lectures 1-7 Flashcards
Which of these is favoured to carry genetic info?
A. DNA
B. Carbohydrates
C. Lipids/phospholipids
D. Proteins
E. Deoxyribose
D.
Proteins are complex polymers of many subunits, many different kinds. All this the “language” between cells. DNA is slightly less favoured because has less complex polymers, only 4 subunits (ATGC), chemically very similar to proteins.
Explain the difference between an S strain and an R strain of streptococcus pneumoniae.
S strain = disease causing. R strain = can’t cause infection
What would happen to a mouse if you put heat-killed S strain and an alive R strain of S.pneumoniae in it? explain
The mouse would die. This is because R cells transform into S cells (R cells take up S traits and become S essentially)
Which of the following is required for a transformation from R to S strain?
A. DNA
B. Carbohydrates
C. Lipids/phospholipids
D. Proteins
E. Deoxyribose
A.
DNA is composed of…
Nitrogenous bases (purines and pyrimidines)
Deoxyribose
Phosphate
Chargaff’s rules
- amount of purines (AG) = amount of pyrimidines(CT) (A-T, G-C)
- Amount of A-T does NOT equal amount of G-C (#G=#C, #A=#T)
DNA can only move from ___’ to ___’ so that makes this the leading strand.
3’ to 5’
Bases are most exposed in the _________ groove
Major
This is where most protein activity occurs, where DNA is “read”
DNA polymerase requires ________ on the ___’ end to begin growing DNA
A. Phosphate, 3’ end
B. OH, 3’ end
C. OH, 5’ end
D. Phosphate, 5’ end
B.
Because polymerase goes 3’ to 5’ it is able to back up and correct mistakes
Why can’t DNA polymerase use rNTPs?
Because ribonucleoside tri-phosphate has an extra OH on its ribose which doesn’t fit DNA polymerases pocket
Most common type of restriction enzyme
Type II
A smaller restriction enzyme will cut ______ frequently than a longer restriction enzyme
more
Why was RNA the first molecule sequenced?
RNA is short, easy to obtain, single-stranded, easy to melt, easy to get pure sample
Explain Sanger sequencing
- DNA of interest into 4 tubes
- Add DNA polymerase, dNTPs, primer and then ddNTP’s corresponding to each base in one tube at a time (ddATP for one tube, ddGTP for another tube etc etc)
- DNAP can add ddNTP but once ddNTP added, can’t add any more dNTP’s to copy DNA further = lots of trunkated DNA that stops at A, T, G, C per tube
- Run each tube in electrophoresis in separate wells (see notebook drawing)
1st generation
What type of sequencing does Illumina use?
What gen?
Shotgun sequencing
2nd generation
PacBio is what generation sequencing?
3rd generation
Which sequencing methods use fluorescently labelled dNTPs?
Illumina, PacBio
Nanopore sequencing includes the nanopore and 3 other items?
what gen?
Motorprotein - denatures ds DNA. Slows the DNA passing through
Y adapter - Ligated to the 5’ end of ds DNA. This is what the tether interacts with
Tether - Interacts with the Y adapter to pull motorprotein and DNA close to the pore
3rd generation
What sequencing methods use short read sequencing, which use long read sequencing?
Short read: Illumina shotgun seq
- highly accurate but PCR required
Long read: Nanopore, pacBio
- less accurate, easier to assemble long fragments
Explain primer walking
Sequence some DNA (800bp), then make primers out of the last section of the sequenced DNA and repeat. Takes an extremely long time
As the genome size increases GC content _________
increases
What are IS elements?
Cause of gene loss and scrambling
Stands for Insertion Sequence = inseq = transposons
As genome size decreases, host dependence and AT content ___________
Increases
If you see many insertions in a gene due to a transposon, that means that the gene is…
not essential
