Introduction

Table of contents
  1. Slides: The flow of genetic information
  2. Activity 1: From DNA to Protein
  3. Activity 2: Exploring phage genomes in NCBI
  4. Activity 3: Search DNA sequences with BLAST

Slides: The flow of genetic information

Activity 1: From DNA to Protein

Rationale

We will start by manually translating a DNA sequence into a protein sequence.

Activity 1 

  1   CTATTATACCAATCGGCTTCATGTATCCGCACGCGGGCGAAATTAGCCCG    50
 51   CGCGAAACCACCTATTAACCTGACGAGGAGGCCCACACGCGAGGAAGATG   100
101   GCGGATAGCTGCATTGAAAACACCATTAGCACCTGGGCGCGCAACATTAA   150
151   CGGCTGATAGACTGTTGCACGTTGGGGGAGAACATCCAGATAGCGCTAGC   200
201   TATGATTTCCTCTGAACTGTTGATAGAGTGGGCTTCCCACGAGCGCGAAT   250
251   AGTAAGCGAATAGAACAAAGACGCCTGCTACAACAGGAGTATCAACCCGT   300
  1. Find all the possible start codons.
  2. Using the DNA codon translation table, translate the DNA sequence into amino acid sequences from the start codon until you hit a stop codon.
  3. Answer the following for each amino acid sequence:
    • What is the amino acid sequence?
    • How long is each amino acid sequence?
    • How long is the nucleotide sequence?
  4. Write your own DNA sequence coding for a small mock protein with 10 amino acids of your choice.

Activity 2: Exploring phage genomes in NCBI

Rationale

NCBI is the National Center for Biotechnology Information, and it’s one of many online resources where biological data is stored. Their website, https://www.ncbi.nlm.nih.gov/, hosts many different databases. We will explore how to use some of them to learn more about the biological sequences we find.

Activity 2.1

  • Follow along:
  1. Go to the the NCBI website and look for the genome with the following accession NC_002371.2
  2. Try to find the following information:
    • Where can you find the accession?
    • How big is the genome?
    • What other properties of the genome can you find in the LOCUS line?
    • What type of phage is it? (Siphoviridae, Podoviridae, Myoviridae, other?)
    • Can you find the bacterial host?
  3. Go back to the top and find the FASTA view. Click it. What do you see? Looks familiar?
  4. Go into the Graphics view. Zoom in, move around, hover over the boxes. What do you see?
    • What does the boxes represent?
    • What are the arrows in the box?
    • Look for the head protein and zoom until you can see the nucleotide sequence. Can you find the START codon?
  5. Go back to the GenBank view. (Make sure Whole sequence is selected in the top right corner!) Scroll down until you find the FEATURES section.
    • Can you find the sequence for the head protein?
    • Can you find a protein that says hypothetical protein? What does this mean?

Activity 2.2

  • Now, you’ll each have an accession code for a phage genome. Follow the instructions bellow and take notes of what you find, so that you tell the rest of the class what you learned about your phage.
  1. Select an accession code from the bag:
    • XXXXXXX
    • XXXXXXX
  2. Go to NCBI and find the genome record.
  3. Find the following information about your phage:
    • How big is the genome?
    • Is the genome DNA or RNA, linear or circular?
    • What type of phage is it? (Siphoviridae, Podoviridae, Myoviridae, other?)
    • Can you find the bacterial host?
    • Can you find the coat protein (or capsid protein)?

Activity 3: Search DNA sequences with BLAST

Rationale

Here, we’ll start with one of the most popular ways to search for sequences, a program called BLAST💥. It’s so popular that it’s become a verb among biologists: “BLASTing”. You can think about it as the Google for biological sequences. We’ll learn how to BLAST a phage genome, which will help us find other related phages.

Activity 3

  1. Open the BLAST website
  2. Click on Nucleotide BLAST
    • When would you use Protein BLAST?
  3. Explore the BLAST window.
    • What is Query?
    • What databases are available?
  4. In a new tab, open NCBI and find the genome record for the phage you selected in the Activity 2.2.
  5. Go to the FASTA view, and copy the DNA sequence of your phage.
  6. Return to the tab with BLAST and copy the sequence into the Query box.
  7. Click on the button that says BLAST and wait for the results.
  8. Take notes about some of the top results of your search.
    • Are there other phages that look a lot like your phage?
    • How similar or how different are they?
    • How do the Query Cover percentages look like?
    • How do the Percent Identity values look like?