002X-f02-10-9780124016675.jpg

 

https://upload.wikimedia.org/wikipedia/commons/0/0a/DNA_alternative_splicing.gif

  • Large ribonucleoprotein complexes.

  • Composed of snRNA (U1, U2, U4, U5, U6) and associated proteins.

  • Recognize conserved splice sites:

    • 5′ splice site → GU.

    • Branch point → Adenine.

    • 3′ splice site → AG.

  • Functions:

    • Excise introns.

    • Join exons precisely.

  • Alternative splicing:

    • Allows multiple proteins from a single gene.

    • Major contributor to protein diversity.

 

 

Ribozymes

 

https://www.researchgate.net/publication/227184428/figure/fig2/AS%3A669081858478091%401536532954444/Schematic-of-a-natural-hammerhead-ribozyme-Hammerhead-ribozymes-consist-of-three.png

 

https://upload.wikimedia.org/wikipedia/commons/e/ea/Hammerhead_ribozyme_ribbons.png

 

https://www.mdpi.com/viruses/viruses-06-02376/article_deploy/html/images/viruses-06-02376-g001.png

  • Ribozymes are RNA molecules with catalytic activity.

  • They can catalyze biochemical reactions without proteins.

  • Prove that RNA can act as both genetic material and enzyme.

  • Examples:

    • RNase P → removes leader sequence from tRNA.

    • Self-splicing introns.

    • Hammerhead ribozyme.

  • Clinical importance:

    • Supports RNA world hypothesis.

    • Target for gene therapy research.


Introns and Exons

 

https://www.researchgate.net/publication/264163152/figure/fig1/AS%3A614075235049472%401523418353453/Fig-2-Schematic-gene-structure-This-gene-has-5-introns-and-6-exons-It-is-assumed.png

 

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https://upload.wikimedia.org/wikipedia/commons/0/0a/DNA_alternative_splicing.gif

  • Genes are composed of:

    • Exons → coding sequences.

    • Introns → non-coding intervening sequences.

  • During transcription, both introns and exons are copied into hnRNA.

  • Introns are removed during splicing.

  • Exons are joined to form mature mRNA.

  • Alternative splicing:

    • Different exon combinations.

    • Produces multiple proteins from a single gene.

  • Introns are common in eukaryotes, rare in prokaryotes.


Reverse Transcriptase

 

https://ars.els-cdn.com/content/image/3-s2.0-B9780128035504000215-f21-07-9780128035504.jpg

 

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  • Reverse transcriptase is an RNA-dependent DNA polymerase.

  • Synthesizes DNA from RNA template.

  • Found in retroviruses (e.g., HIV).

  • Functions:

    • RNA → DNA conversion.

    • DNA integrates into host genome as provirus.

  • Clinical importance:

    • Target of antiretroviral drugs (AZT, nevirapine).

    • Used in molecular biology for cDNA synthesis.


Transfer RNA (tRNA)

 

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https://www.researchgate.net/publication/354273747/figure/fig1/AS%3A1063264561676288%401630513434893/Overview-of-human-cytosolic-tRNAS-anticodon-loop-modifications-known-to-shape-translation.png

 

https://www.researchgate.net/publication/231225238/figure/fig4/AS%3A667635557605382%401536188129404/The-reaction-scheme-for-the-two-steps-of-aminoacylation-reaction-at-the-active-site-of.png

  • tRNA transports amino acids to ribosome.

  • Smallest RNA (~75–90 nucleotides).

  • Cloverleaf structure with:

    • Anticodon loop → recognizes codon on mRNA.

    • Acceptor arm (3′ CCA) → amino acid attachment site.

  • Each amino acid has a specific tRNA.

  • Charging of tRNA:

    • Catalyzed by aminoacyl-tRNA synthetase.

    • Requires ATP.

  • Wobble hypothesis:

    • One tRNA can recognize multiple codons.


Ribosomal RNA (rRNA)

 

https://www.open.edu/openlearn/pluginfile.php/313588/mod_oucontent/oucontent/3807/975837b7/e9c9e8f5/s294_b1_f03_15.eps.png

 

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https://cdn.britannica.com/80/780-050-CC40AEDF/Synthesis-protein.jpg

  • rRNA forms the structural and catalytic core of ribosome.

  • Most abundant RNA (~80%).

  • Prokaryotes:

    • 16S rRNA (30S subunit).

    • 23S + 5S rRNA (50S subunit).

  • Eukaryotes:

    • 18S rRNA (40S).

    • 28S + 5.8S + 5S (60S).

  • rRNA acts as a ribozyme during peptide bond formation.


Ribosomes

 

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  • Ribosomes are ribonucleoprotein complexes.

  • Site of protein synthesis.

  • Types:

    • 70S ribosome → prokaryotes (30S + 50S).

    • 80S ribosome → eukaryotes (40S + 60S).

  • Functional sites:

    • A site → aminoacyl-tRNA binding.

    • P site → peptide bond formation.

    • E site → exit of tRNA.

  • Ribosomes may be:

    • Free → cytosolic proteins.

    • Bound to RER → secretory proteins.


