week 14 LO

Question 1

noncoding RNA

Answer 1

functional RNA molecules that do not code for proteins. They play vital roles in cellular processes, including gene expression regulation and protein synthesis. (miRNA, rRNA, tRNA)

Question 2

genetic engineering

Answer 2

involves the direct manipulation of an organism’s genes, typically involving the introduction, deletion, or modification of specific DNA sequences to alter traits or functions

Question 3

GMO

Answer 3

refers to any organism whose genetic material has been altered using genetic engineering techniques. These modifications are made to introduce new traits or characteristics that do not naturally occur in the species.

Question 4

biopharming

Answer 4

biotechnology process where plants are genetically modified to produce pharmaceuticals, therapeutic proteins, or other valuable molecules.

Question 5

biopharmaceutical products

Answer 5

pharmaceuticals derived from biological sources like cells or living organisms. They differ from chemically synthesized drugs in their production process and complex structure. Examples include vaccines, antibodies, and hormones.

Question 6

PCR

Answer 6

polymerase chain reaction
- used to replicate and amplify a specific DNA segment

Question 7

primer

Answer 7

a short, single-stranded nucleic acid (DNA or RNA) sequence that initiates DNA synthesis

Question 8

Taq DNA polymerase

Answer 8

thermus aquaticus
- Bacteria isolated from hot
springs in Yellowstone
National Park in 1966
* Extreme thermophile
* Optimal growth at 70-75°C
* Taq DNA polymerase was
isolated and later
commercialized in 1980’s

Question 9

palindrome

Answer 9

a DNA sequence that reads the same way backward and forward on the complementary strand

Question 10

sticky ends

Answer 10

Short single-stranded overhangs created by the cleavage of DNA by specific restriction endonucleases, which can potentially base-pair with complementary single-stranded sequences.

Question 11

blunt ends

Answer 11

5’ or 3’ ends of double-stranded DNA lacking any single-stranded overhangs.

Question 12

cloning vector

Answer 12

A piece of DNA derived from a plasmid, virus, or other biological source that can be stably maintained in an organism and into which heterologous pieces of DNA can be inserted

Question 13

multiple cloning site

Answer 13

A vector DNA sequence containing several unique restriction enzyme target sequences facilitating cloning of inserted DNA fragments.

Question 14

selectable gene marker

Answer 14

a gene used to distinguish between cells that have successfully taken up a foreign gene (like a plasmid) and those that haven’t

Question 15

plasmid

Answer 15

a small, circular, double-stranded DNA molecule that exists independently from a host’s chromosomal DNA

Question 16

X-gal

Answer 16

is a chromogenic substrate for the enzyme β-galactosidase

Question 17

expression vector

Answer 17

Cloning vector possessing DNA sequences required for DNA fragments inserted into the vector to be transcribed and translated. Vectors with sequences facilitating expression in eukaryotes are called eukaryotic expression vectors.

Question 18

vector

Answer 18

A DNA fragment with attributes that will allow its amplification (origin of replication) in a biological system and serves as a carrier for foreign DNA inserted into it. Vectors usually also possess genes (e.g., encoding resistance to an antibiotic) that allow selection of hosts carrying the vector.

Question 19

insert

Answer 19

A bacterial DNA sequence that is the target of insertion of a transposable genetic element or is the site of integration of a plasmid such as an F plasmid.

Question 20

Ti plasmid

Answer 20

A large (200 kb) circular plasmid of Agrobacterium tumefaciens that harbors genes for transfer of DNA into plants cells and genes that cause uncontrolled division of plant cells; hence, the tumor-inducing (Ti) plasmid. It has been engineered for the construction of transgenic plants.

Question 21

T-DNA

Answer 21

The portion of the Ti plasmid that is transferred from the bacterium into the nucleus of a plant cell.

Question 22

knockout

Answer 22

Loss-of-function allele of a gene usually obtained via a reverse genetic approach.

Question 23

chimeric

Answer 23

A gene sequence composed of sequences from two or more sources.

Question 24

CRISPR-cas

Answer 24

Complex of the Cas9 protein with tracrRNA and crRNA that acts to target invading nucleic acids in Staphylococcus. This system has been modified for use in gene editing.

Question 25

crRNA

Answer 25

Unique small RNAs derived from CRISPR loci that combine through complementary base pairing with tracrRNAs in the CRISPR-Cas complex.

Question 26

tracrRNA

Answer 26

Small RNA that act to couple crRNAs with a Cas protein in the CRISPR–Cas complex.

Question 27

guideRNA

Answer 27

In RNA editing, the nucleic acid that directs the addition or removal of nucleotides from mRNA. Also known as guide strand. In genome editing, the RNA molecule designed to operate in a CRISPR–Cas complex to target double-strand breaks in a specific DNA molecule or genomic locus.

Question 28

advantages of biopharming

Answer 28

makes complex human proteins makes large amount of protein less expensive clinically equivalent

Question 29

advantages of GMOs

Answer 29

- insect resistance (many) - round-up resistance (many) - cold tolerance (strawberries) - edible vaccines ( potatoes & rice) - vitamin A deficiency (rice) - hemoglobin production (pigs) - healthier fats (pigs)

Question 30

concerns for GMOS

Answer 30

- transfer of genes to other species - out compete native crops - long-term effects on human health are unknown - ownership problems, cost to individual farmers - fields with round-up resistant crops are sprayed with chemicals

Question 31

process of creating GMO

Answer 31

- extract DNA - amplify specific DNA sequence using PCR - use gel electrophoresis, restriction enzymes, and ligase to place the DNA segment into a plasmid - transform E.coli - select for transformed cells and confirm with a restriction digest - move to an expression vector - transform the organism

Question 32

Explain how to create knockout mice

Question 33

Describe why Saccharomyces cerevisiae is widely used as a host for expression of eukaryotic genes

Answer 33

It can be grown easily and manipulated * Its genetics have been studied intensively * Its entire genome has been sequenced * It can post-translationally modify eukaryotic proteins

Question 34

common transformation methods for yeast

Answer 34

* Lithium/heat shock * Electroporation * Biolistic method

Question 35

biolistic method

Answer 35

- Particles (gold or tungsten) are coated with plasmids * Particles are fired at high speed into plant cells * In cells that survive, the DNA may integrate into a plant chromosome * Plants grown from these cells are then screened for the desired phenotype

Question 36

agrobacterium tumefaciens-mediated transformation method

Answer 36

- uses a natural plant transformation system that evolved in the soil bacterium Agrobacterium tumefaciens, which causes crown gall disease * Wild-type strains of the bacterium contain a large plasmid (200 kb) called the tumor- inducing plasmid or Ti plasmid * Part of the plasmid—transfer DNA (T-DNA)—is transferred from the bacterium to plant cell nuclei upon infection Once inside the plant cell, T-DNA can undergo recombination to integrate into random locations of the plant genome * T-DNA contains genes that cause plant cells to divide uncontrollably and produce amino acid by products (opines) that only the bacterium can use as an energy source * Genes involved in the transfer of T-DNA are evolutionarily related to those involved in F factor transfer in E. coli

Question 38

Describe how you can determine the function of a protein by creating transgenic organisms

Answer 38

involves altering the organism’s genome to express, suppress, or modify the gene encoding the protein of interest, then observing the resulting phenotype or molecular changes.