PART 8 Flashcards by Bspharm 2025

▪️Sugar: ribose
▪️Bases: G,C,A,U
▪️Cellular location: nucleus & cytoplasm

RNA (Ribonucleic Acid)

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▪️Product of transcription
▪️carries information for protein synthesis
▪️read in the ribosomes

messenger RNA ( mRNA) REKCA

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▪️component of ribosomes
▪️Prokaryotes
▪️Eukaryotes

Ribosomal RNA (rRNA)

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70s ( 50s +30s)

Prokaryotes

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80s ( 60s + 40s)

Eukaryotes

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Unit of sedimentation

S= Svedberg unit

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▪️adapter molecules
▪️comes the correct amino acids to the site after reading mRNA
▪️cruciform/ clover- shaped
▪️Intrastrand assoc. due to palindromes
▪️(inverted repeats)

Transfer RNA (tRNA)

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Responsible for gene splicing

Small nuclear RNA ( snRNA)

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▪️sugar deoxyribose
▪️Bases: G,C,A,T
▪️Location: Nucleus ( 99%), mitochondria ( 1%)

DNA ( Deoxyribonucleic Acid)

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DNA Structure : Double Helix is proposed by

J. Watson & F. Crick

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used X- ray diff. to elucidate the structure of DNA

Rosalind Franklin & Maurice Wilkins

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▪️Most Common hydrated
▪️intermediate
▪️R-Handed
▪️10.4
▪️wide & deep
▪️narrow & shallow

B-DNA

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▪️Dehydrated form
▪️Broadest
▪️R- handed
▪️11
▪️narrow & deep
▪️Broad & Shallow

A-DNA

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▪️Rare (transient)
▪️narrowest
▪️L- Handed
▪️12
▪️Flat( absent)
▪️Narrow & Deep

Z-DNA

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Complementary Base Pairing

▪️2 H-Bonds

A-T

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Complementary Base Pairing

▪️ 3 H-Bonds
▪️ Stonger & Harder to Separate

G-C

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▪️Amount of A=T and amount of g= C
▪️Total purined (A+G) = Total Pyrimidine ( T+C)
▪️application: DNA Composition
▪️A DNA contains 30 % G what are the % C,A,T?
▪️therefore: 30% C, 30% A, 30% T

Chargaff’s rule

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▪️run in opposite directions
▪️Application: predict the complementary seg. to a single DNA
▪️5’-CGAAT-3’ = Ans: 3’- GCTTA-5’

Anti-parallel strands

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▪️Melting disrupts the base pairing using heat to yield single strands
▪️Melting Temp (Tm) - temp at which ½ of the helical structure is lost (denaturation)
▪️Increase hyperchromicity with increase in temperature

Denaturation and Renaturation

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▪️DNA-directed DNA synthesis
▪️Synthesis of two daughter strands from a parent strand
▪️High fidelity (proofreading is present)
▪️Bidirectional, semi-discontinuous, and semi-conservative

Replication

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Each parent strand serves as a template for complementary daughter strands

Semiconservative

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Uses both strands & proceeds in opposite direction

Bidirectional

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proof reading

High Fidelity of replication

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▪️ Semiconservative
▪️ Bidirectional
▪️ High Fidelity of replication
▪️ Occurs at the S phase of the cell cycle

Replication

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Steps in DNA Replication

Initiation - Elongation- Termination

Recognition of the Origin of Replication (Oric C)

Initiation

“Replication fork/ bubble”

DNA Helicase (DNA B)

What are the 2 problems upon unwinding

Supercoiling Denaturation

Stabilization of Replication Fork ▪️ reliever supercoling (can Break phosphodiester and rejoin them

TOPOISOMERASES

Stabilization of Replication Fork ▪️ Prevent the strands from reassociating / renationation ▪️ protects the DNA from enzymes

SINGLE -STRANDED DNA BINDING PROTEINS ( SSBP)

