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Genetics > Genetics Exam 4 > Flashcards

Genetics Exam 4 Flashcards

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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
Q

quaternary protein structure

A

shape produced by combinations of polypeptides (combinations of tertiary structures)
- multiple polypeptides come together to form a full, functional protein

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26
Q

Disulfide bonds

A

sulfur containing amino acids can interact with each other and form disulfide bridges/bonds
- important in 3D structure

27
Q

kinases

A

phosphorylate proteins

28
Q

phosphatases

A

dephosphorylate proteins

29
Q

What are the main amino acids that are phosphorylated or dephosphorylated?

A
  • Phosphoserine
  • Phosphothreonine
  • Phosphotyrosine
30
Q

What charge does SDS page give proteins?

A

negative

31
Q

Problem with SDS Page

A

Don’t know how many proteins are in each blob

32
Q

What are the two dimensions in 2D SDS Page

A

molecular mass and charge

33
Q

Isoelectric point

A

protein has a net charge of zero

34
Q

What is MALDI-TOF used for

A

used to identify proteins

35
Q

Time of flight

A

something flies through tube and is detected -> smallest has lowest time of flight

36
Q

trypsin

A

hydrolyzes the peptide bond at lysine or arginine residues (cute after arg and lys)

37
Q

Western Blot

A

using antibody against a specific protein to see if it is present in cells

38
Q

Direct vs Indirect Immunoprecipitation

A

Direct: start with antibody and bead, then protein is added
Indirect: Protein and antibody put in first, then beads

39
Q

Limitation of Immunopresipitation

A

cannot establish if the proteins are directly interacting with each other, only that they are part of a complex

40
Q

Co-Immunoprecipitation

A

how to look at what proteins are bound together

41
Q

Chromatin Immunoprecipitation (chip)

A

use antibodies against transcription factor of interest-> can see what genes are being turned on by transcription factor

42
Q

Y2H (Yeast 2 Hybrid)

A

can tell direct interaction of proteins

43
Q

epigenetics

A

area of scientific research that shows how environmental influences actually affect the expression of genes

44
Q

somatic inheritance of epigenetic modifications

A

something environmentally happened in the mother cell-> turns genes on/off-> daughter cell maintains the gene regulation patterns

45
Q

transgenerational inheritance of epigenetic modifications

A

passed from parents to offspring, even multigenerational, same methylation patterns-> can cause disease in later generations

46
Q

How do epigenetic modifications alter accessibility of genes?

A

they alter their chromatin structures
- DNA wrapped tightly around nucleosomes are not transcriptionally active
- making the DNA looser/tighter makes it active/inactive

47
Q

writers

A

introduce modifications on DNA and histone tails

48
Q

readers

A

recognize the modifications and recruit chromatin remodeling enzymes, or recruit transcription factors

49
Q

erasers

A

remove the modifications introduced by the writers

50
Q

IncRNA

A

noncoding RNA that recruits enzymes that modify chromatin
- some recruit remodeling complexes that can condense or decondense chromatin

51
Q

where does methylation occur

A

methylation occurs on cytosines and CpG islands, and on histone tails

52
Q

where are the most CpG sites

A

around the first exon
- frequently located in promoter regions

53
Q

Inhibition

A

-DNA methylation at CpG islands tends to inhibit transcription
- methylation can prevent activators, transcription factors, or RNA polymerase from binding to DNA

54
Q

inheritance of DNA methylation

A

after DNA replication in interphase, methylated DNA on the “old” strand can recruit DNA methylases that add methyl groups to newly synthesized strand

55
Q

How to test methylation patterns

A
  • Bisulfite Conversion
  • Restriction digestion
56
Q

Bisulfite Conversion

A
  • 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
Q

imprinting

A

certain genes are expressed in a parent-of-origin specific manner due to epigenetic modification

58
Q

maternally imprinted

A

gene turned off in the chromosome inherited from mother
- gene on maternally inherited chromosome is transcriptionally silent-> paternally inherited allele is expressed

59
Q

paternally imprinted

A

genes turned off in the chromosomes inherited from our fathers
- gene on paternally inherited chromosome is transcriptionally silent-> maternally inherited allele is expressed

60
Q

Tol2 Transposable element

A
  • 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
Q

transgenic organisms

A
  • permanent change
  • have to do something to cells (shock, poke holes…etc) to be able to do this
62
Q

P element

A
  • transposable element
  • bacterial vector will have two P elements and DNA of interest between them
63
Q

screening

A

doesn’t kill off, gives idea of what is going on

64
Q

selection

A

killing cells off (ex: killing off cells without a plasmid)

Genetics (6 decks)

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