Lecture 2 - Basic molecular mechanisms and nuclei acids Flashcards
4 molecular genetic processes
- Transcription 2. RNA processing 3. Translation 4. Replication
Where 4 molecular genetic processes occur
Transcription + RNA processing + Replication = In nucleus. Translation = In cytosol
4 cell cycle phases
M, G1, S, G2 , M, …
M cell cycle phase (2 things)
Mitosis (nuclear division) and Cytokinesis (cytoplasmic division)
G1 phase (key event)
Growth + Transcription initiation
S
DNA replication
G2 (nothing in particular)
?
DNA : what it contains and where info is stored
- Contains all info required to build CELLS and TISSUES of an organism
- Info stored in UNITS called GENES
Transcription definition
Information stored in DNA is copied into RNA for eventual use
Translation definition
Process where info is used to create a protein of specific amino acid sequence
DNA/RNA basic definition (biochem)
Linear polymers of monomers called nucleotides
Nucleotides (what is it)
pentose phosphate (which backbones deoxyribose in DNA/ribose in RNA) + purin (A G) or pyrimidin base (T C U)
Why DNA more stable (2 reasons) than RNA
- Double stranded. H bonds 2. No hydroxyl on carbon 2’. Hydroxyde catalizes slow hydrolisis of phosphodiester bonds between nucleotides at neutral PH
Effect of base pair composition
DNA more stable if higher % of G-C base pairs because G-C = 3 H bonds and A-T = 2 H bonds so breaking it down is more energy requiring
What would be optimal for high transcription
A-T rich DNA (less energy requiring)
Directionality explanation
Free 5’ phosphate at one end. Free 3’ hydroxyl at other hand. 2 Antiparallel strands
Phosphodiester bond (what is it)
Link between 3’ hydroxyl group of one base to 5’ phosphate group of adjacent base
Natural pair bonding (RNA and DNA) and why + name
A-T (DNA) and A-U (RNA) (cause 2 H bonds) and G-C(cause 3 H bonds) (Watson-Crick base pairing)
Exceptions to natural pair bonding (2)
- G-T and C-T possible (fits within double helix) and possible in artificial DNA in lab
- G-U exists in double-helical regions of RNA (can exist if this form of RNA occurs)
Groove definition
Space between two intertwined strands
Particularities of A DNA if compared to B DNA (3)
- Obtained when most of water is removed from DNA (under lab condition)
- Wider + deeper major groove, More narrow and shallow minor groove
- RNA:DNA or RNA:RNA exists in A DNA form in cells and in vitro
Why DNA flexible
No H bonds parallel to its long axis
What can bend DNA
DNA binding proteins
DNA bending advantage
Necessary for it to be packed in chromatin
TBP ? what does it do
TATA box-binding protein. Must attach to promoters to most of the eukaryotic genes in order to transcript them. (Bends and untwists DNA)
how transcription initiated
promoters in genes
who absorbs more UV light ssDNA or dsDNA
ssDNA
what stabilizes dsDNA and allows it to exist at higher Temp.
G-C base pairs
How to denature dsDNA. what phenomenon do theses conditions influence ?
- Raise Temp. 2. Extremes of pH. 3. Reducing ionic concentration 4. Agents that destabilize hydrogen bonds (formamide or urea). Nucleic acid hybridization depends upon these properties.
how to renature ssDNA (+ one condition)
Reverse conditions (low temp, normal pH, high ionic conentration). + Renaturation depends upon base-pairing so a complementary strand/sequence must exist.
Name of process by which ssDNA (or RNA) anneals to complementary DNA or RNA
Nucleic acid hybridization
What form of DNA appears in prokaryotes and viruses. Two forms and enzyme that changes them.
Circular. Supercoiled to relaxed circle (Topoisomerase 1)
How replication initiated
Complexes attract enzymes. Chromatory modelling complexes recruited to replication site and make DNA accessible.
Why DNA flexible
No H bonds along its axis
Difference between RNA and DNA 3D structure formation
DNA : By interacting with proteins
RNA : Reacts with itself
Specific structures of RNA (3) and how they form
Some regions base-pair to form 1. Hairpin 2. Stem-loop (with double-helical stem region) and 3. Pseudoknot (2 stems and 2 loops)
