DNA And RNA Flashcards
Nucleoside
Sugar and base
How to break down polymers
Hydrolysis
How to make polymers
Condensation/hydrolysis
Directionality of DNA
5’-3’ anti parallel strands
Hydrophobicity of DNA
Backbone - hydrophilic
Bases - hydrophobic
Pyrimidines
C, U, T
Purines
A G
Structure of adenine
Two ring with nh2 substituent
Structure of guanine
Two ring with carboxy substituent
Structure of thymine
Single ring with methyl group and carboxy substituent
Structure of cytosine
Single ring with nh2 substituent
Structure of uracil
Single ring with carboxy substituent (like thymine with no methyl)
How do bases link?
Phosphodiester bonds bt 3’ and 5’ carbon
Hydrogen bonding in DNA
A to T has 2 h bonds
G to C has 3 h bonds
How is DNA denatured
Heat, pH change, DNA rep
Tm
Temperature where half of the DNA denatures
Hershey and chase
DNA, not protein, carries genetic info
Meselson and stahl
Semi conservative model of DNA synthesis
Nucleosome
146 bp wrapping around an octomer of histones
Does DNA synthesis have high fidelity?
Yes, error rate 1 in 10^9-10^10
DnaA
Promotes denaturation by making a bubble
DNA helicase
Unwinds DNA by binding ssDNA
ssDNA bp
Keeps DNA single stranded
Topoisomerase
Cuts strands to relieve coiling
Primase
Synthesizes RNA primers to prime DNA synthesis
DNA polymerase
Replicates DNA
Ligase
Links DNA (Okazaki fragments) with phosphodiester bonds
T or F. DNA synthesis is bidirectional.
Yes. Both strands, 5’ - 3’, at the replication fork
DNA pol I
DNA polymerase activity
3 - 5 exonuclease activity mediates proofreading
5 - 3 exonuclease activity that can remove RNA primer and repair DNA
DNA pol III
DNA polymerase activity
3 - 5 exonuclease activity mediates proofreading
Super high processivity (does most of the adding)
What does exonuclease activity mean?
Can hydrolyzes phosphodiester bonds and can fix and proofread
Roles of RNA
Transmit genetic info
Store genetic info
Catalyze large macromolecules (rRNA and snRNA)
Gene regulation (mi/siRNA)
Non template strand
Coding strand of DNA. The mRNA strand will look like this but with u instead of t
Template strand
Non coding strand of DNA. This is the strand the mRNA will be made from.
Polycistronic
Refers to prok mRNA in that it will contain info for more than one polypeptide chain
Monocistronic
Refers to euk mRNA in that it contains info for only one polypeptide chain
Parts of tRNA
Acceptor stem - charged and where AA is linked
Anticodon loop - base pairs with codon on mRNA
Unique nucleotide bases
Transcription
DNA to mRNA
Bidirectional, depending on which strand is the template strand
RNA polymerase (prokaryotic)
Do not require a primer
No proofreading
Holoenzyme
Holoenzyme
Sigma and core enzyme
Sigma factor binds to promoting region
Promoting region (prokaryotes)
-35 and -10 bases upstream the start of transcription
TATA box
Initiation steps of transcription (proks)
Sigma binds to promoter region of DNA
Sigma opens DNA helix
Sigma leaves, mRNA continues to synthesize (elongation)
Termination of transcription (proks)
Hairpin forms and pinches off of RNA pol
Differences in eukaryotic transcription
No sigma factors, but transcription factors
3 RNA polymerases
In nucleus
Processing with 5’ capping, splicing, and 3’ polyadenylation
Euk rRNA processing
Ribonucelases cleave preribosomal RNA to give different sizes of rRNA
Euk mRNA processing
5’ cap - maintain stability, exit nucleus, efficient translation
Polyadenylation - transcription termination, translation, stability, exit nucleus, endonuclease and polyadenylate polymerase will synthesize RNA beyond cleavage site
Splicing - get introns out
Spliceosome
Recognizes introns and exons and will cut and paste exons
Boundary bt introns and exons is very GC rich
Alternative splicing
Producing 2+ proteins from a single gene
Individual genes express multiple mRNAs
Reverse transcriptase
Makes DNA from viral RNA
Very error prone and high mutation rate = drug resistance
Nucleotide
Sugar, phosphate, base
