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BIO130 > Week 3 > Flashcards

Week 3 Flashcards

1
Q

describe the shape of the genome of e coli

A

circular

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2
Q

conversion: 1000 bp = __ kb

A

1

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3
Q

what does it mean that some mitochondrial genes end up in the nuclear genome

A

that there is a lot of cross talk between the organelles

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4
Q

list the 3 lines of evidence for endosymbiotic theory

A
  • Chloroplast genome and mitochondrial genome are circular
  • Much smaller than bacterial genome (?)
  • Some from mito/chloro genes wound up in nuclear genome
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5
Q

in the human genome, how many bp per genome

A

~3 billion bp per genome

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6
Q

how many genomes from each parent do you get

A

1 from each

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7
Q

how many protein coding genes across 23 pairs of chromosomes

A

~20,000

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8
Q

t/f genome size is always correlated with number of genes/organism complexity

A

false

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9
Q

define haploid

A

half the normal amount of DNA (1 copy of each of the 23 pairs), haploid set 3 bill if diploid is 6 bill

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10
Q

in the human genome:
____% of our genome is repetitive dna and less than ___% of our genome encodes protein (protein-coding exons)

A

50, 1

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11
Q

list what comprises the unique sequences in the human genome

A

protein-coding exons, introns, nonrepetitive dna that is in neither introns nor exons (eg promotor or regulatory seq)

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12
Q

list what comprises the repeated sequences in the human genom

A

mobile genetic elements (LINEs, SINEs, retrotransposons, dna-only transposon), simple repeats, segment duplications (1k-200k bp long)

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13
Q

how were mobile genetic elements named

A

based on the way they are able to copy and insert themselves throughout our genome - make up more than half of the repeated seq in the genome (dna fossils - moved a lot in early evo days but don’t move around that much anymore)

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14
Q

why does dna need to get packaged

A

in a non packaged state, even the small prokaryotic genome would occupy a considerable portion of the cell volume

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15
Q

describe the dna packing in prokaryotes and what it forms

A

dna is condensed through folding and twisting about 1000 fold and is complexed w proteins = forms the prokaryotic nucleoid

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16
Q

how many bp of dna per cell in the human genome

A

6 billion

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17
Q

state the name of the solution of getting eukaryotic genome packed into cells and what it menas

A

the chromosome solution - linear chromosomes instead of circular

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18
Q

what does heating dna double helices do

A

hydrogen bonds between nucleotide pairs broken leading to denaturation to make it into single strands

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19
Q

describe the lab technique of hybridization - FISH (fluorescence in situ hybridisation)

A
  1. probe dna
  2. label w fluorescent dye
  3. denature and hybridize
  4. cool it slowly for renaturation to stay tgt

So many variations, a probe w a DNA or RNA sequence that has a fluorescent tag and tracks where it goes

It is called fish bc we don’t destroy the chromosome, we are trying to study it in its situation

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20
Q

t/f chromatin is dynamic

A

true

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21
Q

what is a karyotype

A

artificial array of chromosomes

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22
Q

define what chromatin is

A

each chromosome contains a single, long, linear dna molecule and associated protein

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23
Q

since chromatin is tightly packed, dna must still be accessible for what 3 processes

A

transcription, replication and repair

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24
Q

define what chromatids are

A

one of the two identical halves of a chromosome that has been replicated in preparation for cell division. they come apart when cell division occurs –> 2 cells after mitosis with identical DNA to parental cell

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25
Q

where on the dna are telomeres and also where on the dna is the centromere

A

telomeres are at ends and centromere is what joins chromatids together in the middle

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26
Q

what is a nucleosome made up on

A

nucleosome core particle + DNA wrapped around + linker DNA

27
Q

the net result of chromatin’s levels of organization is each dna molecule has been packaged into a mitotic chromosome that is ______ fold shorter than its fully extended length

A

10000

28
Q

how did scientists isolate chromatin in a cell in interphase

A

Ruptured the interphase nucleus and let the chromatin spill out and they found the 30nm fiber and then experimentally decondensed it more and applied chemical treatment so we can see the nucleosome

29
Q

what are histones

A

small proteins rich in lysine and arginine, positive charge neutralizes negative charge of dna (DNA tends to be negatively charged due to sugar phosphate backbone, the histones are positively charged so you can wrap the DNA around the histone – can also squish the nucleosomes together bc they aren’t being repelled)

30
Q

what are the 4 core histone proteins and say which are paired tgt in each octamer core

A

h2a and h2b
h3 and h4

31
Q

what terminal is the tail coming off the histone and how can it be modified

A

N-terminal tail (is the squiggles coming off) which can be covalently modified and can be the addition or loss of acetyl, methyl, and phosphate groups

