Transcription and Translation Flashcards
The Central Dogma
- DNA is transcribed into RNA, RNA is translated into a protein
- prokaryotes: both occur in the cytoplasm
- Eukaryotes: transcription occurs in the nucleus, translation in the cytoplasm
RNA v. DNA
- Ribose has a hydroxyl group, deoxyribose has a hydrogen
- RNA has uracil instead of thymine
- 5’ of DNA is a monophosphate, RNA is a triphosphate
- DNA is larger and more stable
- Many believe RNA was the first info storage molecule
Template v. Non-Template Strands
As DNA unwinds:
- one strand is used as a template for RNA (3’-5’), other is non-template
- adenine is match with uracil on the RNA transcript
- RNA polymerase synthesizes RNA from DNA
Initiation and Termination
Involves:
- promoters and terminators
- RNA polymerase and proteins to bind at the DNA duplex at promotor sequences
- Eukaryotic and archaeal promoter sequences are a TATA box
- first nucleotides is placed about 25 nucleotides from the TATA
- transcription continues until a terminator
- In bacteria promotion is done through a sigma factor
Eukaryotic Transcription gene regulation
- through the looping of DNA, transcriptional activator proteins, mediator complex, RNA polymerase II and general transcription factors are brought close enough to start transcription
Transcription Bubble
- transcription takes place in what looks like a bubble that is about 14 pairs in length, RNA-DNA duplex in the bubble is about 8 pair
Polymerization Reaction
- incoming ribonucleoside triphosphate is recognized by the RNA polymerase and joined to the growing transcript
- RNA polymerase positions the oxygen in the hydroxyl group to a position where it can reach the innermost phosphate of the triphosphate (creates ATP/energy)
- Pyrophosphate is released
RNA polymerase in Prokaryotes
- also forms a transcription bubble
- RNA polymerase: separates DNA, allows a duplex to form, elongates transcript, releases transcript, restores helix
- the molecule that combines with the ribosome to direct synthesis is mRNA
Prokaryotic and Eukaryotic primary Transcript
Prokaryotic: coupled transcription and translation, overlap
Eukaryotic: nuclear membrane is the barrier between the processes, primary transcript undergoes chemical modifications called RNA processing
RNA processing
- Addition of a 5’ cap, without the ribosome would not recognize mRNA
- Poly A Tail to the 3’ end of mRNA - polyadenylation, important in termination
- RNA Splicing
RNA splicing
- excision of introns, leaving exons
- sequences near the ends of the intro undergo base pairing in the spliceosome and looped close together
- loop is called the lariat which is broken down
- alternative splicing, different ways to yield different mRNAs
Amino Acid Structure
- function arises from structure
- central carbon atom covalently bonded to an amino, carboxyl, hydrogen and a R side chain
- R groups make each acid unique
Hydrophobic AA
- R group aggregate away from water, buried in interior of fold pattern
- stabilized by weak Van der Waals forces
Hydrophilic AA
- polar charges allow for interaction with water (H bonding)
- fold so they are outside the protein
special AA
- Glycine - R group is hydrogen, symmetrical, increases flexibility of the polypeptide
- Proline - R group linked to the amino group, constraints folding
- Cystine - SH group
peptide bonds
- covalent bonds between the carboxyl and amino of two AAs
- water released in the dehydration synthesis reaction
- results in a primary structure polypeptide chain
Secondary structure
- results from hydrogen bonding in the backbone of the polypeptide
- Alpha helix: h bonds between carbonyl group and amide four ahead
- beta sheet: h bond between carbonyl groups in one AA and an amide in a different part of the polypeptide
Tertiary Structure
- 3D, made of several secondaries
- determined by distribution of R groups
quaternary structure
- a protein
- subunits can be identical (HIV) or different (hemoglobin)
Ribosomes
- protein factories where translation takes place
- complex RNA and protein, bonds with mRNA
- made up of a large and small subunit
- reads a codon (3 nucleotides)
- large subunit has a binding site for tRNA, A (aminoacyl), P (peptidyl) and E (exit) sites
tRNA
- small unit that conducts translation
- self-pairing structure, looks like a clover
- CCA at 3’ end and the 3’ hydroxyl of the A is the attachment site for the AA
- 3 bases in the anticodon loop
tRNA synthetases
- enzymes called aminoacyl tRNA synthetases connect specific AA to specific tRNA molecules
Codon-Anticodon Interaction
- first codon in mRNA pairs with the last base in the anticodon
- codons specify an AA, 20 AA total
- AUG is the start codon
- UAA, UAG, UGA are stop codons
Initiation - Translation
- complex moves along mRNA until AUG
- requires initiation factors bonded to 5’ cap
- recruits the small unit of the ribosome and the large joins when AUG encountered
- initiation factors released
- prokaryotes have a Shine- Delgarno sequence
Elongation - Translation
- Once the tRNA is in place, the bond connecting the AUG to the tRNA is transferred to the Amino group of the next AA forming the first peptide bind
- ribosome shifts the codon right, uncharged tRNA moves to the E site to be ejected, peptide bearing tRNA moves to the P site, A site free for the next tRNA
Termination - Translation
- process continues until a stop codon
- a protein release factor binds to the A site of the ribosome causing the connected polypeptide chain to break creating the carboxyl terminus