Small Nuclear RNA (snRNA)

 

https://upload.wikimedia.org/wikipedia/commons/3/30/Spliceosome_ball_cycle_new2.jpg

 

https://www.fredhutch.org/content/dam/www/science-spotlight/article-images/dvinge%20thumbnail.jpg

 

https://upload.wikimedia.org/wikipedia/commons/3/37/Process_of_RNA_splicing.png

  • snRNA are small RNA molecules found in nucleus.

  • Combined with proteins form spliceosomes.

  • Types:

    • U1, U2, U4, U5, U6.

  • Function:

    • Recognition of splice sites.

    • Removal of introns from hnRNA.

  • Essential for accurate mRNA maturation.


Protein Biosynthesis (Translation)

 

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  • Translation is synthesis of protein from mRNA.

  • Occurs on ribosomes in cytoplasm.

  • Requires:

    • mRNA, tRNA, ribosomes.

    • ATP and GTP.

  • Steps:

    • Initiation → formation of initiation complex.

    • Elongation → peptide chain growth.

    • Termination → release of completed protein.

  • Direction:

    • mRNA read 5′ → 3′.

    • Protein synthesized N-terminal → C-terminal.


Genetic Code

 

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https://image.slidesharecdn.com/geneticcode-110605101532-phpapp02/75/Genetic-code-3-2048.jpg

  • Genetic code is the language converting nucleotide sequence into amino acids.

  • Triplet code → 3 nucleotides = 1 codon.

  • Total codons: 64.

  • Start codon:

    • AUG → methionine.

  • Stop codons:

    • UAA, UAG, UGA.

  • Properties:

    • Universal (with few exceptions).

    • Degenerate → multiple codons for same amino acid.

    • Non-overlapping and comma-less.

  • Mutations affecting genetic code can lead to genetic disorders.

 

Translation

 

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  • Translation is the process by which mRNA directs synthesis of protein.

  • Occurs on ribosomes in the cytoplasm.

  • Requires:

    • mRNA (template)

    • tRNA (adaptor molecule)

    • Ribosomes (site of synthesis)

    • ATP and GTP (energy)

  • Direction:

    • mRNA read 5′ → 3′

    • Polypeptide synthesized N-terminal → C-terminal

  • Multiple ribosomes translating a single mRNA form a polysome.


Initiation of Translation

 

https://media.springernature.com/m685/springer-static/image/art%3A10.1038%2Fnrm2838/MediaObjects/41580_2010_Article_BFnrm2838_Fig1_HTML.jpg

 

https://upload.wikimedia.org/wikipedia/commons/7/79/Shine-Dalgarno_sequence-es.png

 

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  • Initiation begins with formation of initiation complex.

  • Key components:

    • Small ribosomal subunit

    • Initiator tRNA

    • mRNA

    • Initiation factors (IFs/eIFs)

Prokaryotes

  • Initiator tRNA carries N-formyl methionine (fMet).

  • mRNA binds to ribosome via Shine–Dalgarno sequence.

  • Start codon: AUG.

Eukaryotes

  • Initiator tRNA carries methionine.

  • Small subunit binds to 5′ cap and scans for AUG.

  • Start site surrounded by Kozak sequence.

  • Initiator tRNA binds directly to P site.


Elongation of Translation

 

https://cdn.prod.website-files.com/621e95f9ac30687a56e4297e/64adca85e17e00a6bc74360a_V2_1680029238991_80d9ebbc-19dd-4078-b3e9-6aa98014aaae_HIGH_RES.png

 

https://www.mun.ca/biology/scarr/iGen3_06-18_Figure-Lsmc.jpg

 

https://www.frontiersin.org/files/Articles/816398/fmolb-08-816398-HTML/image_m/fmolb-08-816398-g002.jpg

  • Repeating cycle of amino acid addition.

  • Occurs at A, P, and E sites of ribosome.

  • Steps:

    • Aminoacyl-tRNA binding to A site (requires GTP).

    • Peptide bond formation (peptidyl transferase activity of rRNA).

    • Translocation of ribosome along mRNA.

  • Elongation factors:

    • Prokaryotes → EF-Tu, EF-Ts, EF-G

    • Eukaryotes → eEF-1, eEF-2

  • Energy requirement:

    • 1 ATP for tRNA charging.

    • 2 GTP per peptide bond.


Termination of Translation

 

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  • Occurs when ribosome encounters a stop codon.

  • Stop codons:

    • UAA, UAG, UGA

  • No tRNA corresponds to stop codons.

  • Release factors bind to A site.

  • Polypeptide chain released from tRNA.

  • Ribosomal subunits dissociate from mRNA.


Protein Targeting

 

https://www.researchgate.net/publication/333705872/figure/fig1/AS%3A961842532864003%401606332538425/Targeting-signals-Targeting-signals-for-proteins-destined-to-the-ER-mitochondria.png

 

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https://uw.pressbooks.pub/app/uploads/sites/683/2023/05/image84.png

  • Newly synthesized proteins must reach correct cellular location.

  • Signal peptide:

    • Short hydrophobic amino-terminal sequence.

  • Cytosolic proteins:

    • Synthesized on free ribosomes.

  • Secretory and membrane proteins:

    • Targeted to rough endoplasmic reticulum (RER).

  • Signal recognition particle (SRP):

    • Recognizes signal peptide.

    • Directs ribosome to RER membrane.

  • Mitochondrial and nuclear proteins have specific targeting signals.


