1.1.3 Review

Question 1

Bioinformatics

Answer 1

The field of science to store and analyze genetic data

Question 2

Outbreak

Answer 2

A sudden rise in the incidence of a disease

Question 3

Genome

Answer 3

Complete set of DNA in a cell

Question 4

Pathogen

Answer 4

A specific causative agent of a disease

Question 5

Overall goal of 1.1.3

Answer 5

To identify the exact pathogen, we first need a sample of the patient’s lymph fluid. This fluid will contain the patients cells in addition to pathogen cells. From there, we need to isolate the DNA via DNA extraction. From there, will use PCR to amplify pathogen DNA. Then we run another PCR using fluorescently tagged Nucleotides in normal nucleotides to begin the DNA sequencing process. This will produce a set of DNA fragments that differ from a single base. From there, we will use electrophoresis in an automatic sequencer to generate a chromatogram that can then be read to obtain the pathogen sequence. after the sequence is obtain, the species can be identified by using bioinformatics by uploading the sequence into a molecular database.

Question 6

What method was used in the video

Answer 6

Cycle sequencing

Question 7

How long does it take to read an entire genome using this method

Answer 7

A few hours

Question 8

What does it mean to read the Genome

Answer 8

Reading the genome means analyzing the specific nucleotide sequence

Question 9

What is the role of a thermocycler

Answer 9

This is the machine that’s able to raise and lower the temperatures needed for each stage of PCR

Question 10

What kinds of fragments are produced during this process

Answer 10

Fragments that differ in length by a single base

Question 11

What is done to the fragments next

Answer 11

They are sorted by size

Question 12

What is the top stand called

Answer 12

Template

Question 13

Bottom strand

Answer 13

Complementary

Question 14

 what strand is used for the rest of the sequencing process

Answer 14

Complementary

Question 15

Primers

Answer 15

Short DNA fragments that buy specifically to target DNA.  They are starting points that allow DNA polymerase to begin replication

Question 16

DNA polymerase

Answer 16

Is an enzyme that adds complementary nucleotides during the extension phase of PCR

Question 17

Free nucleotides

Answer 17

Served as the building blocks used when the new DNA molecules are built during the extension phase.

Question 18

Fluorescently tagged free nucleotides

Answer 18

Used in cycle sequencing PCR‘s to serve as stop signs in the extension step. They are nucleotides that are fluorescently tagged and will signal DNA polymerase to stop replication. This results in fragments of every length. They are detected by the laser in the sequencing process

Question 19

A

Answer 19

Green

Question 20

C

Answer 20

Blue

Question 21

G

Answer 21

Yellow and black

Question 22

T

Answer 22

Red

Question 23

How does each strand of DNA form

Answer 23

Each strand is built simultaneously. After the primer attaches to the template strand, DNA polymerase adds complementary nucleotides until it adds a fluorescently tagged nucleotide then it stops and that DNA fragment is complete

Question 24

What determines DNA length

Answer 24

When ddTNP is added

Question 25

What does an automatic sequencer do

Answer 25

Search DNA fragments by size by using electricophoresis

Question 26

Capillary tube

Answer 26

Holds the buffer matrix that DNA fragments migrate through

Question 27

What causes DNA to move through the tube

Answer 27

Electrical current that generates positive and negative ends

Question 28

What pieces move the fastest

Answer 28

Smallest

Question 29

Optical detectors

Answer 29

They send out laser beams that detects fluorescent glow and send the signal back to the computer

Question 30

How does the optical detectors work with the computer

Answer 30

They detect the fluorescent glow of the DNA fragments as they move through the capillary tube electrophoresis. That signal is sent back to the computer. Then it generates a chromatogram based on the color and number of the fragment in that spot