Lecture 1: Genes and the Genetic Code

Bioinformatics: Definition?

Overview of Bioinformatics Central Dogma Genes and Genomes

Definition: Computational methods for collecting, organizing, and analyzing large amounts of biological data

Biological Data

Biological Model Computational Algorithms

Biological Data
DNA sequence (A,T,G,C) RNA sequence (A,U,G,C) RNA abundance Protein sequence (20 amino acids) Protein abundance Protein structure and post-translational modifications Protein - protein interactions Protein - DNA (RNA) interactions Metabolic products and pathways

Bioinformatics: Scope
DNA sequence analysis Predicting genes Sequence alignment Phylogenetics Gene expression analysis DNA microarray data analysis High-throughput sequencing Protein sequence analysis Sequence alignment Secondary/tertiary structure prediction Proteomics Protein abundance, modifications, interactions Metabolomics Gene Networks / Mathematical Modeling

Central Dogma

Gene: Definition
Definition: A gene is a sequence of DNA that codes for an RNA; in protein-coding genes, the RNA in turn codes for a protein Transcription:

DNA Reverse Transcription Transcription

RNA Polymerase

RNA Translation Protein RNA

5 GGCAUGGACCAUAGAGGACAGUGACAAAAAA 3

DNA

5 ATGGCATGGACCATAGAGGACAGTGAC 3 Coding strand 3 TACCGTACCTGGTATCTCCTCTCACTG 5 Template strand

+1

Genetic Code
Translation: RNA Protein
5 GGCAUGGACCAUAGAGGACAGUGACAAAAAA 3

Gene Organization: Prokaryotes and Simple Eukaryotes

Transcribed Region Promoter
ATG

G Q Stop

Open reading frame (ORF)

Stop

Gene Elements: An open reading frame (ORF) Start codon (AUG) Intervening codons Stop codon (UAA, UAG, UGA) A promoter DNA sequences that regulate the transcription of the gene

Image from: http://www.mun.ca/biology/scarr/

Gene Organization: Higher Eukaryotes

Enhancer Enhancer .... exon Promoter GT AG Open reading frame (ORF) ATG Transcription RNA GU AG Splicing mRNA AAAAAA Stop ....

Gene Organization: Higher Eukaryotes

Promoter exon GT AG Open reading frame (ORF) ATG Stop

intron

intron

Exons make up the processed mRNA sequence Exons contain the coding sequence, 5 UTR, and 3UTR Classes of Exons 5 exons Internal exons 3 exons intronless genes Introns are spliced out of the mRNA sequence Introns start with GU (GT) and end with an AG sequence

Genome Organization

Regulation of Eukaryotic Gene Expression

NUCLEUS RNA processing control 2 DNA primary RNA transcript 1 mRNA

CYTOSOL mRNA stability control 4 mRNA 3

translation control 5 protein 6 posttranslational control active/ inactive protein

transcriptional control

transport control

nuclear envelope

Provided by Dr. Jaideep Chaudhary

Gene Organization: Prokaryotes and Simple Eukaryotes

Transcribed Region Promoter
ATG

Promoter DNA elements in Transcriptional Control

Transcription Factor Proteins
Transcriptional Machinery

Open reading frame (ORF)

Stop

Gene Elements: An open reading frame (ORF) Start codon (AUG) Intervening codons Stop codon (UAA, UAG, UGA) A promoter DNA sequences that regulate the transcription of the gene

Transcription factor binding sites

TATA box

Transcribed Region

Distal Promoter

Core Promoter

Promoter elements consist of short (~5-20 bp) DNA elements that serve as binding sites for transcription factor proteins Transcription factor proteins can activate or repress the transcription of an adjacent gene