Post-Translational Processing

 

https://www.ptglab.com/media/3598/post-translational-modifications_-an-overview-figure-1.jpg

 

https://media.springernature.com/m685/springer-static/image/art%3A10.1038%2Fs41420-023-01617-5/MediaObjects/41420_2023_1617_Fig1_HTML.png

 

https://pubs.acs.org/cms/10.1021/acs.chemrev.7b00120/asset/images/large/cr-2017-00120d_0014.jpeg

  • Modifications occurring after protein synthesis.

  • Types:

    • Proteolytic cleavage (e.g., proinsulin → insulin).

    • Phosphorylation (serine, threonine, tyrosine).

    • Glycosylation.

    • Hydroxylation (collagen).

    • Acetylation, methylation.

  • Essential for:

    • Functional activity.

    • Stability.

    • Proper localization.


Protein Folding

 

https://cdn.kastatic.org/ka-perseus-images/71225d815cafcc09102504abdf4e10927283be98.png

 

https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41593-018-0235-9/MediaObjects/41593_2018_235_Fig1_HTML.png

 

https://www.researchgate.net/publication/23275541/figure/fig6/AS%3A668495478022147%401536393150345/The-protein-folding-unfolding-and-off-folding-pathways-adapted-from-2-A-native.png

  • Newly synthesized polypeptides fold into native 3-D structure.

  • Driven by:

    • Hydrogen bonds

    • Ionic interactions

    • Hydrophobic interactions

    • Disulfide bonds

  • Proper folding is essential for biological function.

  • Misfolding may lead to:

    • Loss of function.

    • Protein aggregation diseases.


Chaperones

 

https://media.springernature.com/lw1200/springer-static/image/art%3A10.1038%2Fnature10317/MediaObjects/41586_2011_Article_BFnature10317_Fig2_HTML.jpg

 

https://proteopedia.org/wiki/images/9/92/GroEL_reaction.jpg

 

https://physicallensonthecell.org/sites/default/files/chapcycle.gif

  • Chaperones are proteins that assist in proper folding of other proteins.

  • Prevent aggregation of nascent polypeptides.

  • Do not become part of final structure.

  • Examples:

    • Hsp60 (GroEL–GroES system).

    • Hsp70.

  • Require ATP for activity.


Heat Shock Proteins (HSPs)

 

https://www.researchgate.net/publication/34249014/figure/fig5/AS%3A669371307409421%401536601964373/Functions-of-Heat-shock-proteins-Two-of-functions-of-heat-shock-proteins-A-As-new.png

 

https://www.researchgate.net/publication/327215843/figure/fig1/AS%3A663318184341504%401535158787489/Simplified-model-of-the-Hsp70-and-Hsp90-chaperone-cycles-1-Nascent-polypeptides.png

 

https://www.researchgate.net/publication/5415608/figure/fig1/AS%3A624256400515075%401525845732096/ER-stress-protein-misfolding-and-oxidative-stress-are-intimately-interrelated-Protein.png

  • Synthesized in response to cellular stress (heat, toxins, hypoxia).

  • Act as molecular chaperones.

  • Common types:

    • Hsp70 → early folding.

    • Hsp60 → folding in mitochondria.

    • Hsp90 → stabilizes signaling proteins.

  • Clinical relevance:

    • Involved in cancer, neurodegenerative diseases.

    • Protect cells from stress-induced damage.

 

 

 

Inhibitors of Protein Synthesis

 

https://upload.wikimedia.org/wikipedia/commons/b/b1/Ribosome_mRNA_translation_en.svg

 

https://www.frontiersin.org/files/Articles/536313/fchem-08-00276-HTML/image_m/fchem-08-00276-g001.jpg

 

https://tmedweb.tulane.edu/pharmwiki/lib/exe/fetch.php/abx_ribosome2.png

  • Protein synthesis can be inhibited at initiation, elongation, or termination.

  • Most inhibitors act at the ribosomal level.

  • Selectivity is due to structural differences between:

    • Prokaryotic (70S)

    • Eukaryotic (80S) ribosomes

  • Clinical importance:

    • Basis of action of many antibiotics.

    • Useful in cancer chemotherapy and research.


Antibiotics Inhibiting Protein Synthesis

 

https://images.openai.com/static-rsc-3/lo8lMa3HfE1gkR2uKjfPh6zY-XE3ktG8UtzyrxHiawJgEE9nE5FADpw8lh9cMMVLuxvZjxyy-F_ERs0K9QGsnDs47Opb55v0bWhD0L3frz0?purpose=fullsize

 

https://tmedweb.tulane.edu/pharmwiki/lib/exe/fetch.php/abx_ribosome2.png

 

https://d45jl3w9libvn.cloudfront.net/jaypee/static/books/9789386056856/Chapters/images/308-1.jpg

  • Act mainly on prokaryotic ribosomes.

Acting on 30S subunit

  • Aminoglycosides → misreading of mRNA.

  • Tetracyclines → block aminoacyl-tRNA binding.

Acting on 50S subunit

  • Chloramphenicol → inhibits peptidyl transferase.

  • Macrolides (erythromycin) → block translocation.

  • Clindamycin → inhibits peptide bond formation.

  • Linezolid → inhibits initiation complex.


