29.6.2013(biochem-molecular Biology)52 Flashcards by rakesh durai

Smallest of the three major RNA molecules

tRNA

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Ribosomal subunit common to both prokaryotes and eukaryotes

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Attachment of 5 methyl guanosine cap to mRNA

Backwards(5’ to 5’ association)

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Termination factor

P factor(Rho)

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In RNA polymerase the promotor recognition subunit

Sigma factor

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Prokaryote promotor regions

Pribnow box (TATAAT) -9 position
-35 sequence

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Diff btw RNA and DNA polymerase

No need of primer

No exonuclease or endonuclease activity

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Number of high energy bonds used for addition of nucleotide

2 in both DNA and RNA synthesis

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Rho factor has

ATP dependant DNA-RNA helicase activity

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Types of termination of transcription

Rho dependant

Rho independant

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Rho Independant termination

Newly synthesised RNA forms a hairpin loop

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Characteristic of hairpin loop formed in transcription

Palindromic sequences rich in GC stabilise the loop

String of Us in terminal end bond loosely with A in DNA

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Mechanism of action of rifampicin

Binds to beta subunit of RNA polymerase and inhibits it

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Mechanism of action of actinomycin

Binds to DNA template and prevents the movement of RNA polymerase

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Enzymes synthesised by lac operon

Z -beta galactosidase
Y- permease
A -thiogalactoside transacetylase

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Polycistronic messages are produced by

Prokaryotes

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Eukaryotic promotors

TATA box or hogness box -25
CAAT box -80 to -70
GC box

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Transacting elements

Transcription factors

Cis acting elements - promotors

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Cis acting elements

Enhancers(bind activators)

Promotors(bind transcription factor)

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Site of activator binding

Response elements in Enhancers

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Inhibitor of RNA polymerase II

Alpha amanitin

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Diff btw eukaryotic and prokaryotic mRNA

No post transcriptional modification in prokaryotic mRNA

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Difference btw pre tRNA and mature tRNA

Removal of 16 nucleotide sequence at 5’ end by RNAseP
Splicing of intron in anticodon arm
Replacement of uracil residues in 3’ end by CCA
modification of bases

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First post transcriptional modification in eukaryotic hnRNA

7 methyl guanosine cap

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Enzymes involved in mRNA capping

Guanylyl transferase | Guanine 7 methyl transferase

mRNAs lacking polyA tailing

Histones | Some interferons

Steps involved in addition of polyA tail

Polyadenylation signal sequence | Polyadenylate polymerase

Sites in intron

Splice donor site - GU Splice acceptor site- AG Branching site -A

Stop codons

UAA UAG UGA

An accident frozen in time

Adoption of genetic code

Characteristics of genetic code

Universal Specific/unambiguous Degeneracy/redundancy Nonoverlapping/comma less/punctuation less

Activation of Aminoacid

After an amino acid gets attached to tRNA And the tRNA is called charged

Synthesis of a charged tRNA molecule

Aminoacyl tRNA synthetase(has proof reading activity too) | ATP is converted to AMP and PPi

Sites on ribosomes

A - Aminoacyl tRNA acceptor site P- Peptidyl tRNA site E-empty site

Number of high energy bonds cleaved in addition of one Aminoacid to polypeptide chain

4 2 from an ATP in charging of tRNA molecule 1 GTP required for binding of tRNA to A site 1 GTP for translocation step

Mechanism by which tRNA can recognise more than one codon for the same amino acid

Wobble hypothesis

Factors involved in initiation of translation

Prokaryotes IF1,IF2,IF3 Eukaryotes eIF(10 are present)

Initiation of translation in prokaryotes

Shine dalgarno sequence that binds to 16S of 30s ribosomal subunit

Shine dalgarno sequence

6-10 basepairs upstream of AUG | Rich in purines

Initiation of translation in eukaryotes

40S subunit binds to cap structure and moves down till it reaches AUG

Initiator tRNA binds to

P site | All other tRNAs bind to A site

Binding of initiator tRNA to P site is mediated by

IF2 in prokaryotes

Diff btw prokaryotic and eukaryotic initiator tRNA

N-formylmethionine in prokaryotic and mitochondrial initiator tRNA enzyme transformylase catalyses it

Delivery of Aminoacyl tRNAs to A site is facilitated by

Prokaryotes EF-Ts EF-Tu GTP dependant process

Ribosomal subunit with Peptidyl transferase activity

23S

Translocation in prokaryotes is mediated by

EF-G | GTP

Termination is mediated by

``` Release factors RF1 recognises UAA and UAG RF2 recognises UAA and UGA RF3 binds to GTP and activates RF1 and RF2 Eukaryotes- eRF which binds to GTP ```

Polysome

Polyribosome | One mRNA with many ribosomes

MOA of ricin

Removes an adenine from 28S ribosomal subunit

Enzymes destined to lysosomes are tagged by

Mannose-6-phosphate

Amino acids involved in glycosylation

