MATH 5610, Computational Biology

Transcription

1 MATH 5610, Computational Biology Lecture 1 Intro to Molecular Biology Stephen Billups University of Colorado at Denver MATH 5610, Computational Biology p.1/14

2 Announcements Homework 1 due next Tuesday Also, read chapter 1. Sign up for CCB Certificate program. CCB seminar series (1st and 3rd Fridays) Register for discussion board. MATH 5610, Computational Biology p.2/14

3 Outline Course Conduct What is Computational Biology? Overview of topics Intro to Molecular Biology. MATH 5610, Computational Biology p.3/14

4 What is Computational Biology? Synonymous with bioinformatics: (but this is often argued about). Rough definition: the development and use of mathematical or computational tools to study biological systems. Merger of 3 fields: mathematics/statistics, computer science, and biology. New field (became recognized as a field in the 80 s). Amazing potential to impact our lives. Drug Discovery. Diagnosis of disease. Improved agriculture. New materials.... MATH 5610, Computational Biology p.4/14

5 Data Much of bioinformatics is concerned with organizing and understanding biological data, such as Often involves DNA and amino acid sequences or related information such as: Genome sequences Gene expression data Mass spectrometry data Biomedical literature Protein structure data and much more! Hence, the informatics. But bioinformatics goes beyond that. It also includes modeling of biological systems. MATH 5610, Computational Biology p.5/14

6 Biological topics we will examine DNA and protein sequence comparison. Phylogenetic trees. DNA sequence assembly (Human genome project). Gene expression arrays. Gene recognition. Protein and RNA structure prediction. Proteomics. Biological networks. MATH 5610, Computational Biology p.6/14

7 Mathematical/Computational topics Dynamic programming Algorithmic Complexity Graph Theory Hidden Markov Models Machine learning/pattern recognition Optimization Statistical and differential equations models Linear algebra Combinatorics MATH 5610, Computational Biology p.7/14

8 Intro to Molecular Biology DNA/RNA/Proteins Central Dogma Replication/Transcription/Translation MATH 5610, Computational Biology p.8/14

9 DNA DNA: Encodes all inherited information of a living cell. (In particular, genes). Structure: Double helix of two reverse complementary polynucleotide chains. Chains made up of sequence of four nucleotides: {G,A,T,C}. Biological information reduces to sequences constructed from 4 letter alphabet. MATH 5610, Computational Biology p.9/14

10 Nucleotides 4 nucleotides used in DNA: {G,A,T,C} 3 parts to each nucleotide: Phosphate group. Ribose sugar. Nitrogenous base. (Different for each nucleotide). Base Pairing Each nucleotide has a complement: G C A T Nucleotide on one strand binds with its complement on the other strand. MATH 5610, Computational Biology p.10/14

11 Orientation Nucleotides are oriented in relation to the carbon atoms in the Ribose sugar. (see Figure 1.2). Polynucleotide chains are built in a particular direction (5 to 3 ). Nucleotide sequences are listed in 5 to 3 direction. The two strands in a DNA molecule are oriented in opposite directions so are reverse complements. DNA molecule Corresponding strands 5 -CATAGG-3 3 -GTATCC-5 5 -CATAGG-3 5 -CCTATG-3 reverse complements MATH 5610, Computational Biology p.11/14

12 DNA Replication When a cell divides, all of its DNA is replicated. The two strands are separated, each becoming a template to grow the other strand. 5 -CATAGG-3 = 3 -GTATCC-5 5 -CATAGG-3 GTA--> = 3 -GTATCC-5 <--AGG 5 -CATAGG-3 3 -GTATCC-5 3 -GTATCC-5 5 -CATAGG-3 MATH 5610, Computational Biology p.12/14

13 Central Dogma (From: cats.med.uvm.edu/cats_teachingmod/microbiology/courses/genomics/genomics_ ) MATH 5610, Computational Biology p.13/14

14 RNA Transcribed from DNA by RNA polymerase. Made up of Nucleotides. { G, A, U, C } (U instead of T). RNA sequence is complementary to DNA sequence. Many functions of RNA: Messenger RNA (mrna) carries the information that will be translated to make proteins. Transfer RNA (trna) participates in the translation process by recognizing codons in the mrna. Ribosomal RNA (rrna) part of a ribosome. Many others... MATH 5610, Computational Biology p.14/14