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BIOL 200 > PL5 > Flashcards

PL5 Flashcards

1
Q

what is a genome

A

entirety of an organisms hereditary or genomic information

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2
Q

are genomes always DNA

A

usually DNA
but some vriuses have RNA genomes

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3
Q

what is dsDNA (double stranded) measured in

A

base pairs (bp)

1000bp = 1kbp or kb (usually for genes)
1000000 = 1Mbp or Mb (for whole genomes)

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4
Q

is biological complexity related to DNA content in genome

A

NOOOOOOO
just because more DNA does not mean more complex (ex amoeba dubia has more DNA than humans)

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5
Q

how many animal species have been sequenced

A

genomes of 3278 species of animals have been sequenced
~0.2% of animals

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6
Q

name and describe largest sequenced genome

A

australian lungfish xiphophorus = 43 Gb (giga. bases - 14x human genome)
does not have many more genes than other vertebrates but has lots of transposable elements

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7
Q

definition of a gene

A

entire nucleic acid sequence that is necessary for synthesis of a functional product (polypeptide/RNA)

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8
Q

are all coding genes meant to be translated into a functional product

A

NOOOO
Sometimes genes encode RNAs that are not meant to be translated into protein but have a function of their own (genes that encode ribosomal RNA, tRNA, spliceosomes have some RNA parts that are not translated)

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9
Q

what can genes be considered as

A

transcription units

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10
Q

describe a transcription unit

A

segment of DNA that includes all the info needed for primary transcript to be made

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11
Q

what do exons of a gene contain

A

coding region or open reading frame (ORF)

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12
Q

describe open reading frame

A

contained in 3 exons
part of protein encoding gene with AUG (start) which is for initiation of translation and continues until reaches terminator codon
has info that specifies amino acid sequence of proteins

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13
Q

what are control regions

A

promoter - place where RNA polymerase gets recruited
cis regulatory factors = control regions, neighbours promoter, part of gene since they are essential for regulating expression

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14
Q

where are control regions found

A

upstream 5’ end of transcription of mRNA start
controls expression of gene

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15
Q

what do introns do

A

separate exons and are spliced out during mRNA processing (spliced out of primary transcript)

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16
Q

what happens after mRNA is produced, transcribed and terminated

A

enzymatically a series of A residues are added to 3’ end (polyadenylation)
not template driven - added enzymatically
every gene must have poly a site on 3’ end that has signal that directs enzymes that directs termination and addition of all A residues

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17
Q

what do proteins with similar functions often contain

A

similar amino acid sequences that encode functional domains

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18
Q

what can be found using BLAST

A

nucleic acid and protein sequence similarity
match against database and can find highly conserved domains during evolution (usually functional domains)

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19
Q

what is BLAST

A

computer algorithm
aligns 2 or more sequences in optimal way

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20
Q

does protein number or DNA content vary more among species

A

protein number varies much less among species than DNA content

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21
Q

what is difference in genome size often due to

A

Difference in genome size among species is mostly due to different amounts of non-coding DNA and transposable elements

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22
Q

in what type of species is gene density much greater

A

much greater in lower eukaryotes than in more complex eukaryotes

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23
Q

describe lower and higher eukaryotes (what they have)

A

lower eukaryotes have a
lot less genes and higher eukaryotes have a lot more DNA but not as many genes

