Case 2: DNA & RNA Flashcards
Structure of DNA > know structure of nucleotides
One end of the DNA strand has a free hydroxyl group at C-5 of the last 2-deoxyribose and the other end has a free hydroxyl group at C-3. So DNA has a 5’end + 3’ end. DNA is always read in the 5’ end to 3’ end direction.
- backbone > alternating between phosphate and 2-deoxyribose
- 4 nucleotides : adenine (A) & Thymine (T) = purines and Guanine (G) & Cytosine (C) = pyrimidines
- 1 end free hydroxyl group at C-5 and the other end a free hydroxyl group at C-3 > DNA is antiparralel
- double stranded
Structure + function RNA
- Single stranded
- Ribonucleotides: A & U, G & C
- RNA plays a role in protein synthesis + some RNA’s have catalytic + regulatory functions.
Structure + function of mRNA
- messenger RNA > composed of coding/non-coding sequences
- 5’cap added > increases stability + assists binding to ribosime
- poly A-tail > 3’end lots of adenine added, stability + leaving nucleus
- introns (non-coding, pre-mRNA) > removed by splicing
Structure + function tRNA
- tRNA > molecular adapter > bind to mRNA on one end and carry amino acids into position on the other
- tRNA is folded into a cloverleaf structure held together by pairing of complementary nucleotides. This ‘cloverleaf’ is further folded into an L shape. A loop at one end of the folded structure base-pairs with three nucleotides on the mRNA (codons); tRNA (anticodons).
- strict complementary base-pairing > only first 2 nucleotides > 3 position = wobble base
- 3’end of tRNA binds to corresponding amino acid
What is semi-conservative?
each of the two parental DNA strands act as a template for the new DNA strands. So replicated DNA contains one parental strand (old strand) and a ‘daughter strand’ (newly synthesized strand).
DNA replication: initiation > details case
• Initiator proteins
• DNA helicase > Unwinds and separates strands by breaking of hydrogen bonds between the
nitrogenous bases at origin of replication (TATA-region)
● This leads to the formation of a replication fork
● Single-strand binding proteins keep the replication fork apart
• Topoisomerase I & II > Topoisomerase I helps with replication fork movement and removes supercoils in double helix by separation and reconnection of the phosphate backbone (cuts 1 strand) + Topoisomerase, II cuts both strands in DNA and needs ATP for its activity.
• Single-stranded binding proteins
DNA replication: Elongation > details case
• DNA primase > Synthesizes primers of about 20 nucleotides length consisting of RNA in 5’3’ direction
● Attaches to Helicase and forms Primosome
● One primer per replication unit
• RNA primer
• DNA polymerase III > Polymerizes complementary nucleotides from the cytoplasm starting from the primer
● Synthesizes nucleotides in 5’-3’ direction (moves in 3’-5’ direction of template strand)
● Splits off diphosphate of the triphosphate to release energy
● 3’-5’ exonuclease proofreads DNA in 3’-5’ direction for possible errors and fixes them
● Continuously towards replication fork
• DNA polymerase I > Replaces primer RNA with DNA
• DNA ligase > Connects Okazaki fragments through phosphodiester bonds
• Sliding clamp (prevents DNA polymerase II from dissociating from the template strand)
DNA replication: Termination > details case
• DNA polymerase III > The new strands are proofread by DNA polymerase III to make sure there are no mistakes in the new DNA sequence.
• Repair enzymes
- DNA ligase > seals up the sequence of DNA into 2 continuous double strands. Also seals up the nicks > a cut/notch in the DNA molecule due to a break in one phosphodiester bond between adjacent nucleotides of one of the two strands
Transcription RNA : initation > details case
• TATA box
• Promoter sequence
• RNA polymerase II > catalyses the transcription
RNA polymerase holoenzyme (enzyme + cofactor) separates DNA strands and binds to promoter (includes TATA-box ) of the antisense strand (template strand) → it is detected by the 𝛔 (sigma) factor
○ In eukaryotes , multiple transcription factors bind to the strand
Transcription RNA: elongation > details case
Elongation :
Incoming ribonucleotides are used by RNA polymerase II to form the mRNA strand. It does this using complementary base pairing. RNA polymerase II catalyzes the formation of phosphodiester bonds between adjacent ribonucleotides. The mRNA elongates in a 5’ to 3’ direction.
Transcription RNA : termination > details case
• RNA polymerase II (no proof reading capabilities)
• Terminator sequence ( CG rich region)
Elongation will continue until the RNA polymerase encounters a stop sequence. At this point, transcription stops and RNA polymerase II releases the mRNA.
In prokaryotes , a rho-factor leads to the detachment of the polymerase through
the formation of a hairpin structure (rho-dependant termination
What is the leading strand?
Strand that is synthesized continuously ( 5’ to 3’)
What is the lagging strand
strand that is synthesized in pieces (3’ to 5’).
