CMMB 411 Study Guide - Fall 2018, Comprehensive Midterm Notes - Escherichia Coli, Protein, Processivity
12 Oct 2018
School
Course
Professor
CMMB 411
MIDTERM EXAM
STUDY GUIDE
Fall 2018
DNA Topology — Part 1
DNA AS A HARD DRIVE
- One gram of DNA can store 10^18 bytes of information
- A digital movie was stored in the form of DNA in E. coli genome
FEATURES OF THE B FORM DNA
- There are 6 forms of DNA: A, B, C, D, T, and Z
- Forms ABZ are the physiological forms that are very relevant
- Form B is commonly studied in the classroom
- Form Z is very rare and difficult to find as it only appears at a certain time in specific
physiological conditions
- As a result of the rarity of form Z, sometimes it is also mistaken for form B
- 2 important reasons why Z form DNA is hard to prove as physiologically relevant
- A form DNA can be present in spore for a long time, but for the Z form, it is only present
transiently in the cell, therefore, you need to catch it at a very specific time
find more resources at oneclass.com
find more resources at oneclass.com
- Z form DNA needs special purine-pyrimidine segment, making it very difficult to pinpoint
exactly what segment the Z form is
- Important numbers to remember:
- 360° is one helical turn, and per turn, there are 10.5 base pairs1
- The space between two base pairs (axial rise), or the space between two rungs of a DNA
ladder, is 3.4 A (0.34 nm)
- The diameter of the DNA helix is 20 A (2 nm)
- Antiparallel strands
- Antiparallel orientation of DNA strands use Watson and Crick base pairing
- GC having 3 hydrogen bonds
- AT having 2 hydrogen bonds
- Charges in each pair are neutral, making the entire structure stable
- Parallel orientation of DNA strands use Donahue base pairing
- Similar GC and AT pairing, however, due to strands being parallel when:
- Cytosine is flipped 180°, there are only 2 instead of 3 hydrogen bonds linking GC
- Thymine is flipped 180°, there remain 2 hydrogen bonds linking AT
- Thus, due to the change in orientation of the purines, the charges in each base pair do
not cancel out and thus cause the pair to carry a positive charge, resulting in parallel
DNA being unstable
- Problems with parallel orientation:
- Charges do not cancel out, making the DNA structure not neutral and highly unstable
- Number of hydrogen bonds lowers when cytosine rotated 180° to make this Donahue
conformation
- DNA strands could fall apart for animals living in cold environments to prevent this
from happening, there need to be more GC base pairs because they form stronger
and more hydrogen bonds. However, this is not possible in parallel orientation
because GC only form 2 hydrogen bonds instead of 3. Thus, due to a lack of strength
and stability the DNA molecule would fall apart
- Charges
- Positive charge on a base means that base will be in the direction reading from 5’ to 3’
- Negative charge on a base means that the base will be in the direction reading from 3’ to 5’
- Right-handed helix
1 Usually, in the classroom it is taught there are 10 base pairs for simplicity in calculations,
however there are actually 10.5
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
One gram of dna can store 10^18 bytes of information. A digital movie was stored in the form of dna in e. coli genome. There are 6 forms of dna: a, b, c, d, t, and z. Forms abz are the physiological forms that are very relevant. Form b is commonly studied in the classroom. Form z is very rare and difficult to find as it only appears at a certain time in specific physiological conditions. As a result of the rarity of form z, sometimes it is also mistaken for form b. 2 important reasons why z form dna is hard to prove as physiologically relevant. A form dna can be present in spore for a long time, but for the z form, it is only present transiently in the cell, therefore, you need to catch it at a very specific time.