Mitochondrial DNA and RNA

 

https://images.openai.com/static-rsc-3/NTKRxhgRmCuhMF1kJO7n-HEW8BCgR0hZqE942p06ac5-NkAFtYq3Q2KaKcOo0wT1_bTuqyXSCOXqKGJYaHKWnmu9l0Gxyo1gN6YJ8DyvQas?purpose=fullsize

 

https://ars.els-cdn.com/content/image/3-s2.0-B9780128196564000024-f02-02-9780128196564.jpg

 

https://www.greberlab.org/uploads/1/3/3/5/133583913/cover-overview-metal_orig.jpg

  • Mitochondria possess their own DNA and RNA.

  • mtDNA is:

    • Circular

    • Double-stranded

    • Maternally inherited

  • Encodes:

    • 13 proteins (ETC components)

    • 22 tRNAs

    • 2 rRNAs

  • Mitochondrial ribosomes resemble prokaryotic ribosomes.

  • Sensitive to antibiotics affecting bacterial translation.


Oxidative Phosphorylation Diseases

 

https://www.researchgate.net/publication/355227730/figure/fig1/AS%3A1143735240933376%401649699139496/Mitochondrial-oxidative-phosphorylation-OXPHOS-system-and-other-pathways-that-are.png

 

https://www.mda.org/sites/default/files/Mito_mitochondrion.jpg

 

https://upload.wikimedia.org/wikipedia/commons/thumb/e/e6/Tetralogy_of_Fallot.svg/500px-Tetralogy_of_Fallot.svg.png

  • Caused by mutations in mitochondrial or nuclear genes.

  • Lead to defective ATP production.

  • Common features:

    • Myopathy

    • Neurological deficits

    • Lactic acidosis

  • Examples:

    • Leber hereditary optic neuropathy

    • MELAS syndrome

    • MERRF syndrome

  • Inheritance is typically maternal.


Genomics and Proteomics

 

https://www.idex-hs.com/images/default-source/campaigns/proteomics/proteomics-vs-genomics-chart.png?Status=Master&sfvrsn=90e1d65d_1

 

https://upload.wikimedia.org/wikipedia/commons/f/f3/Logo_HGP.jpg

 

https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41586-025-08584-0/MediaObjects/41586_2025_8584_Fig1_HTML.png

  • Genomics:

    • Study of entire genome.

    • Includes gene mapping, sequencing, and function.

  • Proteomics:

    • Study of entire protein complement of a cell.

    • Includes structure, function, interactions.

  • Proteome is more complex than genome due to:

    • Alternative splicing.

    • Post-translational modifications.

  • Clinical applications:

    • Personalized medicine.

    • Disease biomarkers.


MicroRNA (miRNA)

 

https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fncb0309-228/MediaObjects/41556_2009_Article_BFncb0309228_Fig1_HTML.jpg

 

https://www.researchgate.net/publication/330355775/figure/fig1/AS%3A714786165768199%401547429710405/Biogenesis-and-function-of-microRNAs-see-text-RISC-RNA-induced-silencing-complex.jpg

 

https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fsigtrans.2015.4/MediaObjects/41392_2016_Article_BFsigtrans20154_Fig1_HTML.jpg

  • Small non-coding RNA (~22 nucleotides).

  • Regulates gene expression post-transcriptionally.

  • Binds to complementary mRNA sequences.

  • Leads to:

    • Translational repression.

    • mRNA degradation.

  • Important in development, cancer, and apoptosis.


Interfering RNA and RNA Silencing

 

https://www.umassmed.edu/contentassets/4f41e3f4cdb34428827a8397a564e9f8/rnai-pathway-full-text.jpg

 

https://www.researchgate.net/publication/277340532/figure/fig2/AS%3A267881002827787%401440879216262/RNA-silencing-mechanism-For-therapeutic-RNAi-applications-a-lentiviral-vector-or.png

 

https://www.researchgate.net/publication/281383918/figure/fig8/AS%3A356148558483458%401461923841058/Dicer-and-RISC-RNA-induced-silencing-complex-RNAi-is-initiated-by-the-Dicer-enzyme.png

  • RNA interference (RNAi) is sequence-specific gene silencing.

  • Mediated by:

    • siRNA

    • miRNA

  • Mechanism:

    • dsRNA cleaved by Dicer.

    • siRNA incorporated into RISC.

    • Target mRNA degraded.

  • Used in research and therapy.


Antisense Therapy

 

https://www.als.net/images/blog//2020/Antisense_DNA_oligonucleotide.png

 

https://www.azolifesciences.com/image-handler/picture/2020/11/gr1_lrg-1.jpg

 

https://www.researchgate.net/publication/375727393/figure/fig1/AS%3A11431281259300210%401720434373245/Mechanism-of-action-of-antisense-oligonucleotides-Antisense-oligonucleotides-and-siRNA.tif

  • Uses short synthetic DNA or RNA sequences.

  • Complementary to specific mRNA.

  • Binding leads to:

    • Blocked translation.

    • mRNA degradation.

  • Applications:

    • Genetic disorders.

    • Cancer.

    • Viral infections.

  • Example:

    • Antisense therapy in spinal muscular atrophy.


