Gene Expression and Laboratory Techniques

Question 1

What is the first step in oncogenesis?

Answer 1

Tumor initiation

involves changes that allow a single cell to proliferate abnormally; cell bypasses regulatory steps of cell cycle that normally prevent proliferation

Question 2

occurs as a cell develops the ability to proliferate even more aggressively as its descendants are preferentially selected for and come to predominate the growing tumor

Answer 2

tumor progression

malignant cells often unergo mutations allowing them to secrete growth factors to stimulate their own growth

Question 3

when cancer cells gain the ability to migrate to other parts of the body

Answer 3

metastasis

Question 4

what enzymes in a cancerous body digests components of the extracellular matrix and favor metastasis?

Answer 4

proteases

Question 5

promotion of growth of new blood vessels

in cancerous body, these vessels feed the growing tumor

Answer 5

angiogenesis

Question 6

mutagenic compounds

Answer 6

carcinogens

Question 7

____ is associated with mutations that occur by random chance, as a result of carcinogens, and/or the dysregulation of gene expression

Question 8

Name the RNA

what type of RNA activity is abnormal in cancerous cells

Answer 8

miRNA

Question 9

induces the growth of proliferative cells by stimulating te activity of proteins involved in growth and division

Answer 9

tumor promoters

Question 10

genes that promote abnormal growth and proliferation

Answer 10

oncogenes

Question 11

genes that function to prevent tumorigenic properties

Answer 11

tumor suppressor genes

mutation-induced dysfunction -> cell cannot protect itself

main functions: repressing expression of genes that are essential to cell cycle progression, ensuring cell responds appropriately to DNA damage at cell cycle checkpoints, repairing DNA damage, preventing changes in adhesion & proliferation involved metastasis

Question 12

What are the two main genes involved in oncogenesis?

Answer 12

1. oncogenes
2. tumor suppressor genes

Question 13

a cancer-causing virus

Answer 13

tumor virus

e.g Hepatitis B (liver cancer)

many tumor viruses contain retroviral oncogenes, which are reverse-transcribed into the DNA of infected cells. These oncogenes i.e RAS,RAF, and SRC often encode proteins that are key components of signaling pathways that stimulate cell proliferation. Tumor viruses can also hinder the correct function of tumor suppressor genes or promote the function of oncogenes

Question 14

genes that code for growth factors, receptor tyrosine kinases, transcription factors, and regulatory GTPases. They function as oncogenes after mutation or inapropriately elevated expression

Answer 14

proto-oncogenes

turns into oncogene if it mutates in a way that increases its activity

Question 15

TP53 is a ____ gene that encodes the p53 protein involved in responding appropriately to cell damage

Answer 15

tumor suppressor

Question 16

the ____ gene is implicated in half of human cancers

Answer 16

TP53

encodes the p53 protein involved in responding appropriately to cell damage

Question 17

the ____ genes are responsible for repairing and responding to DNA damage

Answer 17

BRCA

implicated in breast and ovarian cancers, have heridary bases

Question 18

DNA sequence that upregulates

Answer 18

enhancer

Question 19

DNA sequence that downregulates

Answer 19

silencer

Question 20

regulatory proteins

Answer 20

transcription factors

Question 21

covalent modifications of histones that upregulates gene expression

Answer 21

acetylation

Question 22

covalent modifications of nucleotides that downregulates gene expression

Answer 22

methylation

Question 23

non-coding RNA sequences that downregulate gene expression

Answer 23

siRNA, and miRNA

Question 24

what’s another name for a restriction enzyme

Answer 24

restriction endonuclease

Question 25

enzymes that cleave DNA at specific recognition sites

Answer 25

restriction endonucleases

Question 26

4 to 8 base pair sequences that are recognized by a restriction enzyme to cleave DNA. Have symmetry of palindromic sequences

Answer 26

recognition site

Question 27

when a sequence of nucleotides of complementary strands of DNA read the same in both directions, either from the 5-prime end or the 3-prime end

Answer 27

palindromic sequences

Question 28

describe blunt vs sticky ends in relation to restriction enzymes

Answer 28

blunt ends: when restriction endonucleeases cleaves a DNA sequnce vertically across the recognition site sticky ends: when restriction endonecleases cleaves a DNA sequence in a zig-zag fashion

Question 29

What is the significance of restriction enzymes?