``` O linked Serine Threonine N linked Asparagine ```

Ubiquitination

ATP dependant protein degradation process

MOA of streptomycin

Binds to 30S ribosome

MOA of tetracyclines

Bind to small ribosomal subunits and prevent the attachment of incoming aminoacyl tRNA

MOA of chloramphenicol

Inhibits Peptidyl transferase

Antibiotic similar to Aminoacyl tRNA

Puromycin

MOA of clindamycin and erythromycin

Inhibits the translocation step in translation by binding to 50S protein

MOA of diphtheria toxin

Inhibits eEF-2 thus preventing translocation

Regulation of PRPP synthetase

Activator- inorganic phosphate | Inhibitor- purine ribonucleotides

Formation of activated ribose

5'-phosphoribosyl pyrophosphate synthetase(PRPP) | Two high energy bonds are broken

Committed step in purine synthesis pathway

Formation of 5' phosphoribosyl amine from PRPP | enzyme- glutaminePRPP amidotransferase

Regulation of glutamine:PRPP amidotransferase

Inhibitors- AMP,GMP,IMP | stimulator- PRPP

Number of ATP utilised in conversion of 5'phosphoribosylamine to IMP

Substances utilised in synthesis of purines

``` Glutamine - N3 and N9 Aspartate- N1 Glycine- N7,C4,C5 Respiratory CO2- C6 N-10 formylTHF -C2 N5,N10 methenyl THF- C8 ```

MOA of mycophenolate

Inhibition of IMP dehydrogenase

AMP synthesis

Enzymes- adenylosuccinate synthetase,adenylosuccinase One GTP Aspartate

GMP synthesis

Enzymes- IMP dehydrogenase(NAD+),GMP synthetase ATP is broken into AMP and PPi Glutamine

Regulation of AMP and GMP synthesis

AMP inhibits adenylosuccinate synthetase | GMP inhibits IMP dehydrogenase

Diff btw nucleoside mono phosphate and diphosphate kinases

Nucleoside diphosphate kinases have broad specificity

Source of phosphate for guanylate kinase

ATP is the source for both adenylate kinase and guanylate kinase

Salvage pathway of purines,substrates and enzymes.

Adenine phosphoribosyl transferase Hypoxanthine guanine phosphoribosyl transferase PRPP release of PPi makes the reaction irreversible

Enzyme involved in the synthesis of deoxyribonucleotides

Ribonucelotide reductase

Regeneration of ribonucleotide reductase

Thioredoxin | Regeneration of thioredoxin is by thioredoxin reductase which utilises NADPH

Ribonucleotide reductase is inhibited by

dATP

Regulation of ribonucleotide reductase

Activity site dATP binds to it and reduces production of any deoxyribonucleotides Substrate specificity site Reduces synthesis of substrate that binds to it but increases synthesis of other deoxyribonucleotides

Conversion of nucleotides to nucleosides

5' nucleotidase

Conversion of nucleoside to nitrogenous base

Purine nucleoside phosphorylase

Role of Xanthine oxidase

Converts hypoxanthine to Xanthine and | Xanthine to Uric acid

Guanase converts guanine to

Xanthine

First genetic disease successfully treated by gene therapy

ADA deficiency

Amino acids required for both purine and pyramidine synthesis

Glutamine | Aspartic acid

Sources of atoms in pyramidine ring

CO2-C2 Glutamine-N3 Aspartate

Regulation of pyramidine synthesis

Mammalian cells CPS2 inhibited by UTP and activated by ATP and PRPP prokaryotes Aspartate transcarbomylase which is inhibited by CTP

Orotic aciduria

UMP synthase deficiency

UMP synthase

OMP decarboxylase | Orotate phosphoribosyl transferase

Location of pyramidine synthesis

Cytosol | Except dihydro orotate dehydrogenase which is present in mitochondria

Diff btw CPS1 and CPS2

``` CPS1 Mitochondria Urea cycle Ammonia is the source of nitrogen Activated by N acetyl glutamate ```

Polypeptide domains involved in pyramidine synthesis

CPS1,Aspartate transcarbomylase,dihydroooratase form a single polypeptide UMP synthase

Nitrogen for CTP synthesis is provided by

Glutamine

Number of high energy bonds needed for synthesis of UMP

MOA of 5-FU

Suicide inhibition of thymidylate synthase

MOA of methotrexate

Inhibition of dihydrofolate reductase

Salvage of pyramidines

Pyramidine bases are not salvaged but pyramidine nucleosides are salvaged by respective kinases

29.6.2013(biochem-molecular Biology)52 Flashcards

(93 cards)