L15: Genomics & Bioinformatics

Question 1

What is genomics?

Answer 1

Study of entire genomes, including gene structure, function & evolution

Question 2

What can genomics seek to identify?

Answer 2

Similarities & differences between genomes of different species
- Compare genomes of diff species
- Compare genoms of diff individual humans

Question 3

Define bioinformatics

Answer 3

Collecting & analysing complex biological data e.g genetic codes

Question 4

What role does bioinformatics play in genomics?

Answer 4

It plays a role in the comparison of DNA sequences from different organisms

Question 5

Advancements in genome sequencing

Answer 5

• Allow rapid genome sequencing
• Large-scale genome analysis led to bioinformatics development

Question 6

4 uses of bioinformatics

Answer 6

1) Organising & analysing genome sequences

2) Identifying genes & predicting protein functions

3) Studying gene regulation & evolution

4) Storing & retrieving genetic data

Question 7

Major aim of genomics

Answer 7

Identify protein coding genes present in the genome

Question 8

Define genome assembly

Answer 8

Stitching together DNA fragments to form a complete genome

Question 9

What is comparative genomics?

Answer 9

Comparing gene sequences between species

Question 10

What is gene identification?

Answer 10

Locating protein-coding regions in DNA

Question 11

What is regulatory region identification?

Answer 11

Finding promotors & enhancers

Question 12

What is evolutionary analysis?

Answer 12

Understanding species relationships

Question 13

What is gene expression studies?

Answer 13

Determining when & where genes are active

Question 14

4 steps in genome sequencing

Answer 14

1) DNA Mapping: identifying fragment locations

2) Fragment Sequencing: determining nucleotide order

3) Sequence Overlap Detection: aligning overlapping fragments

4) Genome Assembly: using software to generate a complete sequence

Question 15

What is the Shotgun Sequencing Method?

Answer 15

Breaks DNA into random fragments, sequences them & reassembles the genome using overlapping regions

FASTER

Question 16

What does genome annotation involve?

Answer 16

Finding functional elements in DNA

Question 17

Key DNA sequences used for gene identification

Answer 17

1) TATA box: promotor region

2) CAAT box: promotor region

3) Start codon (ATG): signals start of synthesis

4) Stop codons (TAA, TAG, TGA): makrs end of gene

5) Poly-A signal (AATAAA): RNA processing

6) Exons & Introns: coding/non-coding region

Question 18

Example of genome annotation

Answer 18

BLAST (basic local alignment search tool): compares DNA & protein sequences between species to find genes

Question 19

What can bioinformatics predice once a gene is identified?

Answer 19

• Amino acid sequence of the protein
• Protein function, based on similarities to known protenis

Question 20

Example of hormone that can predict structure & function

Answer 20

Human Growth Hormone

Question 21

Tools used in prediction

Answer 21

1) CLUSTAL-W: identifies gene families with similar sequences

2) DeepMind AlphaFold: uses AI to predict 3D protein structures

Question 22

What allows the mapping of genes to each of the chromosomes?

Answer 22

Characterisation of the human genome sequence
- locate position of genes coding for specific proteins sequences

Question 23

What can protein structure be identified using?

Answer 23

X-ray diffraction patterns generated from protein crystals

Question 24

Key findings from the Human Genome Project (2003)

Answer 24

1) Genome size: 3 billion nucleotides

2) Protein-coding genes: only 2% of genome codes for proteinns

3) Alternative splicing: allows 1 gene to make multiple proteins

Question 25

What genomic data does NCBI (national center for biotech information) store?

Answer 25

1) gene sequences 2) proteins 3) disease-related mutations 4) cDNA sequences

Question 26

What is the purpose of using restriction enzymes in genomic DNA analysis?

Answer 26

To cut DNA at specific sequences

Question 27

What is the significance of alternative splicing in gene expression?

Answer 27

It allows for multiple proteins from a single gene.

Question 28

How do cDNA sequences differ from genomic DNA sequences?

Answer 28

cDNA sequences lack introns present in genomic DNA

Question 29

How are overlapping sequenced fragments aligned to assemble an entire chromosome?

Answer 29

By identifying overlapping sequence regions

Question 30

How can protein coding genes be identified within a genome?

Answer 30

By identifying specific DNA sequence motifs

Question 31

What is the ENCODE project and what does it aim to identify?

Answer 31

A project to identify all functional elements in the human genome

Question 32

What is the function of transcription factors in gene regulation?

Answer 32

To control gene transcription

Question 33

What role do splice sites play in mRNA processing?

Answer 33

They direct the removal of non-coding RNA segments.

Question 34

What are SNPs and why are they important in human genetics?

Answer 34

Variations at a single position in a DNA sequence

Question 35

What is the significance of conserved genes across different species?

Answer 35

They indicate essentiality and shared ancestry

Question 36

What is the importance of polyadenylation in mRNA stability and translation?

Answer 36

Enhances mRNA stability and enhances translation initiation

Question 37

How do enhancers and silencers influence gene expression?

Answer 37

Enhancers increase gene expression, while silencers decrease gene expression

Question 38

What is the importance of identifying regulatory regions in genomic sequences?

Answer 38

To understand gene expression and cellular function

Question 39

What is synthetic biology and how does it relate to genome studies?

Answer 39

Uses genome studies to design and build new systems

Question 40

How does the quaternary structure of a protein differ from its tertiary structure?

Answer 40

The quaternary structure involves multiple polypeptide chains, unlike the tertiary structure which involves a single chain

Question 41

What is the relationship between amino acid sequence and protein function?

Answer 41

It guides how the molecule folds and interacts.

Question 42

How has the 1000 Genome Project contributed to our understanding of human genetic variation?

Answer 42

By creating a comprehensive catalog of human genetic variants

Question 43

What is the significance of the 100,000 genomes project?

Answer 43

Sequencing patients with rare diseases & cancer to identify disease-causing mutations - To develop personalised medicine. based on genetic profiles

Question 44

What types of genetic diseases can mitochondrial DNA studies help identify?

Answer 44

Maternally inherited mitochondrial diseases

Question 45

What is the significance of the Human Genome Project in modern genetics?

Answer 45

It provided the first comprehensive map of the human genome, revolutionizing biological and medical research

Question 46

What is the role of molecular chaperones in protein folding?

Answer 46

To assist proteins in proper folding and prevent aggregation

Question 47

What is the impact of single nucleotide polymorphisms (SNPs) on human health?

Answer 47

SNPs can influence disease susceptibility and other traits

Question 48

What are some applications of translational medicine in healthcare?

Answer 48

Developing new therapies and diagnostics

Question 49

What is the role of the J Craig Venter Institute in synthetic genome research?

Answer 49

To pioneer the development of the first self-replicating synthetic cell and other advances

Question 50

3 things microbiome sequencing can do

Answer 50

1) Identify differences between individuals 2) Detect changes in disease states 3) Lead to microbiome-based therapies

Question 51

What does the gut microbiome influence?

Answer 51

Digestion, immunity & mental health

Question 52

Applications of synthetic biology

Answer 52

1) Engineering microbes for pollution cleanup 2) Producing biofuels & 1medicines

Question 53

What is the study of: 1) genomics 2) transcriptomics 3) proteomics 4) metabolomics 5) glycomics 6) metagenomics

Answer 53

1) study of entire DNA sequences 2) study of all RNA molecules 3) study of all proteins in a cell/tissue 4) study of metabolic products 5) study of carbs in cells 6) study of microbial communities

Question 54

What does omics flowchart show?

Answer 54

Interactions between DNA, RNA, proteins & metabolites