32
Q

t/f the structure of the nucleosome is highly conserved

A

true

33
Q

t/f the one linker histone (h1) is external to the histone core but apart of the whole nucleosome

A

true

34
Q

H1 changes the trajectory of linker DNA coming out, which allows for what

A

allows for better compaction of the dna

35
Q

what two components are involved in forming chromatin loops

A

sequence specific clamp proteins and cohesins

^ sequence specific clamp proteins recognize particular sequences on the DNA and there’s a special ring protein called cohesin that pull the 30nm fiber together until the clamp proteins meet then we have a loop of chromatin

36
Q

as cells enter mitosis, __________ replace most cohesins to form double loops of chromatin to generate compact chromosome

A

as cells enter mitosis, condensins replace most cohesins to form double loops of chromatin to generate compact chromosome

37
Q

chromatin remodeling complexes and histone modifying enzymes are examples of proteins that can what

A

make changes in chromatin structure and alter access to dna for replication or transcription

38
Q

is it 40% heterochromatin and 60% euchromatin or 60% heterochromatin and 40% euchromatin

A

40% heterochromatin and 60% euchromatin

39
Q

where is heterochromatin found

A

often found by the periphery of the nucleus

40
Q

t/f the degree of chromatin condensation (heterochromatin and euchromatin) is dynamic

A

yes

41
Q

telomeres are made up of ____________ heterochromatin

A

constitutive

42
Q

quiescent is OR is not actively transcribed

A

is not

43
Q

facultative heterochromatin is ________ condensed

A

highly

44
Q

heterochromatic regions of interphase chromosomes are areas where gene expression is ______________

A

suppressed

45
Q

active euchromatic regions of interphase chromosomes are areas where genes tend to be ______________

A

expressed

46
Q

described the condensation of heterochromatin

A

high condensed - the time spent highly condensed varies (ie constitutive vs facultative)

47
Q

described the chromatin of euchromatin

A

relatively non condensed - level of activity varies (ie quiescent vs active) and degree of condensation varies

48
Q

list the types of heterochromatin

A
  • meiotic and mitotic chromosomes
  • centromeres and telomeres
49
Q

localized covalent modification of histones, the presence of chromatin remodeling complexes and rna poly (transcription) complexes modulate the _________ switching from euchromatic to heterochromatic regions along chromosomes

A

reversible

50
Q

expressed genes are re-orientated within the chromatin during interphase, the condensed chromosomal territory tends to be where and where does the expressed gene tend to be

A

condensed chromosomal territory tends to be at the outskirts and expressed gene tended to be more in the center - loop out various parts that need to be transcribed

51
Q

is dna replication conservative or semiconservative?

A

semiconservative

52
Q

dna synthesis causes the nucleotides to be stuck to which end

A

the 3’ end (so 5’ to 3’ direction of chain growth)

53
Q

dna is synthesized from what and rna is synthesized from what

A

dNTPs and NTPs

54
Q

what bond links nucleotides

A

phosphodiester bonds

55
Q

state the 3 main models of the direction of dna replication

A

Linear DNA viruses, plasmids that replicate a bit diff, and the bidirectional method

56
Q

describe the directional method for direction of dna replication

A

bidirectional growth from one starting point (2 forks) which begins from the replication origin. the double helix is opened with the aid of initiator proteins to make the single stranded dna templates ready for dna synthesis.

57
Q

what type of organisms use the bidirectional growth method

A

eukaryotes and bacteria

58
Q

how many origins of replication do bacteria and eukaryotes have and around how does it take

A

bacteria has single and replicates in about an hour

eukaryotes have multiple and can replicate in around 8-10 hours, to replicate an entire cell’s worth of dna

59
Q

describe the 2 possibilities of where dna replication starts

A
  1. random start
  2. always start from the same location on dna (replication origins)
60
Q

list the characteristics of replication origins

A
  • easy to open
  • a-t rich (bc easier to break less h bonds)
  • recognized by initiator proteins that bind to the dna
61
Q

list the procedure of dna replication

A
  1. separate dna strands
  2. synthesize dna
  3. proofread newly synthesized dna
62
Q

list the 6 ingredients for synthesis

A
  1. origin of replication
  2. primers
  3. dNTPs
  4. ATP as an energy source
  5. dna poly
  6. accessory proteins
63
Q

describe what happens at the dna replication forms

A
  • the replication form is asymmetrical: you have a left and right hand fork
  • the leading strand is replicated continuously (5’ to 3’) and lagging strand is discontinuously
  • the most recently synthesized dna is at the end
  • dna polymerase is going from 5’ to 3’ end in an complementary anti parallel fashion
  • okazaki fragment sare used to fill in the lagging strand

BIO130 (12 decks)

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