Fusion Proteins

 

https://upload.wikimedia.org/wikipedia/commons/1/15/PDB_1tmz_EBI.jpg

 

https://www.researchgate.net/publication/45112748/figure/fig1/AS%3A601790143815696%401520489359388/Construction-and-expression-of-G-C-T-fusion-protein-A-Design-of-the-recombinant-fusion.png

 

https://media.springernature.com/lw685/springer-static/image/art%3A10.1208%2Fs12248-023-00873-8/MediaObjects/12248_2023_873_Fig1_HTML.png

  • Fusion proteins are created by joining two genes.

  • Expressed as a single polypeptide.

  • Advantages:

    • Improved stability.

    • Targeted action.

  • Examples:

    • Insulin fusion analogs.

    • Monoclonal antibody fusion proteins.

  • Used in:

    • Biotechnology.

    • Targeted cancer therapy.

    • Research tagging (e.g., GFP fusion).

 

 

FAQs: Transcription and Translation

What is transcription?

Transcription is the process by which RNA is synthesized from a DNA template using RNA polymerase.


Which DNA strand acts as template during transcription?

The antisense (template) strand acts as template; the sense strand has the same sequence as RNA (except T replaced by U).


In which direction does transcription occur?

RNA synthesis occurs in the 5′ → 3′ direction.


What enzyme is responsible for transcription?

RNA polymerase catalyzes transcription.


How many types of RNA polymerase are present in eukaryotes?

Three:

  • RNA polymerase I → rRNA

  • RNA polymerase II → mRNA

  • RNA polymerase III → tRNA and 5S rRNA


What is the role of sigma factor?

Sigma factor helps RNA polymerase recognize promoter sequences in prokaryotes.


What is the TATA box?

A promoter sequence rich in thymine and adenine that helps initiate transcription in eukaryotes.


What are transcription factors?

Proteins required for binding of RNA polymerase II to DNA in eukaryotes.


What is hnRNA?

Heterogeneous nuclear RNA is the primary transcript that undergoes post-transcriptional processing to form mRNA.


What are introns and exons?

  • Introns → non-coding sequences removed during splicing

  • Exons → coding sequences retained in mature mRNA


What is splicing?

Removal of introns and joining of exons to form functional mRNA.


What is a spliceosome?

A ribonucleoprotein complex composed of snRNA and proteins that mediates splicing.


Name the snRNAs involved in splicing.

U1, U2, U4, U5, and U6.


What is alternative splicing?

Process by which different proteins are produced from the same gene by varying exon combinations.


What are ribozymes?

RNA molecules with enzymatic activity, capable of catalyzing reactions.


Give an example of a ribozyme.

RNase P, which processes tRNA.


What is reverse transcriptase?

An RNA-dependent DNA polymerase that synthesizes DNA from RNA.


Where is reverse transcriptase found?

In retroviruses such as HIV.


What is translation?

Translation is the process of protein synthesis from mRNA on ribosomes.


Where does translation occur?

On ribosomes in the cytoplasm.


What are the components required for translation?

mRNA, tRNA, ribosomes, amino acids, ATP, and GTP.


In which direction is protein synthesized?

From N-terminal to C-terminal end.


What is the start codon?

AUG, coding for methionine.


What are stop codons?

UAA, UAG, and UGA.


What is the initiator tRNA?

  • Prokaryotes → fMet-tRNA

  • Eukaryotes → Met-tRNA


What is the Shine–Dalgarno sequence?

A ribosomal binding site on prokaryotic mRNA.


What is the Kozak sequence?

A consensus sequence around the start codon in eukaryotic mRNA.


What are A, P, and E sites of ribosome?

  • A site → aminoacyl-tRNA binding

  • P site → peptide bond formation

  • E site → exit of tRNA


What catalyzes peptide bond formation?

Peptidyl transferase, an rRNA-based ribozyme.


What are release factors?

Proteins that recognize stop codons and terminate translation.


What is a polysome?

Multiple ribosomes translating a single mRNA simultaneously.


What are chaperones?

Proteins that assist in proper folding of newly synthesized polypeptides.


What are heat shock proteins?

Stress-induced chaperone proteins that protect cells during heat, hypoxia, and toxins.


What is post-translational modification?

Chemical modification of proteins after synthesis, such as phosphorylation or glycosylation.


Why is protein folding important?

Correct folding is essential for biological activity and stability of proteins.


What is protein targeting?

Process by which proteins are directed to their correct cellular location.


What is a signal peptide?

A short hydrophobic sequence that directs proteins to RER or specific organelles.


Which particle directs proteins to RER?

Signal recognition particle (SRP).


Which antibiotics inhibit protein synthesis?

Aminoglycosides, tetracyclines, macrolides, chloramphenicol, linezolid.


Why do antibiotics selectively act on bacteria?

Because bacterial ribosomes are 70S, different from eukaryotic 80S ribosomes.


What is mitochondrial DNA?

Circular, double-stranded DNA present in mitochondria, inherited maternally.


Why are mitochondrial ribosomes important?

They resemble bacterial ribosomes and are sensitive to certain antibiotics.


What are oxidative phosphorylation diseases?

Disorders caused by defects in mitochondrial ATP production.


Name common mitochondrial disorders.

MELAS, MERRF, Leber hereditary optic neuropathy.


What is genomics?

