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Genetics > Genetics Exam 4 > Flashcards

Genetics Exam 4 Flashcards

(64 cards)

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1
Q

Next Generation Sequencing Steps

A
  1. Extraction
  2. Library Prep (DNA cut up, adapters added to ends)
  3. Sequencing
  4. Analysis
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2
Q

What vectors can be used for gene cloning?

A

viruses and bacteria

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3
Q

Genetics

A

the study of heredity
- involves the study of functions and composition of the single gene

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4
Q

gene

A

refers to a specific sequence of DNA on a single chromosome

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5
Q

genomics

A

the study of the entirety of and organism’s genes
- addresses all genes and their inter relationships

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6
Q

genome

A

refers to an organism’s entire genetic makeup

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7
Q

nucleotide BLAST

A

search nucleotide database using a nucleotide query

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8
Q

Protein BLAST

A

search protein database using protein query

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9
Q

blastx

A

search protein database using translated nucleotide query

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10
Q

query

A

(input)
- matched up wuth every piece of DNA in the database you chose

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11
Q

max score

A

-score of the single best aligned sequence

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12
Q

query cover

A

percent of query that is aligned with the hit or the percent of the search sequence that overlaps with the aligned segments

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13
Q

E value

A

the number of hits one can “expect” to see by chance when searching a database
- closer to zero= more significant match

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14
Q

Ident (Identity)

A

the extent to which the query and the hit have the same residues at the same positions

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15
Q

When to use FISH

A

single sample, localization and hybridization intensity

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16
Q

When to use qRT-PCR

A

Reaction cycle number to reach the optimal slope, 1-50 genes

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17
Q

Microoarray

A

hybridization intensity, 1000-25,000 genes

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18
Q

RNA Seq

A

transcripts #, whole transcriptome

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19
Q

SYBR Green

A

fluorescent molecule that only fluoresces when incorporated into double stranded DNA
- more PCR product= more fluorescence

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20
Q

TaqMan Assay

A

probe has fluorophore and quencher on same piece, probe is downstream of primer, fluorophore is released when make double stranded DNA
- more PCR= more fluorescence

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21
Q

RNA Seq

A

can tell exact numbers of how many transcripts of each gene there are
- counting the number of mRNAs of a gene in each sample-> can tell the actual up regulation of that gene

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22
Q

Primary protein structure

A

the sequence of amino acids in a polypeptide

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23
Q

Secondary protein structure

A

formation of alpha helices and beta pleated sheets in a polypeptide
- first type of folding (backbone of amino acid strand interacts with other parts of the backbone

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24
Q

tertiary protein structure

A

overall three dimensional shape of a polypeptide (interactions between R groups or R groups and backbone, globular)

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25
quaternary protein structure
shape produced by combinations of polypeptides (combinations of tertiary structures) - multiple polypeptides come together to form a full, functional protein
26
Disulfide bonds
sulfur containing amino acids can interact with each other and form disulfide bridges/bonds - important in 3D structure
27
kinases
phosphorylate proteins
28
phosphatases
dephosphorylate proteins
29
What are the main amino acids that are phosphorylated or dephosphorylated?
- Phosphoserine - Phosphothreonine - Phosphotyrosine
30
What charge does SDS page give proteins?
negative
31
Problem with SDS Page
Don't know how many proteins are in each blob
32
What are the two dimensions in 2D SDS Page
molecular mass and charge
33
Isoelectric point
protein has a net charge of zero
34
What is MALDI-TOF used for
used to identify proteins
35
Time of flight
something flies through tube and is detected -> smallest has lowest time of flight
36
trypsin
hydrolyzes the peptide bond at lysine or arginine residues (cute after arg and lys)
37
Western Blot
using antibody against a specific protein to see if it is present in cells
38
Direct vs Indirect Immunoprecipitation
Direct: start with antibody and bead, then protein is added Indirect: Protein and antibody put in first, then beads
39
Limitation of Immunopresipitation
cannot establish if the proteins are directly interacting with each other, only that they are part of a complex
40
Co-Immunoprecipitation
how to look at what proteins are bound together
41
Chromatin Immunoprecipitation (chip)
use antibodies against transcription factor of interest-> can see what genes are being turned on by transcription factor
42
Y2H (Yeast 2 Hybrid)
can tell direct interaction of proteins
43
epigenetics
area of scientific research that shows how environmental influences actually affect the expression of genes
44
somatic inheritance of epigenetic modifications
something environmentally happened in the mother cell-> turns genes on/off-> daughter cell maintains the gene regulation patterns
45
transgenerational inheritance of epigenetic modifications
passed from parents to offspring, even multigenerational, same methylation patterns-> can cause disease in later generations
46
How do epigenetic modifications alter accessibility of genes?
they alter their chromatin structures - DNA wrapped tightly around nucleosomes are not transcriptionally active - making the DNA looser/tighter makes it active/inactive
47
writers
introduce modifications on DNA and histone tails
48
readers
recognize the modifications and recruit chromatin remodeling enzymes, or recruit transcription factors
49
erasers
remove the modifications introduced by the writers
50
IncRNA
noncoding RNA that recruits enzymes that modify chromatin - some recruit remodeling complexes that can condense or decondense chromatin
51
where does methylation occur
methylation occurs on cytosines and CpG islands, and on histone tails
52
where are the most CpG sites
around the first exon - frequently located in promoter regions
53
Inhibition
-DNA methylation at CpG islands tends to inhibit transcription - methylation can prevent activators, transcription factors, or RNA polymerase from binding to DNA
54
inheritance of DNA methylation
after DNA replication in interphase, methylated DNA on the "old" strand can recruit DNA methylases that add methyl groups to newly synthesized strand
55
How to test methylation patterns
- Bisulfite Conversion - Restriction digestion
56
Bisulfite Conversion
- changes Cs to Us, except methylated Cs will not be changed into Us, so after PCR amplification, there will be Ts where the unmethylated Cs were - if there is still a bunch of Cs after PCR, that tells that the gene is inactive
57
imprinting
certain genes are expressed in a parent-of-origin specific manner due to epigenetic modification
58
maternally imprinted
gene turned off in the chromosome inherited from mother - gene on maternally inherited chromosome is transcriptionally silent-> paternally inherited allele is expressed
59
paternally imprinted
genes turned off in the chromosomes inherited from our fathers - gene on paternally inherited chromosome is transcriptionally silent-> maternally inherited allele is expressed
60
Tol2 Transposable element
- Tol2 ends= insertion sequence. can use these to put a green fluorescent protein into an organism - construct (promoter, green fluorescent protein, Tol2 ends) and transposase will be put into genome - where there is green fluorescence, the gene is turned on
61
transgenic organisms
- permanent change - have to do something to cells (shock, poke holes...etc) to be able to do this
62
P element
- transposable element - bacterial vector will have two P elements and DNA of interest between them
63
screening
doesn't kill off, gives idea of what is going on
64
selection
killing cells off (ex: killing off cells without a plasmid)

Genetics (6 decks)

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