L15: Genomics & Bioinformatics Flashcards
What is genomics?
Study of entire genomes, including gene structure, function & evolution
What can genomics seek to identify?
Similarities & differences between genomes of different species
- Compare genomes of diff species
- Compare genoms of diff individual humans
Define bioinformatics
Collecting & analysing complex biological data e.g genetic codes
What role does bioinformatics play in genomics?
It plays a role in the comparison of DNA sequences from different organisms
Advancements in genome sequencing
- Allow rapid genome sequencing
- Large-scale genome analysis led to bioinformatics development
4 uses of bioinformatics
1) Organising & analysing genome sequences
2) Identifying genes & predicting protein functions
3) Studying gene regulation & evolution
4) Storing & retrieving genetic data
Major aim of genomics
Identify protein coding genes present in the genome
Define genome assembly
Stitching together DNA fragments to form a complete genome
What is comparative genomics?
Comparing gene sequences between species
What is gene identification?
Locating protein-coding regions in DNA
What is regulatory region identification?
Finding promotors & enhancers
What is evolutionary analysis?
Understanding species relationships
What is gene expression studies?
Determining when & where genes are active
4 steps in genome sequencing
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
What is the Shotgun Sequencing Method?
Breaks DNA into random fragments, sequences them & reassembles the genome using overlapping regions
FASTER
What does genome annotation involve?
Finding functional elements in DNA
Key DNA sequences used for gene identification
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
Example of genome annotation
BLAST (basic local alignment search tool): compares DNA & protein sequences between species to find genes
What can bioinformatics predice once a gene is identified?
- Amino acid sequence of the protein
- Protein function, based on similarities to known protenis
Example of hormone that can predict structure & function
Human Growth Hormone
Tools used in prediction
1) CLUSTAL-W: identifies gene families with similar sequences
2) DeepMind AlphaFold: uses AI to predict 3D protein structures
What allows the mapping of genes to each of the chromosomes?
Characterisation of the human genome sequence
- locate position of genes coding for specific proteins sequences
What can protein structure be identified using?
X-ray diffraction patterns generated from protein crystals
Key findings from the Human Genome Project (2003)
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
What genomic data does NCBI (national center for biotech information) store?
1) gene sequences
2) proteins
3) disease-related mutations
4) cDNA sequences
What is the purpose of using restriction enzymes in genomic DNA analysis?
To cut DNA at specific sequences
What is the significance of alternative splicing in gene expression?
It allows for multiple proteins from a single gene.
How do cDNA sequences differ from genomic DNA sequences?
cDNA sequences lack introns present in genomic DNA
How are overlapping sequenced fragments aligned to assemble an entire chromosome?
By identifying overlapping sequence regions
How can protein coding genes be identified within a genome?
By identifying specific DNA sequence motifs
What is the ENCODE project and what does it aim to identify?
A project to identify all functional elements in the human genome
What is the function of transcription factors in gene regulation?
To control gene transcription
What role do splice sites play in mRNA processing?
They direct the removal of non-coding RNA segments.
What are SNPs and why are they important in human genetics?
Variations at a single position in a DNA sequence
What is the significance of conserved genes across different species?
They indicate essentiality and shared ancestry
What is the importance of polyadenylation in mRNA stability and translation?
Enhances mRNA stability and enhances translation initiation
How do enhancers and silencers influence gene expression?
Enhancers increase gene expression, while silencers decrease gene expression
What is the importance of identifying regulatory regions in genomic sequences?
To understand gene expression and cellular function
What is synthetic biology and how does it relate to genome studies?
Uses genome studies to design and build new systems
How does the quaternary structure of a protein differ from its tertiary structure?
The quaternary structure involves multiple polypeptide chains, unlike the tertiary structure which involves a single chain
What is the relationship between amino acid sequence and protein function?
It guides how the molecule folds and interacts.
How has the 1000 Genome Project contributed to our understanding of human genetic variation?
By creating a comprehensive catalog of human genetic variants
What is the significance of the 100,000 genomes project?
Sequencing patients with rare diseases & cancer to identify disease-causing mutations
- To develop personalised medicine. based on genetic profiles
What types of genetic diseases can mitochondrial DNA studies help identify?
Maternally inherited mitochondrial diseases
What is the significance of the Human Genome Project in modern genetics?
It provided the first comprehensive map of the human genome, revolutionizing biological and medical research
What is the role of molecular chaperones in protein folding?
To assist proteins in proper folding and prevent aggregation
What is the impact of single nucleotide polymorphisms (SNPs) on human health?
SNPs can influence disease susceptibility and other traits
What are some applications of translational medicine in healthcare?
Developing new therapies and diagnostics
What is the role of the J Craig Venter Institute in synthetic genome research?
To pioneer the development of the first self-replicating synthetic cell and other advances
3 things microbiome sequencing can do
1) Identify differences between individuals
2) Detect changes in disease states
3) Lead to microbiome-based therapies
What does the gut microbiome influence?
Digestion, immunity & mental health
Applications of synthetic biology
1) Engineering microbes for pollution cleanup
2) Producing biofuels & 1medicines
What is the study of:
1) genomics
2) transcriptomics
3) proteomics
4) metabolomics
5) glycomics
6) metagenomics
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
What does omics flowchart show?
Interactions between DNA, RNA, proteins & metabolites
