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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
Q

what are alu sites

A

remnants of transposable elements (repeated sequences that are highly abundant in human genome)

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26
Q

what are orthologs

A

the same protein in different species
ex= alpha tubulin in humans and flies

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27
Q

what are paralogs

A

closely related proteins in the same species
ex= alpha tubulin and beta tubulin in humans

28
Q

protein coding genes may be…

A

solitary or belong to a gene family

29
Q

what are solitary or single copy genes

A

protein coding genes are represented that are once in genome
25-50%
remainder = duplicates or in multiple copies

30
Q

what can make up a gene family

A

a set of related genes formed by duplication of an original single copy gene

31
Q

what are more than half of genes

A

present in either 2 paralogs ot have gene family

32
Q

describe multicellular and plant genomes

A

lower gene density
with noncoding introns and other noncoding sequences
including long tandem arrays of repeated short sequences

33
Q

what is DNA finger printing

A

compares individual differences in simple sequence tandem arrays

34
Q

describe simple sequence repeats - microsatellite DNA

A

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
Q

what causes neuromuscular diseases (simple sequence repeats - microsatellite DNA )

A

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
Q

how can short repeated sequences be generated

A

by backward slippage during replication

37
Q

describe backwards slippage during replication

A

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
Q

describe simple sequence repeats - minisatellite DNA

A

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
Q

what are centromeres

A

attaches to mitotic spindle

40
Q

what are telomeres

A

ends of chromosomes

41
Q

where is simple sequenced DNA localized

A

much is localized in particular regions of chromosomes

42
Q

what is used for paternity determination and identification of criminals

A

repeated sequences
since they vary extensively in length among individuals

43
Q

what are transposable (mobile) DNA elements (transposons)

A

transposable DNA elements move within genomes by different mechanisms

44
Q

what can mobile DNA elements influences by evolution cause

A

mutations leading to disease
alter expression or nature of protein produced

45
Q

name the 2 major classes of transposons

A

DNA transposons
retrotransposons

46
Q

describe DNA transposons

A

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
Q

describe retro transposons

A

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
Q

how much of human genome is DNA transposons and retrotransposons

A

3% = DNA transposon
40% = retrotransposons

49
Q

describe mechanism for increasing copy number of DNA transposons

A

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
Q

describe general structure of eukaryotic LTR retrotransposons

A

LTR
protein coding region encodes reverse transcriptase, integrase and other proteins - proteins needed for this to move around

51
Q

describe LTR

A

long terminal repeats
highly related to retroviruses

52
Q

what do retrotransposons do not have

A

gene called envelope gene that makes viral coat protein (a retrovirus does have this tho)

53
Q

describe generation of retroviral genomic RNA from integrated retroviral DNA

A

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
Q

describe steps of going from retroviral genome RNA to integrated retroviral DNA - 9 steps (general idea)

A

ensures every nucleotide in retroviral sequence remains intact and is present in DNA copy and gets transferred to new site

55
Q

what are LINEs

A

nonviral DNA retrotransposons
another type of retrotransposon not related to viruses

56
Q

how many LINEs in human genome

A

900,000 of these (54Mb = around 2% of total)
lots of copies are nonfunctional

57
Q

what can happen when line element is inserted

A

line element inserted is actually the mutation that is pathogenic (causes some hemophilias)

58
Q

what is SINA interspersed element

A

very small ~30bp
contains ALU repeat

59
Q

describe ORF1 (of lines)

A

encodes an RNA binding protein involved in nuclear transport of LINE RNA

60
Q

describe ORF2 (of lines)

A

encodes a reverse transcriptase and a nuclease

61
Q

describe mechanism for propagation of lines

A

RNA intermediate then reverse transcriptase to make DNA copy and that is integrated in genome

62
Q

what does TE movement lead to

A

genome changes

63
Q

recombination between repeated elements can…

A

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
Q

what can DNA transposons and LINEs carry when they move

A

unrelated flanking sequences
drives evolution

65
Q

describe DNA transposons and LINEs carrying unrelated flanking sequences with them

A

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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