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24
Q

what is a pseudogene

A

resembles a gene but has many stop codons so not productively expressed

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25
what are alu sites
remnants of transposable elements (repeated sequences that are highly abundant in human genome)
26
what are orthologs
the same protein in different species ex= alpha tubulin in humans and flies
27
what are paralogs
closely related proteins in the same species ex= alpha tubulin and beta tubulin in humans
28
protein coding genes may be...
solitary or belong to a gene family
29
what are solitary or single copy genes
protein coding genes are represented that are once in genome 25-50% remainder = duplicates or in multiple copies
30
what can make up a gene family
a set of related genes formed by duplication of an original single copy gene
31
what are more than half of genes
present in either 2 paralogs ot have gene family
32
describe multicellular and plant genomes
lower gene density with noncoding introns and other noncoding sequences including long tandem arrays of repeated short sequences
33
what is DNA finger printing
compares individual differences in simple sequence tandem arrays
34
describe simple sequence repeats - microsatellite DNA
repeats units are typically 1-4bp in length arrays up to 600bp in length and composed of tandem repeats sometimes found in transcription units or open reading frames expansion underlie several neuromuscular diseases like myotonic dystrophy and spinocerebellar ataxia
35
what causes neuromuscular diseases (simple sequence repeats - microsatellite DNA )
triplet repeats if triplet repeats go over threshold length then starts to make a protein that is pathogenic (because not functional or takes on function that it should not)
36
how can short repeated sequences be generated
by backward slippage during replication
37
describe backwards slippage during replication
leaves out a copy or repeat after 2nd replication = daughter DNA molecule where tandem array has increased by one copy and over time sequences can expand and in some cases cause pathogenicity
38
describe simple sequence repeats - minisatellite DNA
repeat units are 14-100bp in length 20-50 tandem repeat units (diff copies) arrays of 1-5kbp in length often in centromeres and telomeres
39
what are centromeres
attaches to mitotic spindle
40
what are telomeres
ends of chromosomes
41
where is simple sequenced DNA localized
much is localized in particular regions of chromosomes
42
what is used for paternity determination and identification of criminals
repeated sequences since they vary extensively in length among individuals
43
what are transposable (mobile) DNA elements (transposons)
transposable DNA elements move within genomes by different mechanisms
44
what can mobile DNA elements influences by evolution cause
mutations leading to disease alter expression or nature of protein produced
45
name the 2 major classes of transposons
DNA transposons retrotransposons
46
describe DNA transposons
movement only involves DNA and it works by cutting and paste mechanism transposon cuts itself out of location in genome and moves to some other location where it integrates
47
describe retro transposons
movement involves RNA intermediate retrotransposon gets transcribed and then uses reverse transcriptase to make DNA copy of transcript then that copy inserts itself into genome somewhere
48
how much of human genome is DNA transposons and retrotransposons
3% = DNA transposon 40% = retrotransposons
49
describe mechanism for increasing copy number of DNA transposons
If a transposon moves from a region that has replicated to one that has not, copy number will increase by one in one of the daughter chromosomes (moves in front of replication fork after it was first transcribed)
50
describe general structure of eukaryotic LTR retrotransposons
LTR protein coding region encodes reverse transcriptase, integrase and other proteins - proteins needed for this to move around
51
describe LTR
long terminal repeats highly related to retroviruses
52
what do retrotransposons do not have
gene called envelope gene that makes viral coat protein (a retrovirus does have this tho)
53
describe generation of retroviral genomic RNA from integrated retroviral DNA
retroviral genome DNA gets transcribed by RNA polymerase 2 and now have copy of retroviral gene then must make DNA copy of itself and insert into somewhere else
54
describe steps of going from retroviral genome RNA to integrated retroviral DNA - 9 steps (general idea)
ensures every nucleotide in retroviral sequence remains intact and is present in DNA copy and gets transferred to new site
55
what are LINEs
nonviral DNA retrotransposons another type of retrotransposon not related to viruses
56
how many LINEs in human genome
900,000 of these (54Mb = around 2% of total) lots of copies are nonfunctional
57
what can happen when line element is inserted
line element inserted is actually the mutation that is pathogenic (causes some hemophilias)
58
what is SINA interspersed element
very small ~30bp contains ALU repeat
59
describe ORF1 (of lines)
encodes an RNA binding protein involved in nuclear transport of LINE RNA
60
describe ORF2 (of lines)
encodes a reverse transcriptase and a nuclease
61
describe mechanism for propagation of lines
RNA intermediate then reverse transcriptase to make DNA copy and that is integrated in genome
62
what does TE movement lead to
genome changes
63
recombination between repeated elements can...
shuffle exons and produce new genes with new combos of existing exons *targets for homologous recombination called exon shuffling Certain genes have evolved this way produces new genes that shuffle exons
64
what can DNA transposons and LINEs carry when they move
unrelated flanking sequences drives evolution
65
describe DNA transposons and LINEs carrying unrelated flanking sequences with them
LINE element does not have very strong end - so poly A signal is weak transcription continues downstream of LINE element until it gets to next termination site (3' end of gene it is inside) transcript is made with line element and exon from gene it is in so then it gets made into DNA copy and inserts but also inserts new exon - this changes nature of gene

BIOL 200 (29 decks)

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