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Genetics > Lecture 15 > Flashcards

Lecture 15 Flashcards

1
Q

genome

A

complete set of DNA in a single cell of an organism

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2
Q

genomics

A

the study of genomes

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3
Q

structural genomics

A

gene organization and components

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4
Q

functional genomics

A

looking at different species; evolution

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5
Q

metagenomics

A

complex enviromental samples

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6
Q

what is structural genomics?

A
  • sequencing genomes

- analyzing nucleotide sequences to identify genes and sequences such as gene-regulatory elements

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7
Q

protein coding regions

A

-annotation of sequence reveals several identifiable features indicating that the sequence contains a protein-coding gene

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8
Q

examples of protein coding genes

A
  • promoter sequence
  • initiation sequence
  • three exons two unshaded areas between exons represents introns; later spliced out during RNA processing
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9
Q

open reading frames (ORF)

A
  • sequences of triplet nucleotides translated into amino acid sequence of a protein
  • suggestive of protein endoding gene
  • typically begin with inititation sequence ATG
  • ends in a termination sequence TAA, TAG, and TGA
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10
Q

what is functional genomics?

A
  • study if gene functions
  • based on resulting RNAs
  • based on possible proteins they encode and regulatory elements
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11
Q

BLAST searches

A

used to screen databases and compate a sequence to a known sequence

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12
Q

similarity searches

A
  • a genome sequence statistically similar to gene with known function likely encodes for protein with similar function
  • like comparing protions of the human leptin gene (LEP) with its homolog in mice
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13
Q

homologous genes

A

genes that are evolutionarily related

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14
Q

orthologs

A

genes from different species thought to have decended from a common ancestor

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15
Q

paralog

A

homologous genes in same species

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16
Q

protein domains

A

ion channels, membrane-spanning regions, secretions, and ecport signals

17
Q

motifs

A

helix-turn-helix, leucine zipper, or zinc-finger motif

18
Q

protein domains and motifs

A

when a gene sequence is used to predict polypeptide sequence, the polypeptide can be analyzed for specific protein domains and motifs

19
Q

genomic techniques

A
  • range of techniques valuable for functional genomic studies
  • like chromarin immunoprecipitation (ChIP)
20
Q

how is ChIP useful?

A
  • designed to map protein-DNA interactions

- useful for identifying genes regulated by DNA-binding protein (DBP) transcription factors

21
Q

what is the ChIP method?

A
  • DNA is crosslinked to the proteins that are bound to the DNA
  • DNA is isolated and fragmented with DBPs attatched
  • specific DBP is target with an antibody
  • antibody is used to purify the DNA DBP complex
  • crosslink is disrupted
  • DNA is sequenced to reveal the DBP binding site
22
Q

what did the human genome project reveal about the organization of the human genome?

A

-illustrated that all humans and all other species share a common set of genes essential for cellular function, reproduction, and development

23
Q

alternative splicing

A
  • HGP revealed that the number of genes is lower than the number of predicted proteins
  • many genes encode for multiple proteins through alternative splicing
  • can generate multiple mRNAs
24
Q

functional categories assigned for human genes on the basis of

A
  • functions determined previously
  • comparisions to known genes and predicted protein sequences from other species
  • predictions based on annotation and analysis of protein functional domains and motifs
25
Q

single-nucleotide polymorphisms (SNPs)

A
  • single base chnages in genome

- variations associated with disease conditions

26
Q

copy number variations (CNVs)

A

-segments duplicated or deleted

27
Q

what percentage of the human genome is composed of endogenous retroviruses?

A

8%

28
Q

CRISPR-Cas

A
  • Clustered Regularly Interspaced Short Palindromic Repeat

- a short, particularly palindromuc repeated DNA sequences found in the genomes of bacteria and other microorganisms

29
Q

what is the CRISPR-Cas mechanism?

A
  • spacer acquisition
  • crRNA biogenesis (RNA from CRISPR gene)
  • target interference
30
Q

spacer acquisition

A
  • invading phage DNA is cleaved into smaller fragments known as photospacers, which are then inserted into CRISPR loci to become new spacers
  • when new spacers are added to the CRISPR locus, repeat sequences are duplicated such that each spacer is flanked on each side
31
Q

crRNA biogenesis

A
  • CRISPR loci are transcribed starting at the promoter within the leader, into long RNA transcripts
  • processed into short CRISPR-derived RNAs each containing a single spacer flanked on both sides by repeat sequences
32
Q

target interference

A
  • mature aRNAs associate with Cas nucleases, ir nuclease comlexes, and recruit them to complementary sequences in invading phage DNA
  • Cas nucleases then cleave the viral DNA, thus nutreulizing infection
33
Q

CRISPR-Cas type 1

A

requires multi-subunit protein complexes to mediate RNA-guided viral DNA destruction during the interference step

34
Q

CRISPR-Cas type 2

A

-the single Cas9 protein is sufficient, Cas9 also plays a role in spacer aquition and crRNA biogenesis

35
Q

Cas9 during spacer aquisition: cleave invading viral DNA

A
  • Cas9 selects protospacer sequences flanked by a protospacer adjacent motif (P A M) defined by the sequence 5’N G G3’. N = A,G,T or C
  • After protospacer cleavage, the Cas1/Cas2 complex integrates the D N A into a C R I S P R locus
36
Q

Cas9 during crRNA biogenesis

A
  • Noncoding R N A called a transactivating c r R N A (tracrR N A) binds to c r R N A repeat
  • Complex is then bound by Cas9 and cleaved into mature c r R N A/ tracrR N A duplexes by an R Nase that specifically recognizes dsR N A (R Nase Ⅲ)
37
Q

CAs9 during target interference

A
  • Cas9 has two nuclease domains that cleave the target D N A sequence
    • The H N H domain cleaves the strand of viral D N A that is complementary to the c r R N A
    • The R u v C domain cleaves the noncomplementary strand
  • Cas9 will only cleave the D N A if the target is adjacent to a P A M sequence
38
Q

what is the difference between type I and type II CRISPR-Cas Systems?

A
  • type I requires multi-subunit protein complexes to mediate RNA-guided viral DNA destruction during the interference step
  • in type II, the single CAS9 protein is sufficient, Cas9 also plats a role in spacer acquisition and crRNA biogenesis

Genetics (11 decks)

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