Study of the entire genome of an organism.


What is proteomics?

Study of the entire protein complement of a cell.


What is microRNA?

Small non-coding RNA that regulates gene expression post-transcriptionally.


What is RNA interference?

Sequence-specific gene silencing mediated by siRNA and miRNA.


What is antisense therapy?

Use of complementary nucleic acid sequences to block mRNA translation.


What are fusion proteins?

Proteins created by combining two different genes into a single polypeptide.


Why is this chapter clinically important?

Because defects in transcription, translation, folding, or targeting cause genetic disorders, cancer, infections, and metabolic diseases.

 

 

MCQs: Transcription and Translation

1. RNA synthesis occurs in which direction?

A. 3′ → 5′
B. 5′ → 3′
C. N → C
D. C → N

Answer: B


2. Which RNA polymerase synthesizes mRNA in eukaryotes?

A. RNA polymerase I
B. RNA polymerase II
C. RNA polymerase III
D. RNA polymerase IV

Answer: B


3. The promoter sequence recognized by sigma factor in prokaryotes is:

A. Kozak sequence
B. TATA box
C. Pribnow box
D. Poly-A signal

Answer: C


4. Which RNA contains introns?

A. Mature mRNA
B. tRNA
C. rRNA
D. hnRNA

Answer: D


5. Removal of introns is carried out by:

A. Ribosomes
B. RNA polymerase
C. Spliceosome
D. Dicer

Answer: C


6. snRNA involved in splicing include all EXCEPT:

A. U1
B. U2
C. U4
D. U7

Answer: D


7. Which molecule proves that RNA can act as an enzyme?

A. rRNA
B. tRNA
C. Ribozyme
D. miRNA

Answer: C


8. Reverse transcriptase is:

A. DNA-dependent DNA polymerase
B. RNA-dependent RNA polymerase
C. RNA-dependent DNA polymerase
D. DNA-dependent RNA polymerase

