Exam 4 (Topic 16)

Question 1

Enzymes that cleave phosphodiester bonds

Answer 1

Restriction Endonucleases

Question 2

Enzyme that is made by bacteria only to protect from foreign DNA

Answer 2

Restriction Endonucleases

Question 3

Enzyme that only cut DNA at specific nucleotide sequences by chance

Answer 3

Restriction Endonucleases

Question 4

Puts cut DNA back together

Answer 4

DNA ligase

Question 5

In an electric field DNA moves from the negative electrode to the positive electrode and separates based on size

Answer 5

Agarose gel electrophoresis

Question 6

DNA can be stained with a fluorescent dye to visualize with UV light. DNA bands can then be cut out of gel and isolated.

Answer 6

Agarose Gel Electrophoresis

Question 7

The isolation and amplification of a specific region of DNA

Answer 7

DNA Cloning

Question 8

DNA fragments cut by Restriction endonucleases and put back together with DNA ligase

Answer 8

Recombinant DNA

Question 9

Specialized circular DNA molecules used to transform bacteria

Answer 9

DNA Plasmids (recombinant)

Question 10

Multiple Cloning Site (MCS)

Answer 10

Short segment of DNA that allow biologists to insert a piece or pieces of DNA into the region

Question 11

Origin of replication

Answer 11

Tells bacteria to replicate

Question 12

Selection Gene

Answer 12

Code for drug resistance

Question 13

Can be amplified and purified in bacteria

Answer 13

Recombinant DNA

Question 14

The introduction of DNA into bacteria

Answer 14

Transformation

Question 15

Amplifying DNA fragment in vitro (without the use of bacteria)

Answer 15

Polymerase Chain Reaction (PCR)

Question 16

Can make billions of copies of a segment of DNA

Answer 16

Polymerase Chain Reaction (PCR)

Question 17

Extremely sensitive, can detect a single template in a sample

Answer 17

Polymerase Chain Reaction (PCR)

Question 18

For PCR you need the following materials:

Answer 18

Template DNA, Forward and Reverse primers that are complementary to the template DNA, Nucleotides (dATP, dGTP, dCTP, dTTP) to generate new DNA, DNA polymerase

Question 19

PCR Uses

Answer 19

Test for viral infection in a blood sample
Isolate viral genome (usually in the case of HIV)
Forensic medicine

Question 20

A DNA copy of RNA

Answer 20

cDNA

Question 21

How do you create cDNA

Answer 21

Reverse Transcriptase

Question 22

Amplifies the viral genome and detects the amplified DNA on a gel

Answer 22

PCR

Question 23

Regions of DNA on all chromosomes that is highly variable and unique to each individual

Answer 23

Short Tandem Repeats(STRs) in DNA Fingerprint

Question 24

In order to study the function of a gene we must know

Answer 24

its DNA sequence

Question 25

Dideoxy DNA sequencing requires

Answer 25

``` Deoxyribonucleotide (dNTP) Dideoxyribonucleotide Triphosphates (ddNTP)--smalle quantity compared to normale dNTPs 1 Primer to start the PCR reaction Template DNA to be sequenced DNA polymerase ```

Question 26

How often is dideoxyribonucleotides incorporated in new DNA

Answer 26

Rarely

Question 27

Are missing the 3'-OH and terminate replication of that strand

Answer 27

Dideoxyribonucleotides during Chain Termination

Question 28

Old fashion DNA sequencing

Answer 28

Do 4 PCR reaction where each reaction contains a single dideoxyribonucleotide in small amounts and regular deoxyribonucleotides. Generates lots of DNA fragments each varying in size where the the dideoxyribonucleotide was inserted. Run aragrose gel of each PCR reaction

Question 29

DNA sequencing today

Answer 29

Each dideoxyribonucleotide is labeled with a fluorophore (4 bases = 4 colors). We can now measure the fragment size and using a computer that generates a color coded DNA sequence

Question 30

The appearance or behavior an individual organism or protein (red eye vs. white eye)

Answer 30

Phenotype

Question 31

The gene responsible for a given phenotype

Answer 31

Genotype

Question 32

Gene function can be determined by identifying

Answer 32

Mutant Phenotypes

Question 33

We can alter the genotype with the use of

Answer 33

Recombinant DNA technology

Question 34

We can replace a normal gene with a defective gene

Answer 34

Gene Replacement

Question 35

We can remove a gene completely from an organism

Answer 35

Gene Knockout

Question 36

We can add a new gene to an organism

Answer 36

Gene addition

Question 37

Any organism who has had its genome altered in any way

Answer 37

Transgenic Organism

Question 38

Injected C. elegans with dsRNA oligonucleotide that can base pair with mRNA sequence would inhibit protein production.

Answer 38

1998: Craig Mello and Andrew Fire

Question 39

Craig Mello and Andrew Fire

Answer 39

Discovered RNA interference (RNAi) and miRNAs

Question 40

The human genome codes for 400 miRNAs which regulate what?

Answer 40

At least 1/3 of all protein encoding genes

Question 41

Transcribed in the nucleus and exported to the cytoplasm

Answer 41

miRNA

Question 42

RNA Interference miRNA Process

Answer 42

1. dsRNA binds to RISC complex 2. Unwinds dsRNA and makes ssRNA 3. ssRNA/RISC comples binds to complementary sequence on mRNA 4. ssRNA/RISC complex degrades mRNA

Question 43

Generated from foreign dsRNA

Answer 43

siRNA

Question 44

RNA Interference siRNA Process

Answer 44

1. Cleaved by enzyme Dicer into small dsRNA (21 nucleotides) 2. dsRNA binds to RISC complex which unwinds RNA and makes ssRNA, binds to complementary sequence on mRNA and degrades mRNA

Question 45

Enzyme that cleaves dsRNA into small sdRNA

Answer 45

Dicer

Question 46

RNAi in the lab

Answer 46

If you know the gene sequence, design siena complementary to the mRNA that will cause the mRNA to be degraded and the protein will no longer be made

Question 47

hen the mRNA is degraded and the protein will no longer be made

Answer 47

Gene knockdown

Question 48

Knocking down gene expression

Answer 48

Gene knockdown

Question 49

To investigate protein fuction, RNAi can be used to...

Answer 49

decrease the amount of protein made in a cell (knockdown)

Question 50

What is responsible for unwinding double stranded RNA and degrading complementary mRNA?

Answer 50

RISC Complex