Intro to biochem Flashcards
Classes of nucleic acids found in cells
Ribonucleic - 90%
Deoxyribonhuycleic - 10%
Classes of RNA
rRNA - 80%
tRNA - 15%
mRNA - 5%
Functions of DNA
Repositiry of genetic info
Directs its own replication
Directs transcription of complimentary molecules of mRNA
Function of mRNA
Carriers of genetic info
Directs translation of genetic info into proteins
Function of tRNA
Translator of genetic info
Delivers AA during protein synthesis
Function of rRNA
Components of ribosomes
Have structural and functional roles
Purine bases
Adenine
Guanine
Pyrimidine bases
Cytosine
Thymine
Uracil
Nucleoside of adenine
Adenosine
Nuceloside of guanine
Guanosine
Nucleoside of cytosine
Cytidine
Nucleoside of thymine
Thymidine
Nucleoside of uracil
Uridine
How to read nucleic acids
5’ to 3’
Watson - Crick base pairing
A and T form 2 hydrogen bonds
G & C form 3 hydrogen bonds and are more stable
Structure of B-DNA
Double stranded alpha-helix One full turn contains 10 base pairs Width of molecule is 2nm Contains major and minor groove Distance between 2 base plates - 0.34 nm Base pairs are orientated to the right angle of the helix
DNA replication process
DNA Helicase separates parental strand into leading strand and lagging strand
DNA primase and RNA primers re used by DNA polymerase as starting points for replication
Leading strand (5’ to 3’) is replicated in a continuous fashion but the lagging strand is unable to - Okazaki fragnments
RNA primers are removed by exonuclease activity of DNA polymerase and are replaced w/ DNA
DNA Ligase seals fragments to complete synthesis of lagging strand
Length of Okazaki fragments
1,000 to 5,000 bases
Antiviral chemotherapeutic agents
Analogue nucleosides are phosphorylated at 5’ carbon –> triphosphate analogue. Reverse transcriptase then incorporates these into the viral genome and this blocks DNA synthesis –> no more chain elongation
Why is DNA synthesis is blocked in antiviral chemotherapeutic agents
Analogues don’t have hydroxyl groups at 3’ and other atoms/ groups instead
Structure of RNA molecules
Single stranded molecules
Nucleotides joined by phosphodiester bonds
Starts at 5’ end and terminates at 3’ end
Extensive 2’ structures e.g hairpin loop due to intramolecular double stranded regions
RNA polymerases
Synthesis RNA Types are distinguished by the class of which they direct the synthesis
RNA polymerase I
Direct the synthesis of rRNA’s
RNA polymerase II
Direct synthesis of mRNAs
Sensitive to inhibition by alpha-amanitin, found in Amanita phalloides (mushroom)
RNA polymerase III
Direct synthesis of tRNA
Transcription - initiation
Interaction w/ RNA polymerase w/ spp sites on the DNA (promoters)
Promoters
Charcteristic sequences of DNA in front of or upstream of the genes that is to be transcribed
Transcription - elongation
RNA polymerase selects appropriate ribonucleotides and forms phosphodiester bridges between them
Rapid process - 40 nt/ second
Requires double stranded DNA to unwound
How is double stranded DNA unwound in transcription
Topoisomerases I and II
These enzymes are associated w/ the transcription complex and are targets for anti-cancer drugs in chemo
Transcription - termination
Diff types employ diff mechanisms to terminate transcription
RNA polymerase I to terminate transcription
Uses spp protein
RNA polymerase II to terminate transcription
Uses spp termination sequences & protein factors
RNA polymerase III to terminate transcription
Uses spp termination sequences
Features of prokaryotic mRNA’s
Polycistronic
No chemical modification
No splicing
Features of eukaryotic mRNA’s
Monocistronic
Chemical modifications
Splicing - contains introns and axons
Chemical modifications of eukaryotic mRNA
5’: methylated guanine nucleotide cap added
3’: polyA tail added
Monocistronic
Encode for only one protein
Polycistronic
Encodes for multiple proteins
When does transcription and translation occur in prokaryotes
Simultaneously -meaning that transcripts may already be partially transcribed into proteins even before transcription is completed
Why can’t simultaneous transcription and translation occur in eukaryotes
Nuclear envelope acts as a barrier between process of transcription and translation
Structure of tRNA
Acceptor stem T Psi C loop Variable loop Anticodon loop Trinucleotide anticodon D loop
Acceptor stem
Last 3 bases unpaired and form acceptor stem
AA is joined to 3’ end by an ester bond between hydroxy group on adenosine nucleotide and carboxyl group on AA
Trinucleotide anticodon
Trinucleotide codon directs a spp interaction w/ the corresponding don in the mRNA
Secondary structure of tRNA
Cloverleaf
Ribosome-inhibiting antibiotics
As ribosomes in prokaryotes and eukaryotes are different compounds can preferentially target bacteria ribosome
Antibiotics targeting 30S subunit
Streptomycin
Tetracycline
Antibiotics targeting 50S subunits
Erythromycin
Chloramphenol
Nucleotide triphosphates
Substrates for nucleic acid synthesis
When is PPi released
During the incorporation of nucleotide triphosphates into the nascent acid chain
PPi
Pyrophosphate
Tertiary structure of DNA
Chromatin and nucleosomes
DNA is wrapped around histones found in core of nucleosomes, found in chromatin
Each nucleosome has a pice of linker DNA in between which allows extra folding of nucleosome string –> supercoiled structure