Answer: C


9. Reverse transcriptase is characteristically found in:

A. Adenovirus
B. Retrovirus
C. Herpesvirus
D. Poxvirus

Answer: B


10. Which RNA is the smallest?

A. mRNA
B. rRNA
C. tRNA
D. snRNA

Answer: C


11. Amino acid attachment site on tRNA is:

A. Anticodon loop
B. TΨC loop
C. D loop
D. 3′ CCA end

Answer: D


12. Peptide bond formation during translation is catalyzed by:

A. Protein enzyme
B. DNA
C. rRNA
D. tRNA

Answer: C


13. The ribosomal site where peptide bond formation occurs is:

A. A site
B. P site
C. E site
D. S site

Answer: B


14. Start codon for protein synthesis is:

A. UAA
B. UGA
C. AUG
D. UAG

Answer: C


15. Initiator tRNA in prokaryotes carries:

A. Methionine
B. Formyl methionine
C. Valine
D. Glycine

Answer: B


16. Shine–Dalgarno sequence is present in:

A. Eukaryotic mRNA
B. Prokaryotic mRNA
C. tRNA
D. rRNA

Answer: B


17. Kozak sequence is important for:

A. Termination of transcription
B. Translation initiation in eukaryotes
C. Splicing
D. RNA degradation

Answer: B


18. Stop codons include all EXCEPT:

A. UAA
B. UAG
C. UGA
D. AUG

Answer: D


19. Which factor binds to stop codon during translation?

A. Initiation factor
B. Elongation factor
C. Release factor
D. Sigma factor

Answer: C


20. Multiple ribosomes on a single mRNA form:

A. Polycistron
B. Polysome
C. Operon
D. Spliceosome

Answer: B


21. Which antibiotic inhibits peptidyl transferase activity?

A. Tetracycline
B. Aminoglycoside
C. Chloramphenicol
D. Penicillin

Answer: C


22. Tetracyclines inhibit protein synthesis by:

A. Blocking initiation
B. Blocking translocation
C. Preventing aminoacyl-tRNA binding
D. Causing premature termination

Answer: C


23. Why do antibiotics selectively affect bacteria?

A. Higher ATP requirement
B. Presence of cell wall
C. Difference in ribosomal structure
D. Faster metabolism

Answer: C


24. Mitochondrial DNA is inherited from:

A. Father
B. Mother
C. Both parents
D. Autosomes

Answer: B


25. Mitochondrial ribosomes resemble:

A. Eukaryotic cytosolic ribosomes
B. Nuclear ribosomes
C. Prokaryotic ribosomes
D. Lysosomal ribosomes

Answer: C


26. MELAS syndrome is due to defect in:

A. Glycolysis
B. Translation initiation
C. Oxidative phosphorylation
D. DNA replication

Answer: C


27. Study of the entire genome is called:

A. Proteomics
B. Transcriptomics
C. Genomics
D. Metabolomics

Answer: C


28. Which RNA causes post-transcriptional gene silencing?

A. rRNA
B. tRNA
C. miRNA
D. hnRNA

Answer: C


29. Enzyme that cleaves double-stranded RNA in RNA interference is:

A. RISC
B. Dicer
C. Spliceosome
D. RNA polymerase

Answer: B


30. Antisense therapy works by:

A. Increasing transcription
B. Enhancing translation
C. Binding complementary mRNA
D. Activating ribosomes

Answer: C


31. Fusion proteins are produced by:

A. Post-translational modification
B. Joining two genes
C. Alternative splicing
D. RNA editing

Answer: B


32. Which protein assists in correct folding of nascent polypeptides?

A. Transcription factor
B. Chaperone
C. Release factor
D. Signal peptide

Answer: B


33. Heat shock proteins are mainly induced by:

A. Starvation
B. Heat and cellular stress
C. Hypoxia alone
D. Vitamin deficiency

Answer: B


34. Signal recognition particle (SRP) is involved in:

A. DNA replication
B. Protein folding
C. Protein targeting to RER
D. RNA splicing

Answer: C


35. Which modification is essential for collagen stability?

A. Acetylation
B. Phosphorylation
C. Hydroxylation
D. Glycosylation

Answer: C

 

Clinical Problems: Transcription and Translation


Clinical Problem 1

A 6-year-old child presents with delayed development and recurrent infections. Genetic analysis shows a defect in removal of introns from primary RNA transcripts.

Question:
Which molecular process is defective, and what structure is primarily involved?

Answer:

  • Defective process → RNA splicing

  • Structure involved → Spliceosome (snRNA + proteins)

Explanation:
Introns are removed from hnRNA by spliceosomes. Defects lead to abnormal mRNA and defective protein synthesis.


Clinical Problem 2

A patient on long-term chloramphenicol therapy develops bone marrow suppression.

Question:
Explain the biochemical basis of this adverse effect.

Answer:

  • Chloramphenicol inhibits peptidyl transferase activity.

  • Mitochondrial ribosomes resemble prokaryotic ribosomes.

  • Inhibition of mitochondrial protein synthesis → ↓ ATP production → marrow toxicity.


Clinical Problem 3

A newborn presents with muscle weakness, lactic acidosis, and neurological deficits. Family history shows maternal inheritance.

Question:
What is the most likely biochemical defect?

Answer:

  • Defect in mitochondrial oxidative phosphorylation

  • Due to mutation in mitochondrial DNA

Explanation:
Mitochondrial DNA is maternally inherited and encodes key components of the electron transport chain.


Clinical Problem 4

An HIV-positive patient is started on zidovudine (AZT).

Question:
Which enzyme is targeted and why is this effective?

Answer:

  • Target enzyme → Reverse transcriptase

  • Reason → HIV requires reverse transcriptase to convert RNA into DNA for integration into host genome.


Clinical Problem 5

A mutation alters the Kozak sequence of a gene but leaves the coding region intact.

Question:
What will be the effect on protein synthesis?

Answer:

  • Defective initiation of translation

  • Reduced or absent protein synthesis

Explanation:
Kozak sequence is essential for recognition of the start codon in eukaryotes.


Clinical Problem 6

A child has a genetic disorder where multiple proteins are missing despite normal gene count.

Question:
Which mechanism could explain this finding?

Answer:

  • Defective alternative splicing

Explanation:
Alternative splicing allows one gene to produce multiple proteins. Its failure reduces protein diversity.


Clinical Problem 7

A patient develops hearing loss after receiving an aminoglycoside antibiotic.

Question:
What is the mechanism of action of this drug?

Answer:

  • Aminoglycosides bind to 30S ribosomal subunit

  • Cause misreading of mRNA

Clinical correlation:
Ototoxicity occurs due to damage to mitochondrial ribosomes in inner ear cells.


Clinical Problem 8

A researcher observes that a synthetic RNA molecule suppresses expression of a specific gene.

Question:
What mechanism is responsible for this phenomenon?

Answer:

  • RNA interference (RNAi) mediated by siRNA or miRNA

Explanation:
Small RNAs guide RISC to complementary mRNA, leading to degradation or translational repression.


Clinical Problem 9

A child has cystic fibrosis due to a deletion mutation but mRNA is still synthesized.

Question:
At which level is gene expression primarily affected?

Answer:

  • Translation and protein folding

Explanation:
The mutation causes production of a misfolded CFTR protein, which is degraded despite normal transcription.


Clinical Problem 10

A drug blocks binding of aminoacyl-tRNA to ribosome.

Question:
Which class of antibiotic shows this action?

Answer:

  • Tetracyclines


Clinical Problem 11

A patient has a disease caused by accumulation of misfolded proteins in neurons.

Question:
Which protective cellular proteins normally prevent this?

Answer:

  • Chaperones and heat shock proteins (HSPs)

Explanation:
They assist in correct folding and prevent aggregation of nascent proteins.


Clinical Problem 12

A protein synthesized in cytosol fails to reach the rough endoplasmic reticulum.

Question:
Which component is likely defective?

Answer:

  • Signal recognition particle (SRP) or signal peptide


Clinical Problem 13

A mutation changes a codon but still codes for the same amino acid.

Question:
What property of genetic code explains this?

Answer:

  • Degeneracy of genetic code


Clinical Problem 14

A premature stop codon appears in the middle of a gene.

Question:
What is the result at protein level?

Answer:

  • Truncated, non-functional protein

  • Translation terminates early due to release factor binding.


Clinical Problem 15

A novel cancer therapy uses a molecule that binds specifically to mRNA and blocks its translation.

Question:
What type of therapy is this?