TOPOISOMERASES ▪️cleaves one strand ▪️Inhibited by Camptothecins (- tecans)

Type I: Swivelase

TOPOISOMERASES ▪️Cleaves Both Strands; ATP- dependent ▪️Inhibited by Fluroquinolone, Epipodophyllotoxin (-poside) ▪️Doxocrubicin (anthracycline)

Type II : DNA Gyrase & Topoisomerase IV

DNA ELONGATION ▪️ involved in DNA synthesis (5’ -3’ direction) ▪️Unable to initiate polymerization by themselves (requires primer)

DNA Polymerase

DNA ELONGATION ▪️ RNA Polymerase responsible for attaching RNA primer ( w/ free- OH group at the 3’- end)

Primase

▪️continuous synthesis (towards the fork)

Leading strand

▪️Discontinuous synthesis (away from the fork) ▪️Okazaki fragments

Lagging strand

WHAT TYPE OF DNA POLYMERASE ▪️Elongation (5’- 3’ polymerase act.)

DNA Polymerase lll

WHAT TYPE OF DNA POLYMERASE ▪️Proof- reading & repair (3’-5 ‘ exonuclease act.)

DNA Polymerase ll

WHAT TYPE OF DNA POLYMERASE ▪️Removal of RNA Primers ( 5’ -3’ exonucleotide act)

DNA Polymerase I

WHAT TYPE OF DNA POLYMERASE ▪️Both exonucleotide act

DNA Polymerase I & II

Removal of RNA primers and filling of gaps by DNA polymerase

Termination

TERMINATION ▪️ removal of primer

DNA Polymerase I

TERMINATION ▪️ joining the Okazaki fragments

DNA Ligase

▪️DNA-directed RNA synthesis ▪️Product: mRNA ▪️Synthesis of hnRNA (aka pre-mRNA) from DNA

Transcription

▪️Unidirectional - use only one Strand ▪️Lower fidelity compared to replication (no proofreading) ▪️No need for primers before elongation ▪️Involves primarily RNA polymerase- performs majority of the process

Transcription

▪️Haloenzyme ; a2,B, B’, w, Sigma ▪️Core unit: ( a2, B, B’ w) - polymerization ▪️Sigma Factor( o) - recognition of the promoter region

RNA Polymerase (RNAP)

▪️with intrinsic helicase act. ▪️5’ -3’ polymerase act. ▪️can initiate polymerization with primers ▪️but w/ no proof - reading ability

RNA Polymerase (RNAP)

MAMMALIAN RNAP PRODUCT ▪️rRNA

RNAP I

MAMMALIAN RNAP PRODUCT ▪️mRNA ▪️inh. by Alpha - Amanitin Form deathcap

RNAP II

MAMMALIAN RNAP PRODUCT ▪️tRNA

RNAP III

inh. bacterial RNAP in mycobacteria

Rifampicin

binding of RNAP to the promoter region

Initiation

done by the core subunit ( 5’- 3’ direction

Elongation

RNAP ▪️Strand that is copied

Template/ Antisense

RNAP ▪️Strand that is ignored ▪️but it has the same sequence with mRNA

Nontemplate/ Sense Coding Strand

5’ -G-G-C-A-T-A-3’

mRNA

▪️requirement p Factor ( w/ helicase act (ATP - dependent) for termination

Rho (p) - dependent

▪️ formation of hairpin/ loop due to the presence of a polindromic sequence (GC rich) which forces the separation of the RNAP

Rho (p) Independent

Post-transcriptional modifications: ▪️ Protection from degradation ▪️ recognition site for binding to ribosomes

Capping at 5' end

Post-transcriptional modifications: ▪️ addition of a poly-A-Tau at the 3' end

Polyadenylation

Post-transcriptional modifications: ▪️ introns are remove & exons are joined together ▪️ performed by snRNA

Splicing

PART 8 Flashcards

(61 cards)