Bioinformatics

Question 1

How to use plasmids?

Answer 1

1-Design: Select a suitable plasmid vector
2- Construction: Introduce desired DNA sequences
3- Verification: Confirm the successful construction of the recombinant plasmid.
4- Transformation: Transfer the recombinant plasmid into the target organism.
5- Expression: Cultivate transformed cells t

Question 2

Selectable marker (Marker gene)

Answer 2

Gene conferring antibiotic resistance trait

Question 3

Multiple cloning site (MCS)

Answer 3

Region with multiple restriction enzyme recognition sites for inserting foreign DNA.

Question 4

Reporter Gene

Answer 4

A reporter gene is a gene whose activity serves as a visible or measurable indicator of the activity of other genes.

Question 5

PCR

Answer 5

What: Technique to amplify DNA fragments.
Why: Replicate DNA for various analyses.
How: Cyclically heat, cool, and extend DNA using primers and DNA polymerase.

Question 6

Primer design

Answer 6

What: Designing primers that flank a target DNA region for use in PCR.
Why: To amplify specific DNA sequences for various applications such as DNA sequencing and cloning.
How: Utilizing bioinformatics tools to select primer sequences with appropriate length, melting temperature, and specificity to the target DNA region.

Question 7

Restriction Enzymes -Sticky/Blunt

Answer 7

What: Enzymes that cut DNA at specific recognition sequences.
Why: Used in genetic engineering to manipulate DNA.
How: Recognize specific DNA sequences and cleave them at specific sites.

Question 8

Ligation

Answer 8

What: Joining DNA fragments together.
Why: Used in molecular biology to create recombinant DNA molecules.
How: DNA ligase enzyme catalyzes the formation of phosphodiester bonds between DNA fragments.

Question 9

Types of primers for different purposes.

Answer 9

-Normal PCR. [(18-30 bp)]
-Parenthood type PCR. [(Short <15bp)]
-RE- Primers. [(Adding the RE sequence to the primer’s end)]
-Overlapping primers. [(Complement the other primer back)]

Question 10

Design primers need some specs

Answer 10

1-Types of primers for different purposes.
2- Thermodynamics.
3- GC content.
4- AT ending
5- Length of the primers.
6- Primers dimers and self dimers

Question 11

Overlapping PCR

Answer 11

Overlapping PCR involves designing primers with overlapping ends to amplify DNA fragments, which can then be joined together to create a fused DNA sequence.
(PCR Done with fragments that have Tails complement to each other)

Question 12

Extension PCR

Answer 12

PCR done using special primers with Tail

Question 13

Purification PCR

Answer 13

PCR to amplify the full constructed fragment

Question 14

Genomics in bioinformatics

Answer 14

involves using computational tools and techniques to analyze, interpret, and manage large-scale genomic data efficiently.

Question 15

Genomics is a branch of molecular biology that focuses on the:

Answer 15

Structure,
Function,
Evolution,
Mapping,
And Editing of Genomes

Question 16

Analyzes entire genome, providing comprehensive genetic information.

Answer 16

Whole Genome Sequencing (WGS)

Question 17

It makes use of high-throughput techniques, such as as WGS, to sequence DNA fragments rapidly and in parallel.

Answer 17

Next-Generation Sequencing (NGS):

Question 18

Gene structure [Open reading Frame ORF] CDS:

Answer 18

Represents the portion of a gene that potentially encodes a protein product.

Question 19

Gene orientation

Answer 19

Refers to the directionality of a gene on a DNA strand, either forward (+) or reverse (-) relative to a reference point.

Question 20

Gene mining

Answer 20

Involves the identification and extraction of genes or genetic information from genomic data.

Question 21

Annotation

Answer 21

The process of identifying and labeling genes, regulatory sequences, and other functional elements within a genome.

Question 22

Comparative Genomics

Answer 22

Analyzes genome similarities/differences to understand evolution, functions, and variations.

Question 23

Phylogenetics

Answer 23

Reconstructs evolutionary relationships using molecular data to build evolutionary trees.

Question 24

for Gene location (Locus), use:

Answer 24

NCBI, KEGG, UNIPROT

Question 25

For Gene orientation use:

Answer 25

SNAPGENE, Negative strain

Question 26

for Relationship between organisms

Answer 26

MEGA software

Question 27

Biosynthetic gene clusters (BGCs)

Answer 27

Involves identifying the sets of genes responsible for the synthesis of specialized metabolites, such as antibiotics or natural products, within the genomic sequence of microorganisms.

Question 28

Transcriptomics

Answer 28

is the study of all the RNA molecules present in a cell, tissue, or organism at a given time.
-It provides insights into which genes are active and how they are regulated, offering valuable information about cellular processes and functions

Question 29

Next Generation Sequencing (NGS) steps:

Answer 29

1- Extraction
2-library preparation
3-sequencing
4-Analysis

Question 30

Basics of Transcriptomics Analyses?

Answer 30

1-Gene Expression Analysis
2-Sequence Alignment
3-Functional Annotation
4-Differential Gene Expression Analysis
5-Visualization of Transcriptomic Data

Question 31

Studying the levels of RNA molecules produced from different genes in a biological sample.

Answer 31

Gene Expression Analysis

Question 32

The process of arranging DNA or RNA sequences to identify similarities and differences to identify mutations

Answer 32

Sequence Alignment

Question 33

Assigning biological functions to genes based on their sequence characteristics or experimental evidence to roles of genes in various cellular processes.

Answer 33

Functional Annotation

Question 34

Analysis that compares gene expression levels between sample groups to identify genes that are significantly upregulated or downregulated.

Answer 34

Differential Gene Expression (DGE) Analysis

Question 35

Visualization tools allow researchers to explore and interpret transcriptomic data in a more intuitive manner patterns.

Answer 35

Visualization of Transcriptomic Data

Question 36

Gene Ontology

Answer 36

it’s a standardized system for categorizing genes based on their biological functions, molecular roles, and cellular locations

Question 37

a biomedical and genomic information hub through databases, tools, and resources for researchers, healthcare professionals, and the public.

Answer 37

NCBI

Question 38

Tool for comparing DNA and protein sequences.

Answer 38

NCBI BLAST

Question 39

Kyoto Encyclopedia of Genes and Genomes, a database for biological pathways, diseases, drugs, and genomes.

Answer 39

KEGG

Question 40

Deep learning-based protein structure prediction software developed by DeepMind, known for its accuracy in determining protein structures from amino acid sequences

Answer 40

AlphaFold Database

Question 41

Search Tool for the Retrieval of Interacting Genes/Proteins, a database that compiles known and predicted protein-protein interactions.

Answer 41

String Database

Question 42

Arrangement of sequences to identify similarities and differences, often used in bioinformatics to compare DNA, RNA, or protein sequences.

Answer 42

Offline Alignments

Question 43

Molecular Evolutionary Genetics Analysis, software used for conducting molecular evolutionary analysis, phylogenetic tree construction, and Alignment.

Answer 43

MEGA

Question 44

Molecular visualization software used for viewing and analyzing molecular structures in 3D.

Answer 44

PyMol

Question 45

UGENE

Answer 45

a versatile software tool, is a go-to choice for bioinformatics tasks