Answer:

  • Antisense therapy


Clinical Problem 16

A biotechnology lab joins two genes to create a protein with dual function.

Question:
What is this protein called?

Answer:

  • Fusion protein


Clinical Problem 17

A bacterial strain becomes resistant to macrolide antibiotics.

Question:
Which step of translation is normally inhibited by macrolides?

Answer:

  • Translocation step on 50S ribosomal subunit


Clinical Problem 18

A child presents with optic neuropathy and mitochondrial DNA mutation.

Question:
Name the likely disorder.

Answer:

  • Leber hereditary optic neuropathy


Clinical Problem 19

A mutation affects peptidyl transferase activity.

Question:
Which molecule is directly involved?

Answer:

  • rRNA


Clinical Problem 20

A stress-exposed cell increases synthesis of protective proteins.

Question:
Which proteins are upregulated?

Answer:

  • Heat shock proteins (HSPs)

 

Viva Voce: Transcription and Translation

What is transcription?

Synthesis of RNA from a DNA template using RNA polymerase.


Which strand of DNA is transcribed?

The antisense (template) strand.


Direction of RNA synthesis?

5′ → 3′ direction.


Name the enzyme required for transcription.

RNA polymerase.


How many RNA polymerases are present in eukaryotes?

Three.


Which RNA polymerase synthesizes mRNA?

RNA polymerase II.


What is the function of sigma factor?

Recognition of promoter in prokaryotes.


What is the TATA box?

A promoter sequence that helps initiate transcription.


What is hnRNA?

Primary transcript containing introns and exons.


Define introns.

Non-coding sequences removed during RNA processing.


Define exons.

Coding sequences retained in mature mRNA.


What is splicing?

Removal of introns and joining of exons.


Which structure performs splicing?

Spliceosome.


Name the snRNAs involved in splicing.

U1, U2, U4, U5, U6.


What is alternative splicing?

Production of multiple proteins from a single gene.


What are ribozymes?

RNA molecules with enzymatic activity.


Give an example of a ribozyme.

RNase P.


What is reverse transcriptase?

RNA-dependent DNA polymerase.


Where is reverse transcriptase found?

Retroviruses (e.g., HIV).


What is translation?

Protein synthesis from mRNA.


Where does translation occur?

On ribosomes in cytoplasm.


Direction of protein synthesis?

N-terminal → C-terminal.


What is the start codon?

AUG.


What amino acid does AUG code for?

Methionine.


What are stop codons?

UAA, UAG, UGA.


What is the initiator tRNA in prokaryotes?

fMet-tRNA.


What is the initiator tRNA in eukaryotes?

Met-tRNA.


What is the Shine–Dalgarno sequence?

Ribosome-binding site in prokaryotic mRNA.


What is the Kozak sequence?

Sequence around start codon in eukaryotes.


Name the ribosomal sites.

A site, P site, E site.


Which site holds the growing peptide chain?

P site.


Which site binds incoming aminoacyl-tRNA?

A site.


Which site releases tRNA?

E site.


What catalyzes peptide bond formation?

rRNA (peptidyl transferase).


What are elongation factors?

Proteins assisting elongation of polypeptide chain.


What are release factors?

Proteins that recognize stop codons.


What is a polysome?

Multiple ribosomes translating one mRNA.


What are chaperones?

Proteins assisting proper folding of polypeptides.


Do chaperones become part of final protein?

No.


What are heat shock proteins?

Stress-induced chaperone proteins.


Give examples of heat shock proteins.

Hsp70, Hsp60, Hsp90.


What is protein targeting?

Directing proteins to correct cellular location.


What is a signal peptide?

Short hydrophobic sequence guiding protein targeting.


What is the role of SRP?

Directs ribosome-protein complex to RER.


What is post-translational modification?

Chemical modification after protein synthesis.


Give examples of post-translational modifications.

Phosphorylation, glycosylation, hydroxylation.


Why is hydroxylation important?

Essential for collagen stability.


Name antibiotics that inhibit protein synthesis.

Tetracyclines, aminoglycosides, macrolides, chloramphenicol.


Why do antibiotics selectively affect bacteria?

Difference between 70S and 80S ribosomes.


Which antibiotic inhibits peptidyl transferase?

Chloramphenicol.


Which antibiotics act on 30S subunit?

Aminoglycosides, tetracyclines.


What is mitochondrial DNA?

Circular, maternally inherited DNA in mitochondria.


Why are mitochondria sensitive to antibiotics?

Mitochondrial ribosomes resemble bacterial ribosomes.


What are oxidative phosphorylation diseases?

Diseases due to defective mitochondrial ATP synthesis.


Give examples of mitochondrial disorders.

MELAS, MERRF, Leber optic neuropathy.


What is genomics?

Study of the entire genome.


What is proteomics?

Study of the entire protein complement.


What is microRNA?

Small non-coding RNA regulating gene expression.


What is RNA interference?

Sequence-specific gene silencing.


Name enzymes involved in RNA interference.

Dicer and RISC.


What is antisense therapy?

Blocking mRNA using complementary nucleic acid.


What are fusion proteins?

Proteins formed by joining two different genes.


Clinical importance of this chapter?

Explains genetic disorders, antibiotic action, mitochondrial diseases, cancer, and modern gene therapies.


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