Identify a Variant using BLAST

Identify a Variant using BLAST

Teacher Guide &

SEQUENCE COMPARISON IDENTIFY A VARIANT Identify a Variant using BLAST Introduction Background The researchers sequenced your daughters' DNA and identified differences between their genomes and the human reference genome. Based on the variants in your daughters' DNA variants, they eventually identified ten people with similar symptoms and similar variants from four other families. The researchers sequenced those patients' genomes too. In this activity, you will follow the researchers' process to learn how they identified a genetic variant that could be contributing to your daughters' disorder. You will also investigate the types of sequences that researchers can compare and discuss why these researchers might choose to compare certain types of sequences over others.

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SEQUENCE COMPARISON IDENTIFY A VARIANT Central Dogma Review You may have heard of the central dogma of biology: DNA is transcribed into RNA, which is translated into protein. We can compare any of these sequences--DNA, RNA, or protein--across individuals. In this exercise, you will compare individual DNA, RNA, and protein sequences to a reference sequence. Before you begin, let's review core ideas and important vocabulary from the central dogma.

Figure 1. Central Dogma1. A gene is a stretch of DNA, parts of which code for a particular protein. The information contained in the DNA sequence needs to get transported from the nucleus to the cytoplasm in order to be used by the cell to make protein. To accomplish this, the DNA gets transcribed into an RNA molecule, which is processed to form messenger RNA (mRNA). When the cell translates the mRNA into protein, a ribosome will scan the mRNA until it finds a series of three nucleotides called a start codon. The start codon tells the ribosome where in the mRNA the protein coding sequence starts. The ribosome will then add amino acids in a chain until it reaches the series of three nucleotides called the stop codon. This section from the start codon to the stop codon, which gets translated into protein, is called the coding sequence. The coding sequence does not include the sections of the mRNA before the start codon or after the stop codon.

1 Adapted from OpenStax under the Creative Commons Attribution 4.0 International license.

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SEQUENCE COMPARISON IDENTIFY A VARIANT Knowledge Check Order the following sequences from longest to shortest, based on the number of nucleotides. a. mRNA, coding sequence, gene

What are the two main processes of the central dogma?

Glossary Gene ? a DNA sequence that codes for a protein. mRNA ? a molecule that includes the information from a gene that can be used to create protein. Coding sequence ? the portion of an mRNA sequence that codes for a protein. The coding sequence starts with a start codon and ends with a stop codon. Protein sequence ? the sequence of amino acids that make up a fully translated protein.

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SEQUENCE COMPARISON IDENTIFY A VARIANT

Codon Chart

T

TTT Phe (F)

TTC T

TTA Leu (L)

TTG

Second Base

C

A

TCT

TAT

Tyr (Y)

TCC

TAC

Ser (S)

TCA

TAA Stop

TCG

TAG Stop

G

TGT

T

Cys (C)

TGC

C

TGA Stop A

TGG Trp (W) G

CTT

CCT

CAT

CGT

T

His (H)

CTC

CCC

CAC

CGC

C

C

Leu (L)

Pro (P)

Arg (R)

CTA

CCA

CAA

CGA

A

Gln (Q)

CTG

CCG

CAG

CGG

G

First Base

Third Base

ATT

ACT

AAT

AGT

T

Asn (N)

Ser (S)

ATC Ile (I) ACC

AAC

AGC

C

A

Thr (T)

ATA

ACA

AAA

AGA

A

ATG

Start Met (M)

ACG

Lys (K)

Arg (R)

AAG

AGG

G

GTT

GCT

GAT

GGT

T

Asp (D)

GTC

GCC

GAC

GGC

C

G

Val (V)

Ala (A)

Gly (G)

GTA

GCA

GAA

GGA

A

Glu (E)

GTG

GCG

GAG

GGG

G

Figure 2. Codon Chart.

When ribosomes translate mRNA into protein, they read the mRNA in series of three base pairs called a codon. A codon chart helps us to determine which amino acid each mRNA codon will get translated into.

To read a codon chart, find the first base pair in the codon from the left side of the chart to select a row. Then find the second base pair from the top of the chart to select a column. Finally, select the third base pair from the right side of the chart to find your specific codon. The corresponding amino acid will be directly to the right of the codon. Amino acids can be abbreviated in two ways: with a three-letter code or with a one-letter code.

Try it! The codon ACG codes for the amino acid threonine (Thr, T). Can you find this codon on the chart?

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