Answer 29

They cut DNA into fragments that can be "tied" back together by DNA ligase w/o necessariy respecting the original location of the sequences (recombination)

Question 30

DNA molecules used to carry genetic material into a cell where it can be replicated or expressed. Used in DNA recombination processes

Answer 30

vectors | plasmids and bacteriophages

Question 31

vectors in the form of viruses that infect bacteria. They strip out non-essential genes to carry recombinant sequences

Answer 31

bacteriophages

Question 32

short circular DNA molecules that can replicate independently in bacteria

Answer 32

plasmids ## Footnote recombinant plasmids carrying human DNA inseerts can be introudiced into E.coli where they replicate along with the bacteria to yield millions of copies of plasmid DNA. The plasmid DNA can then be isolated, generating recombinant molecules containing a single fragment of human DNA that can be analyzed and further manipulated

Question 33

Describe the steps in the DNA cloning process

Answer 33

1. Host plasmid is cleaved by restriction enzyme 2. DNA fragment of interest is inserted into plasmid 3. Plasmid is annealed by DNA ligase 4. Recombinated DNA is introduced to a bacteria 5. Bacteria carrying the plasmid are selected and reproduce 6. Bacteria replicate the plasmid and pass it on to their offspring, making copies of the DNA it contains 7. DNA/protein is eventually harvested and purified for use

Question 34

antibiotic genes that can kill of bacteria cells that did not take up plasmids, so only cells with plasmid remain | during DNA cloning/purifying process

Answer 34

antibiotic resistance gene

Question 35

genes that distinguish betwen recombinant and non-recombinant plasmids | during DNA cloning process

Answer 35

reporter genes ## Footnote these genes code for a product that creates a obvious phenotypic change (i.e change in color) and contains recognition sites for restriction enzymes that is used in restriction. Thus, E.coli with non-recombinant plasmids will express the reprter gene normally, but those with recombinant plasmids will not, **allowing them to be distinguished and subcultured**

Question 36

# Name the process What does this image depict?

Answer 36

DNA recombination via plasmid vector

Question 37

Explain why a researcher may want to use a bacteriophage instead of a plasmid as a vector

Answer 37

bacteriophages can be used for longer sequences. Plasmids generally contain 2-4kb of DNA, bacteriophages can contain up to 15kb

Question 38

RNA sequences can be cloned through the generation of ______

Answer 38

complementary DNA (cDNA)

Question 39

which enzyme can synthesize a DNA copy of RNA?

Answer 39

reverse transcriptase

Question 40

Descripte the steps in RNA cloning

Answer 40

1. synthezize DNA copy of RNA (cDNA) via reverse trancriptase 2. cDNA is ligated to vector DNA

Question 41

an organism whose genome has been modified

Answer 41

transgenic organism | for research purposes

Question 42

organism in which one or more genes have been disabled

Answer 42

knockout organism | for research purposes

Question 43

involves splicing a functional allele into the cells of a patient with nonfunctional alleles, devastating genetic disorders

Answer 43

gene therapy

Question 44

special cells that have the ability to develop into many different cell types, from muscle cells to brain cells

Answer 44

stem cells

Question 45

a laboratory method used to separate mixtures of DNA, RNA, or proteins according to molecular size and/or charge

Answer 45

gel electrophoresis ## Footnote note: nucleic acids have a high degree of negative charge, thus they will migrate from cathode and towards anode note #2: there is an inverse relationship between molecular size and distance migrated

Question 46

molecular-weight size markers that can be run parallel to the DNA of interest in an electrophoresis experiment to identify the approxiate size of the DNA fragments analyzed

Answer 46

ladders

Question 47

the ability of a single strand DNA or RNA to join with complementary base pair sequences

Answer 47

hybridization ## Footnote important for PCR, watch KA video

Question 48

a specific DNA or RNA fragment that can be labeled radioactively. These are used to detect the presence of nucleotide sequences in analyzed RNA or DNA that are complementary to the sequence in the _____

Answer 48

hybridization probe

Question 49

technology used to identify specific **DNA ** sequences

Answer 49

southern blotting ## Footnote [link](https://www.khanacademy.org/test-prep/mcat/biomolecules/dna-technology/v/southern-blot)

Question 50

technology used to identify specific **RNA** sequences

Answer 50

northern blotting ## Footnote p. 118

Question 51

a laboratory technique used to detect a specific **protein **in a blood or tissue sample.

Answer 51

Western blotting

Question 52

microscope slides that are printed with thousands of tiny spots in defined positions, with each spot containing a known DNA sequence or gene

Answer 52

DNA microarray

Question 53

Uses dideoxynucleotides to terminate synthesis ad elecrophoresis to analyze fragment size

Answer 53

Sanger sequencing ## Footnote [link](https://www.khanacademy.org/science/ap-biology/gene-expression-and-regulation/biotechnology/a/dna-sequencing)

Question 54

a short piece of single-stranded DNA that binds to the template DNA and acts as a "starter" for the polymerase

Answer 54

primer

Question 55

used to make exponentially large number sof copies of DNA in a short amount of time using primers

Answer 55

polymerase chain reaction (PCR)

Question 56

What are differences between Sanger sequencing and PCR?

Answer 56

Sanger sequencing is used to generate every possible length of DNA up to the full length of the target DNA while PCR is used to duplicate the entire DNA sequence