Bioinfor

1. Introduction to computational
Biology Bioinformatics- Lec 4
DR. Zainab Hassan Ali
Embedded Network and Technology DEPT.
FACULTY OF Artificial Intelligence
Kafrelsheik UNIVERSITY
Kafrelsheikh University
Faculty of AI
Biomedical Program
Second Semester- 2022-2023

2. Refresh your knowledge in 10 mins
- State the requirements to complete the operation of DNA replication.
- List the required enzyme to build new DNA from the exiting DNA
template.

3. DNA Damage and Repair
 DNA is stable molecule however damage to DNA inevitable.
 DNA can also be altered by mistakes made during its own replication
or recombination .
 The genetic information encoded in the DNA has to remain
uncorrupted.
 Any chemical changes must be corrected.
 Damage and sequence alterations to DNA are often quickly repaired,
but when they are not, the DNA becomes permanently altered
resulting in the production of Mutation.

4. DNA Damage and Repair
Mutations Categories:
 Somatic Mutations: occur in somatic cell and only affect
the individual in which the mutation arises.
 Germ-line Mutation: alter gametes and passed to the next
generation.

5. DNA Damage and Repair
Mutation types
Nonsense Mutation
Missenses Mutation
Single base pair Sequence of DNA- Stop codon
Insertion Deletion Double
Frame
shift

6. DNA Damage and Repair

7. DNA Damage and Repair
DNA Damage is occurred by i) chemical damage such as a break DNA strand and a
base missing from the backbone of DNA, and ii) physical damage such as radiation,
UV light, and heat.
Source Of Damage
Exogenous Damage
Endogenous Damage
1. UV Light [200-400 nm] radiation from
sun.
2. X-ray gamma.
3. Viruses .
1. DNA replication error

8. DNA Damage and Repair
DNA Damage Types are:
DNA Damage
Single base Two bases Chain breakage Cross Linkage
Alteratio
n
Insertion Deletion
TT diamond
AA diamond

9. DNA Damage and Repair
DNA Repairing: Repairing Types
Excision repair Recombinant repair
The damaged DNA is first removed
and replaced with fresh DNA using
Two Mechanism :
1. Base excision repair.
2. Nucleotide excision repair.
Photoreactive repair
A biological reparative
process in response to DNA
damage caused by
exogenous agents (e.g. UV
light).
The simplest process for repair of
pyrimidine dimers is called
photoreactivation which, as the name
suggests, requires light. Photoreactivation
is catalyzed by a single protein called
photolyase, which uses the energy in a
photon of light to chemically break apart a
pyrimidine dimer in DNA

10. DNA Damage and Repair
DNA Repairing steps:
1- Recognition
2- Removing
3. Repairing
Excision  AB endonuclease
Recombinant repairing  double strands endonuclease
Photoreactive repair  Photoreactive repair endonuclease
Excision
Exonuclease
DNA polymerase-I

11. Alignment in DNA
Sequence alignment is the process of arranging two or more sequences (of DNA, RNA or
protein sequences) in a specific order to identify the region of similarity between them.
Identifying the similar region enables us to infer a lot of information like what traits are
conserved between species, how close different species genetically are, how species
evolve, etc. Biopython provides extensive support for sequence alignment.
Types of alignment:
 Pairwise sequence alignment compares only two sequences at a time and provides
best possible sequence alignments. Pairwise is easy to understand and exceptional to
infer from the resulting sequence alignment.
 Multiple sequence alignment concept, two or more sequences are compared for best
subsequence matches between them and results in multiple sequence alignment in a
single file.

12. Alignment in DNA
 Pairwise sequence alignment:

13. Alignment in DNA
 Pairwise sequence alignment:

14. References
 Jin Xiong. Essential Bioinformatics. Cambridge University Press, New York, USA (2006).
 Sara El-metwally. Bioinformatics Course (MED-121). Faculty of Computers and Information, Mansoura
University, Mansoura, Egypt (2020).
 https://www.genome.gov/
 https://www.yourgenome.org/facts/what-is-dna-replication
 https://www.nigms.nih.gov/education/Documents/Studying_genes_final.pdf
 https://www.nature.com/