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57 Cards in this Set

  • Front
  • Back
RNA silencing characteristics (5)
1)in vivo hybridization technique
2)technology for controlling specific gene expression
3)very powerful inhibition of specific gene fxn
4)can be tailor-made to match an individuals genetics
5)uses 2x-strand RNA to induce gene specific silencing
siRNA mechanism steps(5)
1)dsRNA to a specific gene is introduced into a cell
2)Dicer cuts dsRNA into smaller pieces
3)RISC binds small dsRNA
4)dsRNA is unwound to yield a ssRNA-RISC complex
5)ssRNA-RISC complex cleaves mRNA that are complementary to ssRNA
siRNA and disease therapy show potential for what diseases (6)
3)high cholesterol
5)small-cell lung cancer
6)pancreatic cancer
b)driven heavily by...
a)study and analysis of genomes
b)development of new technologies
What are the 3 levels of genome analyzation
1)genetic map
2)physical map
3)nucleotide sequence
Genetic Map
a)determined by...
b)what is it exactly?
c)time required for it
d)useful for...
a)genetic crosses and mutation mapping (like Mendel's peas)
b)abstract, intellectual construct that lists the order of genes on the chromosome
d)seeing overall organization of a genome and location of specific genes
Physical Map
a)determined by...
a)restriction endonuclease mapping of the DNA molecule
Physical Map Procedure (4)
1)digest DNA w/ restriction enzymes
2)separate fragments by size using gel electrophoresis
3)visualize fragments by DNA specific stain
4)compare fragments
Genomic DNA sequencing
b)is the highest resolution of...
a)entire primary sequence of an organism's DNA molecule
b)genetic mapping
Genomic DNA sequencing relies on...
Dideoxynucleotide DNA sequencing requires... (3)
1)4 reaction mixtures
2)each one "spiked" w/ ONE ddNTP
3)each rxn must contain all four dNTP's too or DNA synthesis will not occur
Why will DNA synthesis not occur if you only have ddNTPs?
they have an H instead of OH is required for DNA synthesis to occur
Whole Genome Genetic analysis allows for...(3)
a)identify genes by predicted fxn or homology
2)rapid ID of both novel genes and sought after genes, but never isolated genes
3)analyze global gene responses
How to sequence a Genome (basically) (6)
1)create a genomic DNA library
2)use automated DNA sequencing to achieve 6-8 coverage
3)assemble sequences into contiguous units (contigs)
4)gap closure
5)edit sequence
6)predict genes and assign fxn
The 2 stratgedies used to sequence the human genome
1)cloned contig
2)directed shotgun
Cloned Contig Sequencing stratgedy steps (5)
1)physical map of chromosome is constructed using restriction enzymes
2)specific restriction fragment is isolated and cloned
3)fragment is cut into small pieces that can be easily sequenced
4)individual DNA sequence reads are assembled by computer to reveal the sequence of the original restriction fragment
5)position of the sequenced region on the chromosome is already known by mapping
Directed shotgun sequencing steps (5)
1)total DNA is isolated from cell
2)shotgun library of entire chromosome is prepared (tons of small fragments)
3)all clones in library are sequenced
4)computer assembles the sequences into contigs
5)as sequences are read the entire chromosome begins to emerge
b)analysis falls into 2 categories
c)key technologies (3)
a)analysis of all proteins being expressed by a cell
b)cell associated proteins AND cell-secreted proteins
c)Microarrays, 2D electrophoresis, mass spectroscopy
Genomics tell you...
Proteomics tell you...
what genes are present

when and if the genes are being transcribed/translated
Unique genes vs. minimal essential genome (in bacteria) and techniques used (2)
minimal essential genome is shared by many bactera but unique genes are only in 1 bacteria (good target for drug)

2)proteomic analysis
What are identified as possible vaccine targets
probable cell surface proteins
Human genome and drug discovery via... (5)
1)transcription factors characterization to uncover gene regulation
2)antisense therapy development
3)protein and cDNA characterizations
4)cell cycle and cell signaling networks
5)facilitate development of antibodies for diagnosis and intervention strategies
study of how an individuals genetic makeup influences drug action, usage, dosing
draws from human genome project and mRNA analysis to attempt to understand the entire genetic profile of an individual
Types of repetitive DNA in genome (4)
1)LINE- long interspersed elements
2)SINE- short interspersed elements
3)SSR- simple sequence repeats
4)SD- large segment duplications
Pharmacogenomics has the potential to identify...
subsets of ppl who are genetically predisposed to toxicity from specific medications and those who are likely not to resond
Mutation def.
heritable change in the sequence of an organism's genome (pass to daughter cells)
Mutant def.
organism that carriers one or more mutations in its genome
TPMT inactiaves...(drug) via...

S-methylation of the drugs
Thiopurine drugs are all...
pro-drugs that must be metabolically activated to exert cytotoxicity
TPMT deficiency can allow...
lethal accumulations of thiopurines
Tools for individual genome analysis (7)
2)immunological detection
3)hybridization techniques (North/South blots)
variations caused by single nucleotide changes
Ultimate goal of SNPs research
analyze SNP profile of person, compare their profile to database and predict person's risk for specific diseases and response to various drugs
Detection of SNPs via...(5)
1)restriction enzyme fragment length polymorphism
2)loss/gain of particular restriction enzyme site in a given gene
3)PCR product length variation
4)presence/absence of a PCR target DNA
5)DNA sequencing
p-glycoprotein fxn
detoxes cell by pumping things out of it
____ gene controls p-glycoprotein
Cancer expresses genes that are...
normally only seen in fetal development
2 genes that are differentially expressed in cancerous ovarian tissue
2 genes that are associated w/ poorer survival in cancer therapy and why

poor response to drugs like cyclophosphamide
Gene involved in longer survival of breast cancer and why
GSTM1, slowed detoxification of drug
Individuals w/ lower levels of ____ have better responses to chemo and why?
MDR1, have less p-glycoprotein to pump chemo agents out of tumors
Technology of Pharmacogenetics and Pharmacogenomics (4)
2)DNA sequencing
3)Nucleic Acid Hydridization (north/south blot)
Genomic analysis uses ____ as genetic source material
Transcriptional analysis uses ____ as genetic source material
2 Tools of Recombinant DNA technology
1)restriction enzymes
Restriction enzymes fxn (2)
1)used to cut DNA
2)molecular scissors
Restriction enzymes recognize....
SPECIFIC SITES @ palindromes
When DNA is treated w/ restriction enzymes what type of ends are created? and desc of each
1)blunt ends, ex: if sequence is GTTAAC and comp. strand is CAATTG, the cut is made b/w T and A
2)uneven, sticky, cohesive ends. ex: if strands are GAATTC and CTTAAG and cut is made b/w G and A
Where does EcoRI cut and what type of ends does it create and what strands does it recognize
b/w G and A, creates sticky ends

What are the sticky or cohesive ends that EcoRI creates and significance of this
ATTC and CTTA, these are capable of complimentary base pairing
BamHI cuts what sequences, what type of ends it creates and source of enzyme
b)sticky ends
c)Bacillus amyloliquefaciens
DNA construct can be created as a result of what?
base pairing (annealing) b/w the overhang regions
DNA construct gets into the cell via...(2)
1)electric shots to membrane to make it more permeable
2)use high salt []s to get DNA into cell
____ binds DNA construct together, and how?

covalently using phosphodiester bonds
After annealing of the sticky ends, these annealed pieces will have...
single strand breaks (called nicks)
Nicks are healed by...
DNA ligase