Module 5

Melanin

________ (dark pigment) which acts like a natural sunscreen which balances vitamin D and folate levels.

complementary DNA

The ________ can be inserted into a plasmid and cloned or amplified by PCR.

What sticks together the DNA fragment through ligation and the sticky ends of the plasmid?

DNA ligase through covalent phosphodiester bonds

what’s the final step after the DNA fragment is attached to the plasmid?

\- the recombinant plasmid is the vector and will replicate in host cells.

Pluripotent or totipotent cells-

early human embryo cells that can become any cell type in the body (except the amniotic sac) and its part of of the inner cell mass.

differentiated cells

cells that have a specific function within a multicellular body

Haplotype

________- set of DNA markers that are inherited together.

MVP

________ is helper T cells some pathogens directly target helper T cells like HIVS.

Who has innate immunity

everyone from bacteria to trees to worms to humans, and can include physical barriers to anti- microbial chemicals defense.

why is a promoter to drive transcription (and translation) of the inserted foreign gene so important?

because without it the plasmid would just re-ligate without the foreign gene so resulting in an empty plasmid

Genetically modified organism (GMO)

any organism that has been manipulated to carry new genetic material, from either a different species or synthesized in the laboratory.

Polymerase Chain Reaction (PCR)

design DNA primers that are complementary to sequence (forward binding to 5 and other one binding to 3)

what does temp 94 to 96 degrees celsius in PCR do?

denatures DNA strands.

why is temp then lowered to 68 degrees in PCR?

primers are able to attatch to sequence.

finally, what does raising the temp slightly to 72 degrees celsius do?

allows for DNA polymerase to create a full sequence (the process of elongation) (bc of DNA polymerase being used that lives in hot springs)

why is bacteria a good way to study a specific protein in more detail?

bc easy to insert a gene and produce multiple copies due to the fast reproduction of bacteria

Perforins

proteins that assemble in the target cell membrane to create holes and destroy the target cell.

Stem cells

those cells that will continue to divide and replenish the bodys cells for the rest of the patients life.

how does CCR5-delta32 help and hurt T cell

Makes the t cell less effective BUT it protects against HIV because the antigens can attach to the t-cell properly.

what is CCR5-delta32

deletion of 32 base pair

phagocytic activity

Antigen- presenting cells (APCs) that have ________ and express Class II Major Histocompatibility (MHC) proteins.

HIV Drugs

________ reduce viral load aka trying to stop the process of making new viruses.

Gene flow

________: mixing of alleles between populations or preference when mating.

Vaccines

________ contain antigens for specific viruses.

Transgenesis

________ adds a new gene.

what are the two methods for molecular cloning?

recombinant DNA technology or PCR, polymerase chain reaction

Recombinant DNA technology

bacterial plasmids are cut with restriction endonuclease (EcoRI) and specific genes are added in.

UV

is good for vitamin D production but bad for breakdown of folate and causes cancer.

hy is cas9 binding to a short guide RNA segment important?

When it binds to the RNA it cuts the DNA at a programmable site.

MHC class I

________ (all cells) activate cytotoxic T cells to destroy cells.

recombinant plasmid

The ________ is the vector and will replicate in host cells.

enzyme Reverse Transcriptase

The ________ is used, along with an oligo- dT primer that is complementary to the polyA tail, to synthesize a complementary DNA.

Antigen receptors

________- a T- cell receptor (TCR) or an antibody molecule (immunoglobulin, Ig)

heavy chain

If antibody uses both ________ and light chain to make a single antigen binding pocket.

what is molecular cloning

cloning or replicating a chosen segment of DNA resulting in GMOs

what are the main differences between recombinant DNA and PCR

PCR can be done in a test tube and doesnt require a living cell

recombinant DNA technology

bacterial plasmids are cut with restriction endonuclease (EcoRI) and specific genes are added in

what enzyme cuts the plasmid at specific sites and how

restriction endonucleases and they cut it in 4, 6, or 8 palindromic sequences with sticky ends

polymerase chain reaction (PCR)

design DNA primers that are complementary to sequence (forward binding to 5 and other one binding to 3)

genetically modified organism (GMO)

any organism that has been manipulated to carry new genetic material, from either a different species or synthesized in the laboratory

non-homologous end-joining

the cells DNA repair system will trim the broken ends and ligate them together which often creates a small deletion as a result of the trimming

**CRISPR**

stands for _C_lustered _R_egularly _I_nterspersed _S_hort _P_alindromic _R_epeats and functions as a library of foreign DNA samples that represent viruses or pathogens that could harm a bacterial species

what is **Cas9**?

it’s a protein enzyme that binds short RNAs made from the CRISPR gene library

describe cas9 steps

cas9 binds to a short guide RNA segment and it cuts the DNA at a programmable site which creates a double-strand DNA break where non-homologous end-joing occurs

differentiated cells

cells that have a specific function within a multicellular body

what is somatic cell nuclear transfer (SCNT)

nuclei (DNA) from a persons skin cells that are in cell cycle arrest due to starvation are transferred into egg cells with no nucleus (DNA) to create stem cells to make new therapies like creating liver, muscle, or nerve cells

what are the difficulties or obstacles for animal cloning

low success rate, high complications, possible premature aging

why is cloning eukaryotic genes difficult/impossible?

contains numerous, large introns which need to be removed and PCR + plasmid vectors have a 10 kilo base-pair-limit

why is the mRNA used in cloning eukaryotic genes?

why is the mRNA used in cloning eukaryotic genes? bc it lacks introns (unlike template DNA) so it’s a compact version of a eukaryotic gene that retains all of the protein coding information.

what is done to mRNA to synthesize a cDNA?

The enzyme Reverse Transcriptase is used, along with an oligo-dT primer that is complementary to the polyA tail, to synthesize a complementary DNA

after reverse transcriptase is used on mRNA and creates a cDNA what’s it used for?

the complementary DNA can be inserted into a plasmid and cloned or amplified by PCR

pluripotent or totipotent cells

early human embryo cells that can become any cell type in the body (except the amniotic sac) and its part of of the inner cell mass

therapeutic cloning

uses enucleated human eggs and somatic cell nuclear transfer technology to create a human embryo that is a genetic clone of the patient

how to obtain embryonic stem cells

induced pluripotent stem cells (iPSCs) which transforms adult differentiated (multipotent) cells into pluripotent cells by using 4-6 different transcription factors

explain dolly

ex of mammilian reproductive cloning, took egg from scottish black sheep and took nucleus from finn-dorset egg and dolly was born and dolly looked like from finn-dorset nucleus donor not egg donor

what is alternatives to embryonic stem cells (avoid ethical issues)

induced pluripotent stem cells (IPSC)

1 purpose of IPSC

can be used for cellular differentiated and then observe genetic abnormality with diff drugs/treatments

who has innate immunity

everyone from bacteria to trees to worms to humans, and can include physical barriers to anti-microbial chemicals defense

who has a more complex adaptive immune system

only jawed vertebrates featuring antibodies and cytotoxic "killer" cells that recognize billions of different molecules with high specificity

antigen receptors

a T-cell receptor (TCR) or an antibody molecule (immunoglobulin, Ig)

"effector" cells

activate and execute the humoral and cellular immune responses

Single Nucleotide Polymorphisms

differentiate different lineages through different nuclutoides

ethical concerns for sourcing of human eggs

\
* remove DNA from a donor egg
* process is inefficient and it destroys the embryo
* implementation into a human’s uterus has high risk of fatality

what are T cells and B cells?

they are lymphocytes, types of white blood cells, that are able to recognize foreign (non-self) antigens.

what do helper T-cells do?

APCs phagocytose pathogens or foreign cells and digest them into peptide fragments and then send the fragments bound to Class II MHC to cell surface for T cells to inspect. Once the T cell recognizes peptide-MHC II complex via its T-cell receptor it activates and divides

what do B cells do?

they recognize and bind antigen via their cell surface Ig. They endocytose, process and present the peptide as fragments on their cell surface MHC II proteins. responsible for humoral (noncellular; mediated by soluble proteins) branch.

what do cytotoxic T cells (CTLs) do?

they look for cells that are presenting non-self or altered peptides on Class I MHC molecules. their T-cell receptors kill the virus or cancer infected cell or cells that express a diff MHC I allele than the host thru signaling apoptosis and then if needed secretes granzymes (destructive enzymes) and perforins,

does MHC Class I present to CTL or helper T cells?

CTL (all cells)

does MHC Class II present to CTL or helper T cells?

helper T cells